# Notebook from VCMason/PyGenToolbox
Path: notebooks/Lyna/ReadSubtractionByGenomeMappingLnc1KD_Late.ipynb

<code>
%load_ext autoreload
%autoreload 2
import datetime
print(datetime.datetime.now())

from pygentoolbox import Tools
from pygentoolbox import ReadSubtractionByGenomeMapping as readsubtract
#dir(pygentoolbox.Tools)
%matplotlib inline
import matplotlib.pyplot as plt2021-09-16 17:03:49.330749
import os
print(os.getcwd())/media/sf_LinuxShare/PyPacks/PyGenToolbox/notebooks/Lyna

fileextension='.fastq.gz'
directory = '/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts'
outplotname = 'Lnc1KD_Late_Inserts_Stacked_Barplot.pdf'
startseqlength = 15
cleanreads=True
blastdatabase = '/media/sf_LinuxShare/Humans/Genome/Seqs/GRCh38_top_level.fa'
aligndatabaselist=['/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome',\
                   '/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector',\
                   '/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome',\
                   '/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac',\
                   '/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES',\
                   '/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1',\
                   '/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2']

readsubtract.main(fileextension, directory, outplotname, startseqlength, cleanreads, blastdatabase, aligndatabaselist)yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  Created
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  Created
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.bam = 6136
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 1277
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  Created
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 6100
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 36
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  Created
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 5987
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 116
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  Created
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 5987
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 0
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  Created
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 5987
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 0
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  Created
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 5701
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 390
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  Created
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 5701
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 0
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_15bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.bam = 11401
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 1890
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 11294
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 107
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 11114
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 181
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 11114
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 0
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 11114
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 0
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 10523
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 816
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 10523
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 0
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_16bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.bam = 14306
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 2736
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 14137
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 169
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 13790
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 347
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 7613
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 8824
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 6559
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1085
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 5877
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 923
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 5166
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1791
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_17bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.bam = 19008
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 3155
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 18662
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 346
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 18229
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 434
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 8996
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 13534
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 7807
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1215
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 6855
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1228
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 5972
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1199
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_18bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.bam = 24122
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 2853
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 23581
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 541
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 22740
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 841
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 10784
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 14822
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 8913
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1898
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 7501
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1836
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 5892
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 2154
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_19bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.bam = 29917
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 3335
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 29160
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 757
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 27412
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 1749
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 13898
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 16487
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 11525
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 2427
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 9662
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 2380
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 7264
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 3110
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_20bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.bam = 39294
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 3547
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 37691
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 1603
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 36412
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 1279
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 17641
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 22219
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 13996
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 3722
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 11210
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 3548
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 6581
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 5525
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_21bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.bam = 137585
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 5126
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 129325
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 8260
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 128060
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 1265
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 55444
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 90604
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 49187
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 6358
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 44925
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 6026
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 26034
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 21514
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_22bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.bam = 1058567
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 22508
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 938826
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 119741
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 931237
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 7589
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 359477
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 595858
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 343429
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 16244
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 331114
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 16511
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 161833
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 175403
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_23bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.bam = 390970
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 10307
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 380272
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 10698
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 377506
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 2767
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 236726
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 151047
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 193219
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 44113
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 132457
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 74560
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 37663
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 111629
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_24bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.bam = 4160550
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 5134
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 4158515
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 2035
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 4139126
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 19390
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 2675762
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 1547760
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 2215036
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 468607
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 910716
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1560634
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 144396
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1006098
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_25bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.bam = 550423
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 5769
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 549727
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 696
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 527786
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 21950
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 400039
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 141258
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 245456
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 156927
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 160962
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 98954
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 78115
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 104598
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_26bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.bam = 418256
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 6386
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 417807
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 449
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 412554
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 5258
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 293281
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 125721
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 102771
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 193771
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 80395
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 26409
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 49618
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 35524
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_27bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.bam = 366942
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 7241
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 366630
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 312
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 362453
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 4178
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 314252
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 54826
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 100978
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 215310
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 88495
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 14527
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 61717
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 28899
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_28bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.bam = 206362
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 8182
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 206109
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 253
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 200623
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 5486
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 159553
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 49112
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 53880
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 106359
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 46606
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 8504
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 32832
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 15310
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_29bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.bam = 86722
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 7839
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 86431
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 291
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 83288
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 3143
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 46234
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 48189
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 25064
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 21291
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 21183
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 4588
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 14958
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 6949
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_30bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.bam = 69059
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 10909
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 68749
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 310
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 60622
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 8127
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 31165
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 39976
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 20536
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 10762
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 18023
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 2933
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 14482
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 4006
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_31bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.bam = 84075
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 14951
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 83783
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 292
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 70697
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 13086
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 26141
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 62966
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 21559
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 4625
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 19652
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 2179
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 17402
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 2500
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_32bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.bam = 210422
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 42240
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 210103
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 319
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 191362
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 18741
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 21799
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 691921
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 19259
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 2563
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 17572
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1945
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 15975
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1899
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_33bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.bam = 93790
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 12920
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 93409
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 381
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 81952
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 11457
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 19533
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 96183
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 17214
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 2344
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 15880
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1549
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 14616
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1427
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_34bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.bam = 99600
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 11004
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 99173
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 427
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 88621
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 10552
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 19192
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 115355
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 17140
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 2073
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 16028
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1268
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 14425
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 2066
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_35bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.bam = 68062
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 9352
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 67658
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 404
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 62393
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 5265
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 17172
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 54925
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 15463
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1732
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 14413
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1227
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 13170
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1491
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_36bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.bam = 44517
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 6397
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 44142
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 375
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 39546
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 4596
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 14709
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 37623
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 13264
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1465
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 12378
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1022
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 11360
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1319
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_37bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.bam = 52878
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 5312
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 52514
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 364
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 47949
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 4565
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 12908
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 69053
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 11480
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1441
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 10661
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 914
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 9619
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1196
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_38bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.bam = 73755
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 6556
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 73412
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 343
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 68602
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 4810
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 12554
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 145978
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 11267
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1298
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 10560
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 796
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 9536
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1140
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_39bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.bam = 54137
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 3856
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 53778
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 359
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 49465
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 4313
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 13402
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 111037
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 12310
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 1100
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 11582
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 812
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 10564
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1097
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_40bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.bam = 32770
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 3404
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 32457
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 313
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 29415
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 3042
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 9767
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 40930
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 8856
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 917
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 8174
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 759
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 7470
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 792
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_41bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
yep your reads must already be clean
Start unpacking trimmed.gz file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.fastq.gz
gzip -f -d -k /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.fastq.gz
Finished unpacking:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.fastq

Starting fastqc
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc  already exists
/media/sf_LinuxShare/Programs/FastQC/fastqc -o /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc -f fastq fastq /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.fastq
Finished fastqc, output at directory:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/fastqc

Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Kpne_CompleteGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.bam = 303928
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.NotMatch4.sort.bam = 11145
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Vector
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam = 302938
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.NotMatch4.sort.bam = 990
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_mtGenome
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam = 221053
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.NotMatch4.sort.bam = 81885
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mac
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam = 175259
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.NotMatch4.sort.bam = 69067
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_MacAndIES
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam = 171767
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.NotMatch4.sort.bam = 3522
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/OESv1
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam = 170257
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.NotMatch4.sort.bam = 1645
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Finished
Starting Hisat2: aligning
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.fastq
Aligning reads to Reference:
/media/sf_LinuxShare/Ciliates/Genomes/Hisat2_Indexes/Pt_51_Mic2
Directory  /media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2  already exists
Finished with Hisat2

Starting samtools converting sam to sorted indexed bam
Finished with Samtools

Start Filtering file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.sort.bam
with flag: 4
Finished
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam = 168458
Finished counting reads in file
Start counting reads in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam
Finished
Number of reads mapped in file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.NotMatch4.sort.bam = 1912
Finished counting reads in file
Start converting bam to fastq
Finished
Converted file:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.bam
to
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/hisat2/210705_SN6662_A_L001_ADPF-118_AdapterTrimmed_R1_50bp.Kpne_CompleteGenome.Match4.sort.Vector.Match4.sort.Pt_mtGenome.Match4.sort.Pt_51_Mac.Match4.sort.Pt_51_MacAndIES.Match4.sort.OESv1.Match4.sort.Pt_51_Mic2.Match4.sort.fastq
Finished
wrote out table of counts aligned to each genome to:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/ReadsMappedToEachReference.tsv

Output Stacked Barplot to:
/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/Lnc1KD_Late_Inserts_Stacked_Barplot.pdf
import os
import glob
import subprocess
from pygentoolbox import SeqsPerFeatureAndFeatureTypeFixed

mappeddirectory='/media/sf_LinuxShare/Projects/Lyna/Hisat2/Pt_51_Mac/lnc1_KD_sRNAs/lnc1KD_late_inserts/33bpMac'
Gff3file = '/media/sf_LinuxShare/Ciliates/Genomes/Annotations/ptetraurelia_mac_51_annotation_v2.0.gff3'
# mappeddirectory = os.path.join(directory, 'hisat2')
# collect sorted sam files generated in the previous step:
samfileextension = '.sort.sam'

# collect sorted sam files generated in the previous step:
#samfileextension = '.sort.sam'
samfilelist = []
for file in os.listdir(mappeddirectory):
    if file.endswith(samfileextension):
        samfilelist.append(os.path.join(mappeddirectory, file))

# count number of reads per feature
# count number of reads per feature type (exon, mRNA, 5' UTR, etc.) and sort so counts are decreasing

#bamfilelist = ['180917_NB501850_A_L1-4_ADPF-29_AdapterTrimmed_R1_33bp.Pt_51_Mac.sort.bam']
# convert bam to sam
#samfilelist = []
#for bam in bamfilelist:
#    bampath = os.path.join(directory, bam)
#    cmd = 'samtools view -h %s' % (bampath)
#    with open(bampath[:-len('.bam')] + '.sam', 'w') as OUT:
#        ps = subprocess.Popen(cmd.split(), stdout=OUT)
#        ps.wait()
#    samfilelist.append(bampath[:-len('.bam')] + '.sam')

SeqsPerFeatureAndFeatureTypeFixed.main(Gff3file, samfilelist)
print(datetime.datetime.now())_____no_output_____
</code>