Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools' Reference genome folder provided is /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ (absolute path is '/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/)' FastQ format assumed (by default) Attention: early reports suggested that high values of -p to have diminishing returns. Please test different values using a small subset of data for your hardware setting. Each Bowtie 2 instance is going to be run with 5 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark'): /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Output will be written into the directory: /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark/ Summary of all aligner options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Running Bismark Parallel version. Number of parallel instances to be spawned: 5 Current working directory is: /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz and /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6899329) Using the subset file >1G4_R1_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6899329) Using the subset file >1G4_R1_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6899329) Using the subset file >1G4_R1_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6899329) Using the subset file >1G4_R1_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz for PID: 70152 and offset 5 (sequences written out: 6899328) Using the subset file >1G4_R1_001.fastp-trim.fq.gz.temp.5.gz< as new in-file 1 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6899329) Using the subset file >1G4_R2_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6899329) Using the subset file >1G4_R2_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz for PID: 70152 and offset 5 (sequences written out: 6899328) Using the subset file >1G4_R2_001.fastp-trim.fq.gz.temp.5.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6899329) Using the subset file >1G4_R2_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6899329) Using the subset file >1G4_R2_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 2 (instead of >/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1G4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz to 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz (6899329 sequences in total) Writing a C -> T converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz (6899329 sequences in total) Writing a C -> T converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz (6899329 sequences in total) Writing a C -> T converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz (6899329 sequences in total) Writing a C -> T converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz (6899328 sequences in total) Writing a C -> T converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz to 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz (6899329 sequences in total) Input files are 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz (6899329 sequences in total) Input files are 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz (6899329 sequences in total) Input files are 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz (6899328 sequences in total) Input files are 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz (6899329 sequences in total) Input files are 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:51374:1070_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 GATTTTTGTTTAGTTTTTTGTGTAAAGTATATGTTTGTTGGAAGTTATAATTATGGTGGATAAAGTGGATAGTTAAGATTTTAAATTTAAAGTAAAAGAAATTATAAAGGTTTTAAGAAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51374:1070_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATTTACACACAACAAACACACATATTACAAACTATCCACAAATCATACTACAAACTTCTACTAAAACAAACACACAAATAAAAATCTACAAACAAACTTTAATTACCTATAAACTCTTCTTCAC IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:33061:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TTTTGTTATATGAAAAAATATTTGTTATTGTAGTTAAATAGTTGTTTAATATGTTTAGGATTTTGTTTTGTTTTGTAATGGATAGTTTTTAGGAGTGTAAATATAAAAATTTTTAGGTTGAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33061:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TTTATATTTACACTCCTAAAAACTATCCATTACAAAACAAAACAAAATCCTAAACATATTAAACAACTATTTAACTACAATAACAAATATTTTTTCATATAACAAAAAACACCCAAACCAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50686:1056_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATATTATTTTGGATGATAAGTTTTATATTAAGTTGATTGATTTTGGTTTAGTAGTTTATATGGAGGAAGGGAAGAAGTTTAGTAT IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50686:1056_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATAAACTACTAAACCAAAATCAATCAACTTAATATAAAACTTATCATCCAAAATAATATTTTCATCCTTTTAT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31734:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TGTATTTTTTATTGTTTATAGTAAAGTTTTTATTGAAGGTTGAATTTTGTTTTAATGATTGTAAAAGATTTGTTGAGTTGTTGTTTTATTTTTTTTTATTGAATTTTTTTGATTTGAGATAGAGT -II9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIIIIIII99IIII9IIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31734:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TAACTTCATTTCTAAAACCAAAAATATAAACAATACCTTTTCTTTATCAAAAAAAATAAAACTCTATCTCAAATCAAAAAAATTCAATATAAAAAAATAAAACAACAACTCAACAAATCTTTTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31864:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 GGTGGATGGATTGTGTTTATTATTTGTTTTAGATTAGTAAAATTGGTTATTGTTGTATGGTATTTTGTTATTAGAATTGTATAAGTAGTGGAAGAAGATGTTGGTTTATGTTATTATTTAGATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31864:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 CCACCACTTCAAATACAATAAATCCAAAACCTTTATTACCATTAATAAATAATCAATATAATCAAAACCCTAATTACAATTTCCAAATCTAAATAATAACATAAACCAACATCTTCTTCCACTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:33061:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TTTTATTATATAAAAAAATATTTATTATTATAATTAAATAATTATTTAATATATTTAAAATTTTATTTTATTTTATAATAAATAATTTTTAAAAATATAAATATAAAAATTTTTAAATTAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33061:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TTTATATTTATATTTTTAAAAATTATTTATTATAAAATAAAATAAAATTTTAAATATATTAAATAATTATTTAATTATAATAATAAATATTTTTTTATATAATAAAAAATATTTAAATTAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31864:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATAAACAAATTACATTTATTATTTATTTTAAATTAATAAAATTAATTATTATCATACAATATTTTATTATTAAAATCATATAAATAATAAAAAAAAATATTAATTTACATTATTATTTAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31864:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TTGTTGTTTTGAATATAATAAATTTAAAATTTTTATTATTGTTAATAAATAATTGATATAATTGAAATTTTAATTATGATTTTTAAATTTAAATAATAATGTAAATTAATATTTTTTTTTATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50686:1056_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATATTATTTTAAATAATAAATTTTATATTAAATTAATTAATTTTAATTTAATAATTTATATAAAAAAAAAAAAAAAATTTAATAT IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50686:1056_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATAAATTATTAAATTAAAATTAATTAATTTAATATAAAATTTATTATTTAAAATAATATTTTTATTTTTTTAT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:51374:1070_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATTTTTATTTAATTTTTTATATAAAATATATATTTATTAAAAATTATAATTATAATAAATAAAATAAATAATTAAAATTTTAAATTTAAAATAAAAAAAATTATAAAAATTTTAAAAAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51374:1070_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATTTATATATAATAAATATATATATTATAAATTATTTATAAATTATATTATAAATTTTTATTAAAATAAATATATAAATAAAAATTTATAAATAAATTTTAATTATTTATAAATTTTTTTTTAT IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31734:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TATATTTTTTATTATTTATAATAAAATTTTTATTAAAAATTAAATTTTATTTTAATAATTATAAAAAATTTATTAAATTATTATTTTATTTTTTTCTATTAAATTTTTTTAATTTAAAATAAAAT -II9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIIIIIII99IIII9IIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31734:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TAATTTTATTTTTAAAATTAAAAATATAAATAATATTTTTTTTTTATTAAAAAAAATAAAATTTTATTTTAAATTAAAAAAATTTAATATAAAAAAATAAAATAATAATTTAATAAATTTTTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50686:1056_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATATTATTTTAAATAATAAATTTTATATTAAATTAATTAATTTTAATTTAATAATTTATATAAAAAAAAAAAAAAAATTTAATAT IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50686:1056_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATAAATTATTAAATTAAAATTAATTAATTTAATATAAAATTTATTATTTAAAATAATATTTTTATTTTTTTAT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31864:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATAAACAAATTACATTTATTATTTATTTTAAATTAATAAAATTAATTATTATCATACAATATTTTATTATTAAAATCATATAAATAATAAAAAAAAATATTAATTTACATTATTATTTAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31864:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TTGTTGTTTTGAATATAATAAATTTAAAATTTTTATTATTGTTAATAAATAATTGATATAATTGAAATTTTAATTATGATTTTTAAATTTAAATAATAATGTAAATTAATATTTTTTTTTATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:51374:1070_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATTTTTATTTAATTTTTTATATAAAATATATATTTATTAAAAATTATAATTATAATAAATAAAATAAATAATTAAAATTTTAAATTTAAAATAAAAAAAATTATAAAAATTTTAAAAAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51374:1070_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATTTATATATAATAAATATATATATTATAAATTATTTATAAATTATATTATAAATTTTTATTAAAATAAATATATAAATAAAAATTTATAAATAAATTTTAATTATTTATAAATTTTTTTTTAT IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31734:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TATATTTTTTATTATTTATAATAAAATTTTTATTAAAAATTAAATTTTATTTTAATAATTATAAAAAATTTATTAAATTATTATTTTATTTTTTTCTATTAAATTTTTTTAATTTAAAATAAAAT -II9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIIIIIII99IIII9IIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31734:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TAATTTTATTTTTAAAATTAAAAATATAAATAATATTTTTTTTTTATTAAAAAAAATAAAATTTTATTTTAAATTAAAAAAATTTAATATAAAAAAATAAAATAATAATTTAATAAATTTTTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:33061:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TTTTATTATATAAAAAAATATTTATTATTATAATTAAATAATTATTTAATATATTTAAAATTTTATTTTATTTTATAATAAATAATTTTTAAAAATATAAATATAAAAATTTTTAAATTAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33061:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TTTATATTTATATTTTTAAAAATTATTTATTATAAAATAAAATAAAATTTTAAATATATTAAATAATTATTTAATTATAATAATAAATATTTTTTTATATAATAAAAAATATTTAAATTAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50686:1056_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 AATATTATTTTGGATGATAAGTTTTATATTAAGTTGATTGATTTTGGTTTAGTAGTTTATATGGAGGAAGGGAAGAAGTTTAGTAT IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50686:1056_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATAAACTACTAAACCAAAATCAATCAACTTAATATAAAACTTATCATCCAAAATAATATTTTCATCCTTTTAT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:51374:1070_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 GATTTTTGTTTAGTTTTTTGTGTAAAGTATATGTTTGTTGGAAGTTATAATTATGGTGGATAAAGTGGATAGTTAAGATTTTAAATTTAAAGTAAAAGAAATTATAAAGGTTTTAAGAAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51374:1070_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TATTTACACACAACAAACACACATATTACAAACTATCCACAAATCATACTACAAACTTCTACTAAAACAAACACACAAATAAAAATCTACAAACAAACTTTAATTACCTATAAACTCTTCTTCAC IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIII YT:Z:UP >>> Writing bisulfite mapping results to 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:31864:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 GGTGGATGGATTGTGTTTATTATTTGTTTTAGATTAGTAAAATTGGTTATTGTTGTATGGTATTTTGTTATTAGAATTGTATAAGTAGTGGAAGAAGATGTTGGTTTATGTTATTATTTAGATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31864:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 CCACCACTTCAAATACAATAAATCCAAAACCTTTATTACCATTAATAAATAATCAATATAATCAAAACCCTAATTACAATTTCCAAATCTAAATAATAACATAAACCAACATCTTCTTCCACTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:33061:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TTTTGTTATATGAAAAAATATTTGTTATTGTAGTTAAATAGTTGTTTAATATGTTTAGGATTTTGTTTTGTTTTGTAATGGATAGTTTTTAGGAGTGTAAATATAAAAATTTTTAGGTTGAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33061:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TTTATATTTACACTCCTAAAAACTATCCATTACAAAACAAAACAAAATCCTAAACATATTAAACAACTATTTAACTACAATAACAAATATTTTTTCATATAACAAAAAACACCCAAACCAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:31734:1084_1:N:0:AAGACACC+TCGGTTAC/1 77 * 0 0 * * 0 0 TGTATTTTTTATTGTTTATAGTAAAGTTTTTATTGAAGGTTGAATTTTGTTTTAATGATTGTAAAAGATTTGTTGAGTTGTTGTTTTATTTTTTTTTATTGAATTTTTTTGATTTGAGATAGAGT -II9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIIIIIII99IIII9IIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31734:1084_2:N:0:AAGACACC+TCGGTTAC/2 141 * 0 0 * * 0 0 TAACTTCATTTCTAAAACCAAAAATATAAACAATACCTTTTCTTTATCAAAAAAAATAAAACTCTATCTCAAATCAAAAAAATTCAATATAAAAAAATAAAACAACAACTCAACAAATCTTTTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6741144 (97.71%) aligned concordantly 0 times 52964 (0.77%) aligned concordantly exactly 1 time 105221 (1.53%) aligned concordantly >1 times 2.29% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6893572 (99.92%) aligned concordantly 0 times 364 (0.01%) aligned concordantly exactly 1 time 5393 (0.08%) aligned concordantly >1 times 0.08% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6894728 (99.93%) aligned concordantly 0 times 368 (0.01%) aligned concordantly exactly 1 time 4233 (0.06%) aligned concordantly >1 times 0.07% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6742553 (97.73%) aligned concordantly 0 times 53373 (0.77%) aligned concordantly exactly 1 time 103403 (1.50%) aligned concordantly >1 times 2.27% overall alignment rate Processed 6899329 sequences in total Successfully deleted the temporary files 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6899329 Final Cytosine Methylation Report ================================= Total number of C's analysed: 6919682 Total methylated C's in CpG context: 124699 Total methylated C's in CHG context: 11189 Total methylated C's in CHH context: 128996 Total methylated C's in Unknown context: 1700 Total unmethylated C's in CpG context: 993146 Total unmethylated C's in CHG context: 1154789 Total unmethylated C's in CHH context: 4506863 Total unmethylated C's in Unknown context: 28375 C methylated in CpG context: 11.2% C methylated in CHG context: 1.0% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 5.7% 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6741158 (97.71%) aligned concordantly 0 times 52953 (0.77%) aligned concordantly exactly 1 time 105218 (1.53%) aligned concordantly >1 times 2.29% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6741983 (97.72%) aligned concordantly 0 times 53591 (0.78%) aligned concordantly exactly 1 time 103755 (1.50%) aligned concordantly >1 times 2.28% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6894894 (99.94%) aligned concordantly 0 times 405 (0.01%) aligned concordantly exactly 1 time 4030 (0.06%) aligned concordantly >1 times 0.06% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6893654 (99.92%) aligned concordantly 0 times 371 (0.01%) aligned concordantly exactly 1 time 5304 (0.08%) aligned concordantly >1 times 0.08% overall alignment rate Processed 6899329 sequences in total Successfully deleted the temporary files 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6899329 Final Cytosine Methylation Report ================================= Total number of C's analysed: 6922896 Total methylated C's in CpG context: 127218 Total methylated C's in CHG context: 11063 Total methylated C's in CHH context: 127202 Total methylated C's in Unknown context: 1731 Total unmethylated C's in CpG context: 993910 Total unmethylated C's in CHG context: 1153102 Total unmethylated C's in CHH context: 4510401 Total unmethylated C's in Unknown context: 28323 C methylated in CpG context: 11.3% C methylated in CHG context: 1.0% C methylated in CHH context: 2.7% C methylated in Unknown context (CN or CHN): 5.8% 6899328 reads; of these: 6899328 (100.00%) were paired; of these: 6740676 (97.70%) aligned concordantly 0 times 53088 (0.77%) aligned concordantly exactly 1 time 105564 (1.53%) aligned concordantly >1 times 2.30% overall alignment rate 6899328 reads; of these: 6899328 (100.00%) were paired; of these: 6894738 (99.93%) aligned concordantly 0 times 345 (0.01%) aligned concordantly exactly 1 time 4245 (0.06%) aligned concordantly >1 times 0.07% overall alignment rate 6899328 reads; of these: 6899328 (100.00%) were paired; of these: 6893647 (99.92%) aligned concordantly 0 times 363 (0.01%) aligned concordantly exactly 1 time 5318 (0.08%) aligned concordantly >1 times 0.08% overall alignment rate 6899328 reads; of these: 6899328 (100.00%) were paired; of these: 6741653 (97.71%) aligned concordantly 0 times 53802 (0.78%) aligned concordantly exactly 1 time 103873 (1.51%) aligned concordantly >1 times 2.29% overall alignment rate Processed 6899328 sequences in total Successfully deleted the temporary files 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6899328 Final Cytosine Methylation Report ================================= Total number of C's analysed: 6948683 Total methylated C's in CpG context: 127040 Total methylated C's in CHG context: 11496 Total methylated C's in CHH context: 128477 Total methylated C's in Unknown context: 1625 Total unmethylated C's in CpG context: 995649 Total unmethylated C's in CHG context: 1158721 Total unmethylated C's in CHH context: 4527300 Total unmethylated C's in Unknown context: 28182 C methylated in CpG context: 11.3% C methylated in CHG context: 1.0% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 5.5% Now waiting for all child processes to complete 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6741023 (97.71%) aligned concordantly 0 times 52929 (0.77%) aligned concordantly exactly 1 time 105377 (1.53%) aligned concordantly >1 times 2.29% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6893498 (99.92%) aligned concordantly 0 times 394 (0.01%) aligned concordantly exactly 1 time 5437 (0.08%) aligned concordantly >1 times 0.08% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6894828 (99.93%) aligned concordantly 0 times 364 (0.01%) aligned concordantly exactly 1 time 4137 (0.06%) aligned concordantly >1 times 0.07% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6742067 (97.72%) aligned concordantly 0 times 53878 (0.78%) aligned concordantly exactly 1 time 103384 (1.50%) aligned concordantly >1 times 2.28% overall alignment rate Processed 6899329 sequences in total Successfully deleted the temporary files 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6899329 Final Cytosine Methylation Report ================================= Total number of C's analysed: 6937686 Total methylated C's in CpG context: 126750 Total methylated C's in CHG context: 11511 Total methylated C's in CHH context: 130376 Total methylated C's in Unknown context: 1739 Total unmethylated C's in CpG context: 993665 Total unmethylated C's in CHG context: 1157631 Total unmethylated C's in CHH context: 4517753 Total unmethylated C's in Unknown context: 28210 C methylated in CpG context: 11.3% C methylated in CHG context: 1.0% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 5.8% 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6741166 (97.71%) aligned concordantly 0 times 53347 (0.77%) aligned concordantly exactly 1 time 104816 (1.52%) aligned concordantly >1 times 2.29% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6894749 (99.93%) aligned concordantly 0 times 390 (0.01%) aligned concordantly exactly 1 time 4190 (0.06%) aligned concordantly >1 times 0.07% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6893495 (99.92%) aligned concordantly 0 times 371 (0.01%) aligned concordantly exactly 1 time 5463 (0.08%) aligned concordantly >1 times 0.08% overall alignment rate 6899329 reads; of these: 6899329 (100.00%) were paired; of these: 6741687 (97.72%) aligned concordantly 0 times 54031 (0.78%) aligned concordantly exactly 1 time 103611 (1.50%) aligned concordantly >1 times 2.28% overall alignment rate Processed 6899329 sequences in total Successfully deleted the temporary files 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G4_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6899329 Final Cytosine Methylation Report ================================= Total number of C's analysed: 6966099 Total methylated C's in CpG context: 127270 Total methylated C's in CHG context: 11681 Total methylated C's in CHH context: 134174 Total methylated C's in Unknown context: 1846 Total unmethylated C's in CpG context: 1000156 Total unmethylated C's in CHG context: 1161993 Total unmethylated C's in CHH context: 4530825 Total unmethylated C's in Unknown context: 28855 C methylated in CpG context: 11.3% C methylated in CHG context: 1.0% C methylated in CHH context: 2.9% C methylated in Unknown context (CN or CHN): 6.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1G4_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark/1G4_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_PE_report.txt into >>> /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark/1G4_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G4_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 34496644 Final Cytosine Methylation Report ================================= Total number of C's analysed: 34695046 Total methylated C's in CpG context: 632977 Total methylated C's in CHG context: 56940 Total methylated C's in CHH context: 649225 Total methylated C's in Unknown context: 8641 Total unmethylated C's in CpG context: 4976526 Total unmethylated C's in CHG context: 5786236 Total unmethylated C's in CHH context: 22593142 Total unmethylated C's in Unknown context: 141945 C methylated in CpG context: 11.3% C methylated in CHG context: 1.0% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 5.7% Deleting temporary report files... Bismark completed in 0d 2h 6m 30s ==================== Bismark run complete ====================