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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_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/1F9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_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/1F9_R1_001.fastp-trim.fq.gz for PID: 70158 and offset 5 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_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/1F9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7579783) Using the subset file >1F9_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/1F9_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/1F9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_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/1F9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_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/1F9_R2_001.fastp-trim.fq.gz for PID: 70158 and offset 5 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1F9_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/1F9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7579783) Using the subset file >1F9_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/1F9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1F9_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/1F9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1F9_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/1F9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1F9_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/1F9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7579782) Using the subset file >1F9_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/1F9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz (7579783 sequences in total) Writing a C -> T converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz (7579782 sequences in total) Writing a C -> T converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz (7579782 sequences in total) Writing a C -> T converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz (7579782 sequences in total) Writing a C -> T converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz (7579782 sequences in total) Writing a C -> T converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1F9_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 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz (7579782 sequences in total) Input files are 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F9_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 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz (7579782 sequences in total) Input files are 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F9_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 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz (7579783 sequences in total) Input files are 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F9_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 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz (7579782 sequences in total) Input files are 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F9_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)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50201:1056_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTGGTGTTTATGTATATGTGAGAAGAAATAGGTTGTTGTTTAAGTATATATTATGAAGATAATAGGTTATTTTTGAATTATTTTTGGTTTTTTTGTTAAATTTTGTTAAATTTAATATTTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50201:1056_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AAATTATAAATTAAATAACCATATTACAAAAAACAAAAAATCATCAAACTACTACACCATTCATTAACCAAAAAACTATAAAAAATAAATTCATTCAAACTTTAAATCAAAATAAACTTATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:41809:1070_1:N:0:CTCGAACA+GGAATTGC/1 99 ptg000023l_CT_converted 26475013 42 125M = 26475016 128 GAAAAGAGTGTTAGGGTGTAGTATTTAAATGAAGAAAATGTATGTGTAGTATTTTTTGTTGTTATAGGAAGTTTTTTAGGGGGAGTTTTTGTATTTAATGTTATTGTGGTTGTTTAAGTTTTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41809:1070_2:N:0:CTCGAACA+GGAATTGC/2 147 ptg000023l_CT_converted 26475016 42 125M = 26475013 -128 AAGAGTGTTAGGGTGTAGTATTTAAATGAAGAAAATGTATGTGTAGTATTTTTTGTTGTTATAGGAAGTTTTTTAGGGGGAGTTTTTGTATTTAATGTTATTGTGGTTGTTTAAGTTTTTAGAAA IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:42278:1070_1:N:0:CTCGAACA+GGAATTGC/1 99 ptg000024l_CT_converted 787577 42 125M = 787758 305 TTTGTAAAATGAATGAATTTTTTGTGTTATTTATTGTATTGTTGATATGTTTTTGTTTATGGTTTAGTAGAGTTATTAAATTTAATTGAATTTTTGTTATATTATTGTTTTTATTTTATTGAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII9III99IIII9IIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-8 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:42278:1070_2:N:0:CTCGAACA+GGAATTGC/2 147 ptg000024l_CT_converted 787758 42 26M1I98M = 787577 -305 TATTTTTATTAGATAGTAGTTAGGAATTTTTTTTTGATGGTTTGAGGATGTTTTTATAATTATTATAATAAGGAGGATATTATTTTATTGTGTTGAAGTTTTTGTTTTTTATTTTTGTTGTAGTG IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:124 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:40854:1070_1:N:0:CTCGAACA+GGAATTGC/1 99 ptg000034l_CT_converted 2718509 2 125M = 2718568 185 TTAAAGTGTTTGTTATGTATTTTATAGAAATAAGATGAGAAGTTTAGGGAATAAAGTTTTTGAAAAAGTTATAATAAGATATAAATTTAGGAATGATTATTAGTTAGTTTTTGTTTGAAAAAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-54 XS:i:-65 XN:i:0 XM:i:9 XO:i:0 XG:i:0 NM:i:9 MD:Z:22G5G2G23A1G3T9A36A0G15 YS:i:-50 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40854:1070_2:N:0:CTCGAACA+GGAATTGC/2 147 ptg000034l_CT_converted 2718568 2 87M1D38M = 2718509 -185 TTGAAAAAGTTATAATAAGATATAAATTTAGGAATGATTATTAGTTAGTTTTTGTTTGAAAAAGGTTAAGATTTATAAATGTTTTTTTTTTTTATTATAGTAAATAGAAAGGATTGATATTTGTT IIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-IIII-IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-50 XS:i:-44 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:2T9A36A0G25G10^G5G11G20 YS:i:-54 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:40854:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTAAAATATTTATTATATATTTTATAAAAATAAAATAAAAAATTTAAAAAATAAAATTTTTAAAAAAATTATAATAAAATATAAATTTAAAAATAATTATTAATTAATTTTTATTTAAAAAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40854:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AATAAATATTAATTTTTTTTATTTATTATAATAAAAAAAAAAAATATTTATAAATTTTAATTTTTTTTAAATAAAAATTAATTAATAATTATTTTTAAATTTATATTTTATTATAATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIII-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:42278:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTTATAAAATAAATAAATTTTTTATATTATTTATTATATTATTAATATATTTTTATTTATAATTTAATAAAATTATTAAATTTAATTAAATTTTTATTATATTATTATTTTTATTTTATTAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII9III99IIII9IIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42278:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 TATTATAATAAAAATAAAAAATAAAAATTTTAATATAATAAAATAATATTTTTTTTATTATAATAATTATAAAAATATTTTTAAATTATTAAAAAAAAATTTTTAATTATTATTTAATAAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:50201:1056_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTAATATTTATATATATATAAAAAAAAATAAATTATTATTTAAATATATATTACAAAAATAATAAATTATTTTTAAATTATTTTTAATTTTTTTATTAAATTTCATTAAATTTAATATTTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50201:1056_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AAATTATAAATTAAATAATTATATTATAAAAAATAAAAAATTATTAAATTATTATATTATTTATTAATTAAAAAATTATAAAAAATAAATTTATTTAAATTTTAAATTAAAATAAATTTATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:41809:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 AAAAAAAATATTAAAATATAATATTTAAATAAAAAAAATATATATATAATATTTTTTATTATTATAAAAAATTTTTTAAAAAAAATTTTTATATTTAATATTATTATAATTATTTAAATTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41809:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 TTTTTAAAAATTTAAATAATTATAATAATATTAAATATAAAAATTTTTTTTAAAAAATTTTTTATAATAATAAAAAATATTATATATATATTTTTTTTATTTAAATATTATATTTTAATATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:42278:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTTATAAAATAAATAAATTTTTTATATTATTTATTATATTATTAATATATTTTTATTTATAATTTAATAAAATTATTAAATTTAATTAAATTTTTATTATATTATTATTTTTATTTTATTAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII9III99IIII9IIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42278:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 TATTATAATAAAAATAAAAAATAAAAATTTTAATATAATAAAATAATATTTTTTTTATTATAATAATTATAAAAATATTTTTAAATTATTAAAAAAAAATTTTTAATTATTATTTAATAAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:50201:1056_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTAATATTTATATATATATAAAAAAAAATAAATTATTATTTAAATATATATTACAAAAATAATAAATTATTTTTAAATTATTTTTAATTTTTTTATTAAATTTCATTAAATTTAATATTTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50201:1056_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AAATTATAAATTAAATAATTATATTATAAAAAATAAAAAATTATTAAATTATTATATTATTTATTAATTAAAAAATTATAAAAAATAAATTTATTTAAATTTTAAATTAAAATAAATTTATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:41809:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 AAAAAAAATATTAAAATATAATATTTAAATAAAAAAAATATATATATAATATTTTTTATTATTATAAAAAATTTTTTAAAAAAAATTTTTATATTTAATATTATTATAATTATTTAAATTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41809:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 TTTTTAAAAATTTAAATAATTATAATAATATTAAATATAAAAATTTTTTTTAAAAAATTTTTTATAATAATAAAAAATATTATATATATATTTTTTTTATTTAAATATTATATTTTAATATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:40854:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTAAAATATTTATTATATATTTTATAAAAATAAAATAAAAAATTTAAAAAATAAAATTTTTAAAAAAATTATAATAAAATATAAATTTAAAAATAATTATTAATTAATTTTTATTTAAAAAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40854:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AATAAATATTAATTTTTTTTATTTATTATAATAAAAAAAAAAAATATTTATAAATTTTAATTTTTTTTAAATAAAAATTAATTAATAATTATTTTTAAATTTATATTTTATTATAATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIII-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:42278:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTTGTAAAATGAATGAATTTTTTGTGTTATTTATTGTATTGTTGATATGTTTTTGTTTATGGTTTAGTAGAGTTATTAAATTTAATTGAATTTTTGTTATATTATTGTTTTTATTTTATTGAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII9III99IIII9IIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42278:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 CACTACAACAAAAATAAAAAACAAAAACTTCAACACAATAAAATAATATCCTCCTTATTATAATAATTATAAAAACATCCTCAAACCATCAAAAAAAAATTCCTAACTACTATCTAATAAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:50201:1056_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 TTGGTGTTTATGTATATGTGAGAAGAAATAGGTTGTTGTTTAAGTATATATTATGAAGATAATAGGTTATTTTTGAATTATTTTTGGTTTTTTTGTTAAATTTTGTTAAATTTAATATTTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50201:1056_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AAATTATAAATTAAATAACCATATTACAAAAAACAAAAAATCATCAAACTACTACACCATTCATTAACCAAAAAACTATAAAAAATAAATTCATTCAAACTTTAAATCAAAATAAACTTATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:41809:1070_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 GAAAAGAGTGTTAGGGTGTAGTATTTAAATGAAGAAAATGTATGTGTAGTATTTTTTGTTGTTATAGGAAGTTTTTTAGGGGGAGTTTTTGTATTTAATGTTATTGTGGTTGTTTAAGTTTTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41809:1070_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 TTTCTAAAAACTTAAACAACCACAATAACATTAAATACAAAAACTCCCCCTAAAAAACTTCCTATAACAACAAAAAATACTACACATACATTTTCTTCATTTAAATACTACACCCTAACACTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:40854:1070_1:N:0:CTCGAACA+GGAATTGC/1 83 ptg000023l_GA_converted 12815483 0 125M = 12815424 -184 ACCTTTTTCAAACAAAAACTAACTAATAATCATTCCTAAATTTATATCTTATTATAACTTTTTCAAAAACTTTATTCCCTAAACTTCTCATCTTATTTCTATAAAATACATAACAAACACTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-42 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:43T19A5T32C18A3 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40854:1070_2:N:0:CTCGAACA+GGAATTGC/2 163 ptg000023l_GA_converted 12815424 0 125M = 12815483 184 AACAAATATCAATCCTTTCTATTTACTATAATAAAAAAAAAAAACATTTATAAATCTTAACCTTTTTCAAACAAAAACTAACTAATAATCATTCCTAAATTTATATCTTATTATAACTTTTTCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIII-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII AS:i:-24 XS:i:-36 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:20C22C58T19A2 YS:i:-30 YT:Z:CP Reading in the sequence files 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz >>> Writing bisulfite mapping results to 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz (7579782 sequences in total) Input files are 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F9_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 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:51528:1056_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 ATAGGATTTAAAGTTGGATTAATATTTTTATTTTTTTTTTTTTTTTTGTAATATGTGGTTTATGGTGAATAAAGTGATTAGTTTTTTTGTGGTTTTTATTTTGTGTAGGAAGTTTTGGTAGTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIII9IIII--9-III99IIIII9I9I9I9II-II9I9IIIIII-9III9I9II9IIII9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51528:1056_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AACTACAAAAAAAATACTTAAAAAACTAAAAAAACTACCAAAACTTCCTACACAAAATAAAAACCACAAAAAAACTAATCACTTTATTCACCATAAACCACATATT III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-IIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:51528:1056_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 ATAAAATTTAAAATTAAATTAATATTTTTATTTTTTTTTTTTTTTTTATAATACATAATTTACAACAAATAAAACAATTAATTTTTTTATAATTTTTATTTTACATAAAAAATTTTAATAATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIII9IIII--9-III99IIIII9I9I9I9II-II9I9IIIIII-9III9I9II9IIII9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51528:1056_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AATTATAAAAAAAATATTTAAAAAATTAAAAAAATTATTAAAATTTTTTATGTAAAATAAAAATTATAAAAAAATTAATTGTTTTATTTGTTGTAAATTATGTATT III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-IIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:51528:1056_1:N:0:CTCGAACA+GGAATTGC/1 77 * 0 0 * * 0 0 ATAAAATTTAAAATTAAATTAATATTTTTATTTTTTTTTTTTTTTTTATAATACATAATTTACAACAAATAAAACAATTAATTTTTTTATAATTTTTATTTTACATAAAAAATTTTAATAATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIII9IIII--9-III99IIIII9I9I9I9II-II9I9IIIIII-9III9I9II9IIII9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51528:1056_2:N:0:CTCGAACA+GGAATTGC/2 141 * 0 0 * * 0 0 AATTATAAAAAAAATATTTAAAAAATTAAAAAAATTATTAAAATTTTTTATGTAAAATAAAAATTATAAAAAAATTAATTGTTTTATTTGTTGTAAATTATGTATT III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-IIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F9_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: LH00526:197:22KFKVLT4:3:1101:51528:1056_1:N:0:CTCGAACA+GGAATTGC/1 83 ptg000004l_GA_converted 10233232 42 78M1D47M = 10233202 -156 AAAACTACCAAAACTTCCTACACAAAATAAAAACCACAAAAAAACTAATCACTTTATTCACCATAAACCACATATTACAAAAAAAAAAAAAAAAATAAAAATATTAATCCAACTTTAAATCCTAT 9IIII9II9I9III9-IIIIII9I9II-II9I9I9I9IIIII99III-9--IIII9IIIIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20T57^A47 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51528:1056_2:N:0:CTCGAACA+GGAATTGC/2 163 ptg000004l_GA_converted 10233202 42 106M = 10233232 156 AACTACAAAAAAAATACTTAAAAAACTAAAAAAACTACCAAAACTTCCTACACAAAATAAAAACCACAAAAAAACTAATCACTTTATTCACCATAAACCACATATT III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-IIIIIII9 AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:50T55 YS:i:-14 YT:Z:CP >>> Writing bisulfite mapping results to 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1128:20098:2009_1:N:0:CTCGAACA+GGAATTGC ntLink_0 1 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1407:30885:23623_1:N:0:CTCGAACA+GGAATTGC ptg000004l 15492347 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2116:48178:29548_1:N:0:CTCGAACA+GGAATTGC ptg000117l 1 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2266:37229:27937_1:N:0:CTCGAACA+GGAATTGC ptg000117l 30003 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2192:6665:1896_1:N:0:CTCGAACA+GGAATTGC ptg000083l 1 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2243:46033:10707_1:N:0:CTCGAACA+GGAATTGC ptg000007l 12295855 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2485:49327:21647_1:N:0:CTCGAACA+GGAATTGC ptg000066l 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1198:38855:13663_1:N:0:CTCGAACA+GGAATTGC ptg000083l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1238:44172:14125_1:N:0:CTCGAACA+GGAATTGC ptg000007l 12295855 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1293:32365:14083_1:N:0:CTCGAACA+GGAATTGC ptg000015l 14997091 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1287:41259:14321_1:N:0:CTCGAACA+GGAATTGC ptg000130l 35789 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2165:9214:17907_1:N:0:CTCGAACA+GGAATTGC ptg000097l 1 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2190:24629:13271_1:N:0:CTCGAACA+GGAATTGC ptg000155l 36824 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2370:47652:2695_1:N:0:CTCGAACA+GGAATTGC ptg000146l 38970 Processed 7000000 sequence pairs so far 7579783 reads; of these: 7579783 (100.00%) were paired; of these: 7562938 (99.78%) aligned concordantly 0 times 6893 (0.09%) aligned concordantly exactly 1 time 9952 (0.13%) aligned concordantly >1 times 0.22% overall alignment rate 7579783 reads; of these: 7579783 (100.00%) were paired; of these: 3373942 (44.51%) aligned concordantly 0 times 1651056 (21.78%) aligned concordantly exactly 1 time 2554785 (33.71%) aligned concordantly >1 times 55.49% overall alignment rate 7579783 reads; of these: 7579783 (100.00%) were paired; of these: 3367296 (44.42%) aligned concordantly 0 times 1652824 (21.81%) aligned concordantly exactly 1 time 2559663 (33.77%) aligned concordantly >1 times 55.58% overall alignment rate 7579783 reads; of these: 7579783 (100.00%) were paired; of these: 7561290 (99.76%) aligned concordantly 0 times 7142 (0.09%) aligned concordantly exactly 1 time 11351 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate Processed 7579783 sequences in total Successfully deleted the temporary files 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7579783 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213637397 Total methylated C's in CpG context: 3374367 Total methylated C's in CHG context: 190754 Total methylated C's in CHH context: 815571 Total methylated C's in Unknown context: 5861 Total unmethylated C's in CpG context: 29844584 Total unmethylated C's in CHG context: 36026748 Total unmethylated C's in CHH context: 143385373 Total unmethylated C's in Unknown context: 304078 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2473:30342:25177_1:N:0:CTCGAACA+GGAATTGC ptg000121l 50718 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7562987 (99.78%) aligned concordantly 0 times 6861 (0.09%) aligned concordantly exactly 1 time 9934 (0.13%) aligned concordantly >1 times 0.22% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7561538 (99.76%) aligned concordantly 0 times 7104 (0.09%) aligned concordantly exactly 1 time 11140 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3371838 (44.48%) aligned concordantly 0 times 1652452 (21.80%) aligned concordantly exactly 1 time 2555492 (33.71%) aligned concordantly >1 times 55.52% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3367963 (44.43%) aligned concordantly 0 times 1653910 (21.82%) aligned concordantly exactly 1 time 2557909 (33.75%) aligned concordantly >1 times 55.57% overall alignment rate Processed 7579782 sequences in total Successfully deleted the temporary files 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7579782 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213726683 Total methylated C's in CpG context: 3374274 Total methylated C's in CHG context: 189867 Total methylated C's in CHH context: 812718 Total methylated C's in Unknown context: 5624 Total unmethylated C's in CpG context: 29847406 Total unmethylated C's in CHG context: 36034051 Total unmethylated C's in CHH context: 143468367 Total unmethylated C's in Unknown context: 303635 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7563010 (99.78%) aligned concordantly 0 times 6884 (0.09%) aligned concordantly exactly 1 time 9888 (0.13%) aligned concordantly >1 times 0.22% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3365794 (44.40%) aligned concordantly 0 times 1655958 (21.85%) aligned concordantly exactly 1 time 2558030 (33.75%) aligned concordantly >1 times 55.60% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7561657 (99.76%) aligned concordantly 0 times 7040 (0.09%) aligned concordantly exactly 1 time 11085 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3374128 (44.51%) aligned concordantly 0 times 1651813 (21.79%) aligned concordantly exactly 1 time 2553841 (33.69%) aligned concordantly >1 times 55.49% overall alignment rate Processed 7579782 sequences in total Successfully deleted the temporary files 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7579782 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213765677 Total methylated C's in CpG context: 3372865 Total methylated C's in CHG context: 190916 Total methylated C's in CHH context: 816083 Total methylated C's in Unknown context: 5544 Total unmethylated C's in CpG context: 29860678 Total unmethylated C's in CHG context: 36051713 Total unmethylated C's in CHH context: 143473422 Total unmethylated C's in Unknown context: 302681 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Now waiting for all child processes to complete 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7562860 (99.78%) aligned concordantly 0 times 6938 (0.09%) aligned concordantly exactly 1 time 9984 (0.13%) aligned concordantly >1 times 0.22% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7561673 (99.76%) aligned concordantly 0 times 7034 (0.09%) aligned concordantly exactly 1 time 11075 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3368030 (44.43%) aligned concordantly 0 times 1653271 (21.81%) aligned concordantly exactly 1 time 2558481 (33.75%) aligned concordantly >1 times 55.57% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3367498 (44.43%) aligned concordantly 0 times 1653875 (21.82%) aligned concordantly exactly 1 time 2558409 (33.75%) aligned concordantly >1 times 55.57% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7562821 (99.78%) aligned concordantly 0 times 7075 (0.09%) aligned concordantly exactly 1 time 9886 (0.13%) aligned concordantly >1 times 0.22% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3371330 (44.48%) aligned concordantly 0 times 1653881 (21.82%) aligned concordantly exactly 1 time 2554571 (33.70%) aligned concordantly >1 times 55.52% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 3369865 (44.46%) aligned concordantly 0 times 1653640 (21.82%) aligned concordantly exactly 1 time 2556277 (33.72%) aligned concordantly >1 times 55.54% overall alignment rate 7579782 reads; of these: 7579782 (100.00%) were paired; of these: 7561684 (99.76%) aligned concordantly 0 times 6960 (0.09%) aligned concordantly exactly 1 time 11138 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate Processed 7579782 sequences in total Successfully deleted the temporary files 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7579782 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213867578 Total methylated C's in CpG context: 3367370 Total methylated C's in CHG context: 189632 Total methylated C's in CHH context: 813696 Total methylated C's in Unknown context: 5668 Total unmethylated C's in CpG context: 29891181 Total unmethylated C's in CHG context: 36057150 Total unmethylated C's in CHH context: 143548549 Total unmethylated C's in Unknown context: 303297 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Processed 7579782 sequences in total Successfully deleted the temporary files 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7579782 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213749862 Total methylated C's in CpG context: 3367940 Total methylated C's in CHG context: 189416 Total methylated C's in CHH context: 813920 Total methylated C's in Unknown context: 5578 Total unmethylated C's in CpG context: 29869999 Total unmethylated C's in CHG context: 36041327 Total unmethylated C's in CHH context: 143467260 Total unmethylated C's in Unknown context: 304060 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1F9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1F9_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1F9_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/1F9_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1F9_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/1F9_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F9_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: 37898911 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1068747197 Total methylated C's in CpG context: 16856816 Total methylated C's in CHG context: 950585 Total methylated C's in CHH context: 4071988 Total methylated C's in Unknown context: 28275 Total unmethylated C's in CpG context: 149313848 Total unmethylated C's in CHG context: 180210989 Total unmethylated C's in CHH context: 717342971 Total unmethylated C's in Unknown context: 1517751 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Deleting temporary report files... Bismark completed in 0d 4h 46m 39s ==================== Bismark run complete ====================