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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_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/1A5_R1_001.fastp-trim.fq.gz for PID: 80681 and offset 5 (sequences written out: 8416550) Using the subset file >1A5_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/1A5_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/1A5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_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/1A5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_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/1A5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_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/1A5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_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/1A5_R2_001.fastp-trim.fq.gz for PID: 80681 and offset 5 (sequences written out: 8416550) Using the subset file >1A5_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/1A5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A5_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/1A5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A5_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/1A5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A5_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/1A5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A5_R1_001.fastp-trim.fq.gz.temp.2.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/1A5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8416551) Using the subset file >1A5_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/1A5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A5_R1_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 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz (8416550 sequences in total) Writing a C -> T converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz (8416551 sequences in total) Writing a C -> T converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz (8416551 sequences in total) Writing a C -> T converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz (8416551 sequences in total) Writing a C -> T converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz (8416551 sequences in total) Writing a C -> T converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A5_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 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz (8416551 sequences in total) Input files are 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:44714:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 ATTTAATTTGAAATGATTTGAGTAAATATAATTGTGGTTTAGGAGTTGAGGAATTTTGGGATTTTTTAAATTTATTAATTATTTTGTTGATAATTGTTTGTTGTGGTGTGGTAGTTTGTAGAAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44714:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 ATCCAACTCAAAATAATCTAAACAAACATAACTATAATTCAAAAACTAAAAAATTTTAAAATTTCTTAAATTCACCAACCACTTCATTAACAATAATTATTTATTATATAACTATCAATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII9IIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:44714:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 ATTTAATTTAAAATAATTTAAATAAATATAATTATAATTTAAAAATTAAAAAATTTTAAAATTTTTTAAATTTATTAATTATTTTATTAATAATTATTTATTATAATATAATAATTTATAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44714:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 ATTTAATTTAAAATAATTTAAATAAATATAATTATAATTTAAAAATTAAAAAATTTTAAAATTTTTTAAATTTATTAATTATTTTATTAATAATAATTATTTATTATATAATTATTAATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII9IIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A5_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz (8416550 sequences in total) Input files are 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A5_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)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:44714:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 ATTTAATTTAAAATAATTTAAATAAATATAATTATAATTTAAAAATTAAAAAATTTTAAAATTTTTTAAATTTATTAATTATTTTATTAATAATTATTTATTATAATATAATAATTTATAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44714:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 ATTTAATTTAAAATAATTTAAATAAATATAATTATAATTTAAAAATTAAAAAATTTTAAAATTTTTTAAATTTATTAATTATTTTATTAATAATAATTATTTATTATATAATTATTAATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII9IIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A5_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz (8416551 sequences in total) Input files are 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A5_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)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:47288:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 AATTTTTGGATTTTTGTTTTGAGTTTTTTTGAATTATTATTGAAGAATGTATGTTTTTATTTTTATGTGTTTTTTGTTAGTGGGAGTTATTAATTTTTTAGTATAATGTTTTTAATTTAGTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:47288:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 AAACCACTCTTAATTAATATTTAACTAAATTAAAAACATTATACTAAAAAATTAATAACTCCCACTAACAAAAAACACATAAAAATAAAAACATACATTCTTCAATAATAATTCAAAAAAACTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:44714:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 ATTTAATTTGAAATGATTTGAGTAAATATAATTGTGGTTTAGGAGTTGAGGAATTTTGGGATTTTTTAAATTTATTAATTATTTTGTTGATAATTGTTTGTTGTGGTGTGGTAGTTTGTAGAAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44714:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 ATCCAACTCAAAATAATCTAAACAAACATAACTATAATTCAAAAACTAAAAAATTTTAAAATTTCTTAAATTCACCAACCACTTCATTAACAATAATTATTTATTATATAACTATCAATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII9IIIII9I YT:Z:UP >>> Writing bisulfite mapping results to 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:51593:1056_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TGGATAGTAAGATATTTATTATTATAAGTTTTTTAATTATATTTTTTGAATTGTGTATGGTTTAAAAGGAAAGATTTGTATTTTATTAATTTTTTATTTAATTTTATTAGATAATT IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51593:1056_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 AATTAATAAAATACAAATCTTTCCTTTTAAACCATACACAATTCAAAAAATATAATTAAAAAACTTATAATAATAAATATCTTACTATCCAAAAATCTTTCCAACTCTTTCCAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A5_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz (8416551 sequences in total) Input files are 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:48833:1070_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TGTTTTTATTTATAATTTTTAATTAATATTTAGTATTGAATTTGAATGTAGGAAATGGTATTTTTGGGTTTTTAGATTTTAAAATTTTTTGGAGAAGTATGTTTTTATATTTTTTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48833:1070_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 TCCAAAAAATTTTAAAATCTAAAAACCCAAAAATACCATTTCCTACATTCAAATTCAATACTAAATATTAATTAAAAATTATAAATAAAAACACAAATAAAATTTAATATAAAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:47288:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 AATTTTTAAATTTTTATTTTAAATTTTTTTAAATTATTATTAAAAAATATATATTTTTATTTTTATATATTTTTTATTAATAAAAATTATTAATTTTTTAATATAATATTTTTAATTTAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:47288:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 AAATTATTTTTAATTAATATTTAATTAAATTAAAAATATTATATTAAAAAATTAATAATTTTTATTAATAAAAAATATATAAAAATAAAAATATATATTTTTTAATAATAATTTAAAAAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:51593:1056_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TAAATAATAAAATATTTATTATTATAAATTTTTTAATTATATTTTTTAAATTATATATAATTTAAAAAAAAAAATTTATATTTTATTAATTTTTTATTTAATTTTATTAAATAATT IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51593:1056_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 AATTAATAAAATATAAATTTTTTTTTTTAAATTATATATAATTTAAAAAATATAATTAAAAAATTTATAATAATAAATATTTTATTATTTAAAAATTTTTTTAATTTTTTTTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A5_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)) Reading in the sequence files 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:47288:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 AATTTTTAAATTTTTATTTTAAATTTTTTTAAATTATTATTAAAAAATATATATTTTTATTTTTATATATTTTTTATTAATAAAAATTATTAATTTTTTAATATAATATTTTTAATTTAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:47288:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 AAATTATTTTTAATTAATATTTAATTAAATTAAAAATATTATATTAAAAAATTAATAATTTTTATTAATAAAAAATATATAAAAATAAAAATATATATTTTTTAATAATAATTTAAAAAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:48833:1070_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TATTTTTATTTATAATTTTTAATTAATATTTAATATTAAATTTAAATATAAAAAATAATATTTTTAAATTTTTAAATTTTAAAATTTTTTAAAAAAATATATTTTTATATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48833:1070_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 TTTAAAAAATTTTAAAATTTAAAAATTTAAAAATATTATTTTTTATATTTAAATTTAATATTAAATATTAATTAAAAATTATAAATAAAAATATAAATAAAATTTAATATAAAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:51593:1056_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TAAATAATAAAATATTTATTATTATAAATTTTTTAATTATATTTTTTAAATTATATATAATTTAAAAAAAAAAATTTATATTTTATTAATTTTTTATTTAATTTTATTAAATAATT IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51593:1056_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 AATTAATAAAATATAAATTTTTTTTTTTAAATTATATATAATTTAAAAAATATAATTAAAAAATTTATAATAATAAATATTTTATTATTTAAAAATTTTTTTAATTTTTTTTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:48833:1070_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TATTTTTATTTATAATTTTTAATTAATATTTAATATTAAATTTAAATATAAAAAATAATATTTTTAAATTTTTAAATTTTAAAATTTTTTAAAAAAATATATTTTTATATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48833:1070_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 TTTAAAAAATTTTAAAATTTAAAAATTTAAAAATATTATTTTTTATATTTAAATTTAATATTAAATATTAATTAAAAATTATAAATAAAAATATAAATAAAATTTAATATAAAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:47288:1084_1:N:0:AAGACCGT+CAATCGAC/1 83 ptg000015l_GA_converted 2139449 42 125M = 2139430 -144 TTTAACTAAATTAAAAACATTATACTAAAAAATTAATAACTCCCACTAACAAAAAACACATAAAAATAAAAACATACATTCTTCAATAATAATTCAAAAAAACTCAAAACAAAAATCCAAAAATT IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:47288:1084_2:N:0:AAGACCGT+CAATCGAC/2 163 ptg000015l_GA_converted 2139430 42 125M = 2139449 144 AAACCACTCTTAATTAATATTTAACTAAATTAAAAACATTATACTAAAAAATTAATAACTCCCACTAACAAAAAACACATAAAAATAAAAACATACATTCTTCAATAATAATTCAAAAAAACTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 >>> Writing bisulfite mapping results to 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:51593:1056_1:N:0:AAGACCGT+CAATCGAC/1 83 ntLink_6_GA_converted 10288123 42 116M = 10288148 141 AATTATCTAATAAAATTAAATAAAAAATTAATAAAATACAAATCTTTCCTTTTAAACCATACACAATTCAAAAAATATAATTAAAAAACTTATAATAATAAATATCTTACTATCCA IIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:109A6 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51593:1056_2:N:0:AAGACCGT+CAATCGAC/2 163 ntLink_6_GA_converted 10288148 42 116M = 10288123 -141 AATTAATAAAATACAAATCTTTCCTTTTAAACCATACACAATTCAAAAAATATAATTAAAAAACTTATAATAATAAATATCTTACTATCCAAAAATCTTTCCAACTCTTTCCAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:84A31 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:48833:1070_1:N:0:AAGACCGT+CAATCGAC/1 83 ptg000016l_GA_converted 6724690 42 118M = 6724715 143 CTAAAAAAATATAAAAACATACTTCTCCAAAAAATTTTAAAATCTAAAAACCCAAAAATACCATTTCCTACATTCAAATTCAATACTAAATATTAATTAAAAATTATAAATAAAAACA IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:118 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:48833:1070_2:N:0:AAGACCGT+CAATCGAC/2 163 ptg000016l_GA_converted 6724715 42 118M = 6724690 -143 TCCAAAAAATTTTAAAATCTAAAAACCCAAAAATACCATTTCCTACATTCAAATTCAATACTAAATATTAATTAAAAATTATAAATAAAAACACAAATAAAATTTAATATAAAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:118 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz (8416551 sequences in total) Input files are 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A5_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 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A5_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)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:39131:1084_1:N:0:AAGACCGT+CAATCGAC/1 99 ntLink_8_CT_converted 13835481 6 107M1I17M = 13835618 262 TTTTTTATTTGTTTTGGTATTATAGGGGTTGTATTTTTTTGGTTTTTATTGTATTTTAGTAATAGATATTAGTTTGTTAATATTAGAGGTTAATGGTTTTTTAATTGTTTTTTTTAAATGTGGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-14 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:124 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39131:1084_2:N:0:AAGACCGT+CAATCGAC/2 147 ntLink_8_CT_converted 13835618 6 125M = 13835481 -262 AGTATTTGGTTTTATATTTTATTTGTTTTATATTGTGTTATTTGGTGATATTGTTAGGAAGTATAATATGGGTTTTTATTTTTATGTTGATGATATTTAGTTGTATTTGTTTTTTGATTTTAAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-8 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:39131:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TTTTTTATTTATTTTAATATTATAAAAATTATATTTTTTTAATTTTTATTATATTTTAATAATAAATATTAATTTATTAATATTAAAAATTAATAATTTTTTAATTATTTTTTTTAAATATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39131:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 TTTTAAAATTAAAAAATAAATATAATTAAATATTATTAATATAAAAATAAAAATTTATATTATATTTTTTAATAATATTATTAAATAATATAATATAAAATAAATAAAATATAAAATTAAATATT IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:39131:1084_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TTTTTTATTTATTTTAATATTATAAAAATTATATTTTTTTAATTTTTATTATATTTTAATAATAAATATTAATTTATTAATATTAAAAATTAATAATTTTTTAATTATTTTTTTTAAATATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39131:1084_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 TTTTAAAATTAAAAAATAAATATAATTAAATATTATTAATATAAAAATAAAAATTTATATTATATTTTTTAATAATATTATTAAATAATATAATATAAAATAAATAAAATATAAAATTAAATATT IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A5_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: LH00526:197:22KFKVLT4:3:1101:39131:1084_1:N:0:AAGACCGT+CAATCGAC/1 83 ptg000008l_GA_converted 18417027 1 10M1I114M = 18416889 -262 CTCCACATTTAAAAAAAACAATTAAAAAACCATTAACCTCTAATATTAACAAACTAATATCTATTACTAAAATACAATAAAAACCAAAAAAATACAACCCCTATAATACCAAAACAAATAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS: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 LH00526:197:22KFKVLT4:3:1101:39131:1084_2:N:0:AAGACCGT+CAATCGAC/2 163 ptg000008l_GA_converted 18416889 1 125M = 18417027 262 TCTTAAAATCAAAAAACAAATACAACTAAATATCATCAACATAAAAATAAAAACCCATATTATACTTCCTAACAATATCACCAAATAACACAATATAAAACAAATAAAATATAAAACCAAATACT IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS: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 >>> Writing bisulfite mapping results to 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1140:24330:23847_1:N:0:AAGACCGT+CAATCGAC ptg000119l 15546 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 LH00526:197:22KFKVLT4:3:1254:5499:11114_1:N:0:AAGACCGT+CAATCGAC ptg000048l 76430 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1332:4811:2695_1:N:0:AAGACCGT+CAATCGAC ptg000025l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1330:21061:15358_1:N:0:AAGACCGT+CAATCGAC ptg000007l 12295855 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36015:7037_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36023:7023_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36007:7023_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36031:7037_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:35999:7037_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1476:39988:15596_1:N:0:AAGACCGT+CAATCGAC ptg000048l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2178:45823:7009_1:N:0:AAGACCGT+CAATCGAC ptg000020l 17861296 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2207:28902:29324_1:N:0:AAGACCGT+CAATCGAC ptg000080l 40111 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2253:33604:9699_1:N:0:AAGACCGT+CAATCGAC ptg000090l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2277:21182:22936_1:N:0:AAGACCGT+CAATCGAC ptg000083l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2335:13187:27755_1:N:0:AAGACCGT+CAATCGAC ptg000122l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2360:20988:29156_1:N:0:AAGACCGT+CAATCGAC ptg000080l 40104 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2470:21757:26956_1:N:0:AAGACCGT+CAATCGAC ptg000056l 59091 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1205:31014:18916_1:N:0:AAGACCGT+CAATCGAC ptg000011l 2 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1231:2270:17683_1:N:0:AAGACCGT+CAATCGAC ptg000039l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1312:32414:18454_1:N:0:AAGACCGT+CAATCGAC ptg000066l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1356:22388:16647_1:N:0:AAGACCGT+CAATCGAC ptg000093l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1339:21886:11268_1:N:0:AAGACCGT+CAATCGAC ptg000002l 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1388:30731:11254_1:N:0:AAGACCGT+CAATCGAC ptg000105l 83227 Processed 6000000 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 LH00526:197:22KFKVLT4:4:1458:2303:18440_1:N:0:AAGACCGT+CAATCGAC ptg000053l 71533 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2101:24354:5230_1:N:0:AAGACCGT+CAATCGAC ptg000074l 12235 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2209:39017:4614_1:N:0:AAGACCGT+CAATCGAC ptg000006l 3 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2219:28797:1939_1:N:0:AAGACCGT+CAATCGAC ptg000027l 16268248 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2167:16432:14013_1:N:0:AAGACCGT+CAATCGAC ptg000130l 1 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 LH00526:197:22KFKVLT4:4:2284:12094:4376_1:N:0:AAGACCGT+CAATCGAC ptg000102l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2194:33733:25444_1:N:0:AAGACCGT+CAATCGAC ptg000117l 29993 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2237:18649:8270_1:N:0:AAGACCGT+CAATCGAC ptg000047l 1 Processed 8000000 sequence pairs so far 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8395413 (99.75%) aligned concordantly 0 times 7603 (0.09%) aligned concordantly exactly 1 time 13535 (0.16%) aligned concordantly >1 times 0.25% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8397089 (99.77%) aligned concordantly 0 times 7493 (0.09%) aligned concordantly exactly 1 time 11969 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3592890 (42.69%) aligned concordantly 0 times 1762653 (20.94%) aligned concordantly exactly 1 time 3061008 (36.37%) aligned concordantly >1 times 57.31% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3597358 (42.74%) aligned concordantly 0 times 1762559 (20.94%) aligned concordantly exactly 1 time 3056634 (36.32%) aligned concordantly >1 times 57.26% overall alignment rate Processed 8416551 sequences in total Successfully deleted the temporary files 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8416551 Final Cytosine Methylation Report ================================= Total number of C's analysed: 229832367 Total methylated C's in CpG context: 3828758 Total methylated C's in CHG context: 204569 Total methylated C's in CHH context: 907358 Total methylated C's in Unknown context: 7051 Total unmethylated C's in CpG context: 32221624 Total unmethylated C's in CHG context: 38683902 Total unmethylated C's in CHH context: 153986156 Total unmethylated C's in Unknown context: 335336 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2491:42804:26802_1:N:0:AAGACCGT+CAATCGAC ptg000083l 3 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8395496 (99.75%) aligned concordantly 0 times 7631 (0.09%) aligned concordantly exactly 1 time 13424 (0.16%) aligned concordantly >1 times 0.25% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3592709 (42.69%) aligned concordantly 0 times 1761781 (20.93%) aligned concordantly exactly 1 time 3062061 (36.38%) aligned concordantly >1 times 57.31% overall alignment rate Processed 8000000 sequence pairs so far 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8397143 (99.77%) aligned concordantly 0 times 7583 (0.09%) aligned concordantly exactly 1 time 11825 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3600140 (42.77%) aligned concordantly 0 times 1758856 (20.90%) aligned concordantly exactly 1 time 3057555 (36.33%) aligned concordantly >1 times 57.23% overall alignment rate Processed 8416551 sequences in total Successfully deleted the temporary files 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8416551 Final Cytosine Methylation Report ================================= Total number of C's analysed: 229642498 Total methylated C's in CpG context: 3827876 Total methylated C's in CHG context: 204565 Total methylated C's in CHH context: 911778 Total methylated C's in Unknown context: 6698 Total unmethylated C's in CpG context: 32234565 Total unmethylated C's in CHG context: 38646517 Total unmethylated C's in CHH context: 153817197 Total unmethylated C's in Unknown context: 335013 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8395217 (99.75%) aligned concordantly 0 times 7596 (0.09%) aligned concordantly exactly 1 time 13738 (0.16%) aligned concordantly >1 times 0.25% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8396965 (99.77%) aligned concordantly 0 times 7431 (0.09%) aligned concordantly exactly 1 time 12155 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3596418 (42.73%) aligned concordantly 0 times 1761106 (20.92%) aligned concordantly exactly 1 time 3059027 (36.35%) aligned concordantly >1 times 57.27% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3600443 (42.78%) aligned concordantly 0 times 1761551 (20.93%) aligned concordantly exactly 1 time 3054557 (36.29%) aligned concordantly >1 times 57.22% overall alignment rate Processed 8416551 sequences in total Successfully deleted the temporary files 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8416551 Final Cytosine Methylation Report ================================= Total number of C's analysed: 229741478 Total methylated C's in CpG context: 3828962 Total methylated C's in CHG context: 204218 Total methylated C's in CHH context: 914129 Total methylated C's in Unknown context: 6818 Total unmethylated C's in CpG context: 32229963 Total unmethylated C's in CHG context: 38657548 Total unmethylated C's in CHH context: 153906658 Total unmethylated C's in Unknown context: 334501 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8396891 (99.77%) aligned concordantly 0 times 7472 (0.09%) aligned concordantly exactly 1 time 12188 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3595123 (42.71%) aligned concordantly 0 times 1762083 (20.94%) aligned concordantly exactly 1 time 3059345 (36.35%) aligned concordantly >1 times 57.29% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 3601066 (42.79%) aligned concordantly 0 times 1761361 (20.93%) aligned concordantly exactly 1 time 3054124 (36.29%) aligned concordantly >1 times 57.21% overall alignment rate 8416551 reads; of these: 8416551 (100.00%) were paired; of these: 8395083 (99.74%) aligned concordantly 0 times 7536 (0.09%) aligned concordantly exactly 1 time 13932 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate Processed 8416551 sequences in total Successfully deleted the temporary files 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8416551 Final Cytosine Methylation Report ================================= Total number of C's analysed: 229749883 Total methylated C's in CpG context: 3826457 Total methylated C's in CHG context: 204871 Total methylated C's in CHH context: 915016 Total methylated C's in Unknown context: 7021 Total unmethylated C's in CpG context: 32232667 Total unmethylated C's in CHG context: 38670087 Total unmethylated C's in CHH context: 153900785 Total unmethylated C's in Unknown context: 334550 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2466:47441:13957_1:N:0:AAGACCGT+CAATCGAC ptg000083l 2 8416550 reads; of these: 8416550 (100.00%) were paired; of these: 8397050 (99.77%) aligned concordantly 0 times 7474 (0.09%) aligned concordantly exactly 1 time 12026 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 8416550 reads; of these: 8416550 (100.00%) were paired; of these: 3591275 (42.67%) aligned concordantly 0 times 1764575 (20.97%) aligned concordantly exactly 1 time 3060700 (36.37%) aligned concordantly >1 times 57.33% overall alignment rate 8416550 reads; of these: 8416550 (100.00%) were paired; of these: 8395359 (99.75%) aligned concordantly 0 times 7453 (0.09%) aligned concordantly exactly 1 time 13738 (0.16%) aligned concordantly >1 times 0.25% overall alignment rate 8416550 reads; of these: 8416550 (100.00%) were paired; of these: 3601214 (42.79%) aligned concordantly 0 times 1759076 (20.90%) aligned concordantly exactly 1 time 3056260 (36.31%) aligned concordantly >1 times 57.21% overall alignment rate Processed 8416550 sequences in total Successfully deleted the temporary files 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A5_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8416550 Final Cytosine Methylation Report ================================= Total number of C's analysed: 229695226 Total methylated C's in CpG context: 3836824 Total methylated C's in CHG context: 205311 Total methylated C's in CHH context: 917681 Total methylated C's in Unknown context: 7100 Total unmethylated C's in CpG context: 32201612 Total unmethylated C's in CHG context: 38654089 Total unmethylated C's in CHH context: 153879709 Total unmethylated C's in Unknown context: 335924 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1A5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1A5_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1A5_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/1A5_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1A5_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/1A5_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A5_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: 42082754 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1148661452 Total methylated C's in CpG context: 19148877 Total methylated C's in CHG context: 1023534 Total methylated C's in CHH context: 4565962 Total methylated C's in Unknown context: 34688 Total unmethylated C's in CpG context: 161120431 Total unmethylated C's in CHG context: 193312143 Total unmethylated C's in CHH context: 769490505 Total unmethylated C's in Unknown context: 1675324 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Deleting temporary report files... Bismark completed in 0d 5h 48m 36s ==================== Bismark run complete ====================