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/1H9_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/1H9_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/1H9_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/1H9_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/1H9_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/1H9_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/1H9_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/1H9_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= 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/1H9_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/1H9_R2_001.fastp-trim.fq.gz 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/1H9_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/1H9_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/1H9_R1_001.fastp-trim.fq.gz for PID: 91335 and offset 5 (sequences written out: 8258719) Using the subset file >1H9_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/1H9_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/1H9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8258720) Using the subset file >1H9_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/1H9_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/1H9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8258720) Using the subset file >1H9_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/1H9_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/1H9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8258720) Using the subset file >1H9_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/1H9_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/1H9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8258719) Using the subset file >1H9_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/1H9_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/1H9_R2_001.fastp-trim.fq.gz for PID: 91335 and offset 5 (sequences written out: 8258719) Using the subset file >1H9_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/1H9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H9_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/1H9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8258720) Using the subset file >1H9_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/1H9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H9_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/1H9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8258720) Using the subset file >1H9_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/1H9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H9_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/1H9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8258720) Using the subset file >1H9_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/1H9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H9_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/1H9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8258719) Using the subset file >1H9_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/1H9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H9_R1_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 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz (8258719 sequences in total) Writing a C -> T converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz (8258720 sequences in total) Writing a C -> T converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz (8258720 sequences in total) Writing a C -> T converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz (8258720 sequences in total) Writing a C -> T converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz (8258719 sequences in total) Writing a C -> T converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H9_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 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz (8258720 sequences in total) Input files are 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40304:1070_1:N:0:GGACATCA+TGCAGGTA/1 99 ptg000004l_CT_converted 3787886 8 99M9I17M = 3788034 273 TTTTGTTGAATTTTATTATGGTTTGAGTGTAGTAGTAAAAGATTTGTTTTTGTAGTTATGTTGTATGTGTAAAATTAATGATAAAATGTAATAAAGAGTAGTAAAAAGTTTTTTTTTGTGGTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-68 XN:i:0 XM:i:6 XO:i:1 XG:i:9 NM:i:15 MD:Z:20A17G20A1A22T9G21 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40304:1070_2:N:0:GGACATCA+TGCAGGTA/2 147 ptg000004l_CT_converted 3788034 8 125M = 3787886 -273 ATTTAAGTATAGTATTTTTTGTTGTAGGTAGGTTTTTTGTAAGTTTTAGATTAAATGTAAGAAAAGTAAGTAAAATTTTTTATTTTTTTTATTTATTTTATAGTTATTTTTGATTTGAATAATGT II9IIIIIIIIII99IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1A25T69A27 YS:i:-68 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40304:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTTATTAAATTTTATTATAATTTAAATATAATAATAAAAAATTTATTTTTATAATTATATTATATATATAAAATTAATAATAAAATATAATAAAAAATAATAAAAAATTTTTTTTTATAATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40304:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 ATATTATTTAAATTAAAAATAATTATAAAATAAATAAAAAAAATAAAAAATTTTATTTATTTTTTTTATATTTAATTTAAAATTTATAAAAAATTTATTTATAATAAAAAATATTATATTTAAAT IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII99IIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40304:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTTATTAAATTTTATTATAATTTAAATATAATAATAAAAAATTTATTTTTATAATTATATTATATATATAAAATTAATAATAAAATATAATAAAAAATAATAAAAAATTTTTTTTTATAATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40304:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 ATATTATTTAAATTAAAAATAATTATAAAATAAATAAAAAAAATAAAAAATTTTATTTATTTTTTTTATATTTAATTTAAAATTTATAAAAAATTTATTTATAATAAAAAATATTATATTTAAAT IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII99IIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40304:1070_1:N:0:GGACATCA+TGCAGGTA/1 83 ptg000004l_GA_converted 2507005 0 17M9I99M = 2506848 -273 ATAACCACAAAAAAAAACTTTTTACTACTCTTTATTACATTTTATCATTAATTTTACACATACAACATAACTACAAAAACAAATCTTTTACTACTACACTCAAACCATAATAAAATTCAACAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-66 XN:i:0 XM:i:4 XO:i:1 XG:i:9 NM:i:13 MD:Z:30A0A29A23A30 YS:i:-26 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40304:1070_2:N:0:GGACATCA+TGCAGGTA/2 163 ptg000004l_GA_converted 2506848 0 119M1I5M = 2507005 273 ACATTATTCAAATCAAAAATAACTATAAAATAAATAAAAAAAATAAAAAATTTTACTTACTTTTCTTACATTTAATCTAAAACTTACAAAAAACCTACCTACAACAAAAAATACTATACTTAAAT IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII99IIIIIIIIII9II AS:i:-26 XS:i:-48 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:27T8T60A26 YS:i:-56 YT:Z:CP >>> Writing bisulfite mapping results to 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz (8258719 sequences in total) Input files are 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:45434:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTTGTGTTATGTTGAGGGAAAAGTAAGTTATTTATTAAGTAGTTGTTTGATGAAAAATGTATTTAATTTGTATTTATTTTTTGAAAGATTAATAAATAATTTGTTATGATATTGTAATTTATAA IIII9IIIIII9-I9IIIIIIIIIIII9II9IIII-IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIIIIIIII9-I9IIIIIII9IIIII-II--IIII9IIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45434:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 TCTTATATTATATTAAAAAAAAAACAAATCATCTATCAAATAACTATTTAATAAAAAATACATTCAATTTATATTTACTTCCTAAAAAATCAACAAATAATCTATCATAATACTATAATTCACAA IIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-IIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:45434:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTTATATTATATTAAAAAAAAAATAAATTATTTATTAAATAATTATTTAATAAAAAATATATTTAATTTATATTTATTTTTTAAAAAATTAATAAATAATTTATTATAATATTATAATTTATAA IIII9IIIIII9-I9IIIIIIIIIIII9II9IIII-IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIIIIIIII9-I9IIIIIII9IIIII-II--IIII9IIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45434:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 TTTTATATTATATTAAAAAAAAAATAAATTATTTATTAAATAATTATTTAATAAAAAATATATTTAATTTATATTTATTTTTTAAAAAATTAATAAATAATTTATTATAATATTATAATTTATAA IIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-IIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:45434:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTTATATTATATTAAAAAAAAAATAAATTATTTATTAAATAATTATTTAATAAAAAATATATTTAATTTATATTTATTTTTTAAAAAATTAATAAATAATTTATTATAATATTATAATTTATAA IIII9IIIIII9-I9IIIIIIIIIIII9II9IIII-IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIIIIIIII9-I9IIIIIII9IIIII-II--IIII9IIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45434:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 TTTTATATTATATTAAAAAAAAAATAAATTATTTATTAAATAATTATTTAATAAAAAATATATTTAATTTATATTTATTTTTTAAAAAATTAATAAATAATTTATTATAATATTATAATTTATAA IIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-IIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:45434:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTTGTGTTATGTTGAGGGAAAAGTAAGTTATTTATTAAGTAGTTGTTTGATGAAAAATGTATTTAATTTGTATTTATTTTTTGAAAGATTAATAAATAATTTGTTATGATATTGTAATTTATAA IIII9IIIIII9-I9IIIIIIIIIIII9II9IIII-IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIIIIIIII9-I9IIIIIII9IIIII-II--IIII9IIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45434:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 TCTTATATTATATTAAAAAAAAAACAAATCATCTATCAAATAACTATTTAATAAAAAATACATTCAATTTATATTTACTTCCTAAAAAATCAACAAATAATCTATCATAATACTATAATTCACAA IIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-IIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Created C -> T as well as G -> A converted versions of the FastQ file 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz (8258720 sequences in total) Input files are 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H9_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)) Reading in the sequence files 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:40482:1070_1:N:0:GGACATCA+TGCAGGTA/1 99 ptg000016l_CT_converted 2168285 2 125M = 2168326 152 AATGAGTGGTGGTAAAGAAAATATGTGTTTAGTTTTGGGATTATTGTTAAGAATTTTGAAGTTTTTGAGAATGATATTTTTGATTGTAAGGTTTTGTGGGTGGTAGGTAAGTGTGAATGGAATTT IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII 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:-52 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40482:1070_2:N:0:GGACATCA+TGCAGGTA/2 147 ptg000016l_CT_converted 2168326 2 104M13I3M1I4M = 2168285 -152 TATTGTTAAGAATTTTGAAGTTTTTGAGAATGATATTTTTGATTGTAAGGTTTTGTGGGTGGTAGGTAAGTGTGAATGGAATTTTGTTGGTTTTTTTGTTTTGTGTTTTGTTTATTAGAATGTTT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-52 XS:i:-49 XN:i:0 XM:i:0 XO:i:2 XG:i:14 NM:i:14 MD:Z:111 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40482:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 AATAAATAATAATAAAAAAAATATATATTTAATTTTAAAATTATTATTAAAAATTTTAAAATTTTTAAAAATAATATTTTTAATTATAAAATTTTATAAATAATAAATAAATATAAATAAAATTT IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40482:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 AAATATTTTAATAAATAAAATATAAAGTAAAAAAATTAATAAAATTTTATTTATATTTATTTATTATTTATAAAATTTTATAATTAAAAATATTATTTTTAAAAATTTTAAAATTTTTAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40482:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 AATAAATAATAATAAAAAAAATATATATTTAATTTTAAAATTATTATTAAAAATTTTAAAATTTTTAAAAATAATATTTTTAATTATAAAATTTTATAAATAATAAATAAATATAAATAAAATTT IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40482:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 AAATATTTTAATAAATAAAATATAAAGTAAAAAAATTAATAAAATTTTATTTATATTTATTTATTATTTATAAAATTTTATAATTAAAAATATTATTTTTAAAAATTTTAAAATTTTTAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40482:1070_1:N:0:GGACATCA+TGCAGGTA/1 83 ptg000015l_GA_converted 979011 0 125M = 978984 -152 AAATTCCATTCACACTTACCTACCACCCACAAAACCTTACAATCAAAAATATCATTCTCAAAAACTTCAAAATTCTTAACAATAATCCCAAAACTAAACACATATTTTCTTTACCACCACTCATT IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII 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:-52 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40482:1070_2:N:0:GGACATCA+TGCAGGTA/2 163 ptg000015l_GA_converted 978984 0 4M1I2M13I105M = 979011 152 AAACATTCTAATAAACAAAACACAAAACAAAAAAACCAACAAAATTCCATTCACACTTACCTACCACCCACAAAACCTTACAATCAAAAATATCATTCTCAAAAACTTCAAAATTCTTAACAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 AS:i:-52 XS:i:-52 XN:i:0 XM:i:0 XO:i:2 XG:i:14 NM:i:14 MD:Z:111 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz (8258720 sequences in total) Input files are 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40822:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 GAATATTTTTTAAATATGTTGTTAGAGGTTGGTTTGGGGAGGATGGGTTGAGGGTGTGAAGATGGTATTTTTGGTAATTTAGTAGGTGGTTGTGGATATGATTGTTGTTGTTGTTGTTGTTGTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40822:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 AAAAAATCAATTTTAACATAAAATCTACACATTTTATATTTCAACCTCAATTTCCCCAACAAATACAATACATAACACAACAACAACAAAAACAACAACAAAAACAACAACAACAATCATATCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIII99IIIIIIIIII9IIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40822:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 AAATATTTTTTAAATATATCATTAAAAATTAATTTAAAAAAAATAAATTAAAAATATAAAAACAATATTTTTAATAATTTAATAAATAATTATAAATATAATTATTATTATTATTATTATTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40822:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 AAAAAATTAATTTTAATATAAAATTTATATATTTTATATTTTAATTTTAATTTTTTTAATAAATATAATATATAATATAATAATAATAAAAATAATAATAAAAATAATAATAATAATTATATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIII99IIIIIIIIII9IIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40822:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 AAATATTTTTTAAATATATCATTAAAAATTAATTTAAAAAAAATAAATTAAAAATATAAAAACAATATTTTTAATAATTTAATAAATAATTATAAATATAATTATTATTATTATTATTATTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40822:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 AAAAAATTAATTTTAATATAAAATTTATATATTTTATATTTTAATTTTAATTTTTTTAATAAATATAATATATAATATAATAATAATAAAAATAATAATAAAAATAATAATAATAATTATATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIII99IIIIIIIIII9IIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40822:1070_1:N:0:GGACATCA+TGCAGGTA/1 83 ptg000008l_GA_converted 6694926 23 125M = 6694822 -229 CAACAACAACAACAACAACAACAATCATATCCACAACCACCTACTAAATTACCAAAAATACCATCTTCACACCCTCAACCCATCCTCCCCAAACCAACCTCTAACAACATATTTAAAAAATATTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:68T5C11A17T20 YS:i:-42 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40822:1070_2:N:0:GGACATCA+TGCAGGTA/2 163 ptg000008l_GA_converted 6694822 23 125M = 6694926 229 AAAAAATCAATTTTAACATAAAATCTACACATTTTATATTTCAACCTCAATTTCCCCAACAAATACAATACATAACACAACAACAACAAAAACAACAACAAAAACAACAACAACAATCATATCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIII99IIIIIIIIII9IIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIII-III AS:i:-42 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:55A45C14C0A1C1A1A1 YS:i:-24 YT:Z:CP >>> Writing bisulfite mapping results to 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz (8258719 sequences in total) Input files are 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H9_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 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40968:1070_1:N:0:GGACATCA+TGCAGGTA/1 99 ntLink_6_CT_converted 13841862 21 125M = 13841856 -131 TTTGTTATTGTGGTTTTGGTTTTGTTTTTTTTAAGTTGGTTGAGATGTTTTTGGTAGGTTAGGTATTAGGAATAAGTTGATAAGGGATGAATTATTAGGTATTATGGGAAAAAGTTTGTAAGAAT IIIIIIIIIIIIIIIII9II9II-IIIIIII-I9I9IIIIII-IIIIII9II9IIIIIII99III9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIII--IIIIIIIIIII-IIIII9IIII- AS:i:-18 XS:i:-50 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:22G8A17A75 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40968:1070_2:N:0:GGACATCA+TGCAGGTA/2 147 ntLink_6_CT_converted 13841856 21 125M = 13841862 131 GTTGATTTTGTTATTGTGGTTTTGGTTTTGTTTTTTTAAAGTTGGTTGAGATGTTATTGGTAGGTTAGGTATTAGGAATAAGTTGATAAGGGATGAATTATTAGGTATTATGGGAAAAAGTTTGT IIIIIIIIIIII-IIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9III AS:i:-6 XS:i:-38 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:28G96 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40968:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTATTATTATAATTTTAATTTTATTTTTTTCAAATTAATTAAAATATTCTTAATAAATTAAATATTAAAAATAAATTAATAAAAAATAAATTATTAAATATTATAAAAAAAAATTTATAAAAAT IIIIIIIIIIIIIIIII9II9II-IIIIIII-I9I9IIIIII-IIIIII9II9IIIIIII99III9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIII--IIIIIIIIIII-IIIII9IIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40968:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 ATAAATTTTTTTTTATAATATTTAATAATTTATTTTTTATTAATTTATTTTTAATATTTAATTTATTAATAATATTTTAATTAATTTTAAAAAAATAAAATTAAAATTATAATAATAAAATTAAT III9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIII-IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40968:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTATTATTATAATTTTAATTTTATTTTTTTCAAATTAATTAAAATATTCTTAATAAATTAAATATTAAAAATAAATTAATAAAAAATAAATTATTAAATATTATAAAAAAAAATTTATAAAAAT IIIIIIIIIIIIIIIII9II9II-IIIIIII-I9I9IIIIII-IIIIII9II9IIIIIII99III9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIII--IIIIIIIIIII-IIIII9IIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40968:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 ATAAATTTTTTTTTATAATATTTAATAATTTATTTTTTATTAATTTATTTTTAATATTTAATTTATTAATAATATTTTAATTAATTTTAAAAAAATAAAATTAAAATTATAATAATAAAATTAAT III9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIII-IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H9_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: LH00526:197:22KFKVLT4:3:1101:40968:1070_1:N:0:GGACATCA+TGCAGGTA/1 77 * 0 0 * * 0 0 TTTGTTATTGTGGTTTTGGTTTTGTTTTTTTTAAGTTGGTTGAGATGTTTTTGGTAGGTTAGGTATTAGGAATAAGTTGATAAGGGATGAATTATTAGGTATTATGGGAAAAAGTTTGTAAGAAT IIIIIIIIIIIIIIIII9II9II-IIIIIII-I9I9IIIIII-IIIIII9II9IIIIIII99III9IIIIII9IIIIIIIIIIIIIIIIIIII-IIIIII--IIIIIIIIIII-IIIII9IIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40968:1070_2:N:0:GGACATCA+TGCAGGTA/2 141 * 0 0 * * 0 0 ACAAACTTTTTCCCATAATACCTAATAATTCATCCCTTATCAACTTATTCCTAATACCTAACCTACCAATAACATCTCAACCAACTTTAAAAAAACAAAACCAAAACCACAATAACAAAATCAAC III9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIII-IIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1178:29250:6589_1:N:0:GGACATCA+TGCAGGTA ptg000066l 66346 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1188:50800:14447_1:N:0:GGACATCA+TGCAGGTA ptg000055l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1197:40717:6967_1:N:0:GGACATCA+TGCAGGTA ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1242:14150:11324_1:N:0:GGACATCA+TGCAGGTA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1242:14166:11324_1:N:0:GGACATCA+TGCAGGTA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1254:1081:11366_1:N:0:GGACATCA+TGCAGGTA ptg000181l 31375 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1441:47190:6379_1:N:0:GGACATCA+TGCAGGTA ptg000097l 1 Processed 2000000 sequence pairs so far 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 LH00526:197:22KFKVLT4:3:2194:35910:22040_1:N:0:GGACATCA+TGCAGGTA ptg000015l 14997092 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2207:29444:6533_1:N:0:GGACATCA+TGCAGGTA ntLink_1 163091 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2243:40895:13607_1:N:0:GGACATCA+TGCAGGTA ptg000066l 66359 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 LH00526:197:22KFKVLT4:3:2324:44358:3213_1:N:0:GGACATCA+TGCAGGTA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2404:19199:16367_1:N:0:GGACATCA+TGCAGGTA ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2417:18050:2919_1:N:0:GGACATCA+TGCAGGTA ptg000025l 21443081 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 LH00526:197:22KFKVLT4:4:1165:51633:8718_1:N:0:GGACATCA+TGCAGGTA ptg000015l 14997091 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1173:35060:4292_1:N:0:GGACATCA+TGCAGGTA ptg000007l 12295855 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1329:36387:12304_1:N:0:GGACATCA+TGCAGGTA ntLink_3 131384 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1440:8688:25514_1:N:0:GGACATCA+TGCAGGTA ptg000027l 16268299 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2191:13179:9503_1:N:0:GGACATCA+TGCAGGTA ptg000117l 30008 Processed 7000000 sequence pairs so far 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 LH00526:197:22KFKVLT4:4:2238:31783:21451_1:N:0:GGACATCA+TGCAGGTA ptg000015l 14997091 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2336:16440:23272_1:N:0:GGACATCA+TGCAGGTA ntLink_2 399363 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2286:46397:28287_1:N:0:GGACATCA+TGCAGGTA ptg000077l 42461 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2405:28951:9825_1:N:0:GGACATCA+TGCAGGTA ptg000080l 40132 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2380:34316:21269_1:N:0:GGACATCA+TGCAGGTA ptg000077l 42461 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2421:13648:3900_1:N:0:GGACATCA+TGCAGGTA ptg000077l 42461 Processed 8000000 sequence pairs so far 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 8237189 (99.74%) aligned concordantly 0 times 8584 (0.10%) aligned concordantly exactly 1 time 12947 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 3636297 (44.03%) aligned concordantly 0 times 1724447 (20.88%) aligned concordantly exactly 1 time 2897976 (35.09%) aligned concordantly >1 times 55.97% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 3630291 (43.96%) aligned concordantly 0 times 1727032 (20.91%) aligned concordantly exactly 1 time 2901397 (35.13%) aligned concordantly >1 times 56.04% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 8236102 (99.73%) aligned concordantly 0 times 8789 (0.11%) aligned concordantly exactly 1 time 13829 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate Processed 8258720 sequences in total Successfully deleted the temporary files 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8258720 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224440589 Total methylated C's in CpG context: 3356878 Total methylated C's in CHG context: 210772 Total methylated C's in CHH context: 897207 Total methylated C's in Unknown context: 6179 Total unmethylated C's in CpG context: 32373997 Total unmethylated C's in CHG context: 38032330 Total unmethylated C's in CHH context: 149569405 Total unmethylated C's in Unknown context: 316856 C methylated in CpG context: 9.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 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 LH00526:197:22KFKVLT4:4:2476:49149:18706_1:N:0:GGACATCA+TGCAGGTA ptg000083l 2 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 3629116 (43.94%) aligned concordantly 0 times 1727564 (20.92%) aligned concordantly exactly 1 time 2902040 (35.14%) aligned concordantly >1 times 56.06% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 3636378 (44.03%) aligned concordantly 0 times 1723393 (20.87%) aligned concordantly exactly 1 time 2898949 (35.10%) aligned concordantly >1 times 55.97% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 8235828 (99.72%) aligned concordantly 0 times 8704 (0.11%) aligned concordantly exactly 1 time 14188 (0.17%) aligned concordantly >1 times 0.28% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 8236614 (99.73%) aligned concordantly 0 times 8751 (0.11%) aligned concordantly exactly 1 time 13355 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate Processed 8258720 sequences in total Successfully deleted the temporary files 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8258720 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224460579 Total methylated C's in CpG context: 3370536 Total methylated C's in CHG context: 213328 Total methylated C's in CHH context: 898118 Total methylated C's in Unknown context: 6091 Total unmethylated C's in CpG context: 32366217 Total unmethylated C's in CHG context: 38031643 Total unmethylated C's in CHH context: 149580737 Total unmethylated C's in Unknown context: 317106 C methylated in CpG context: 9.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 8236901 (99.74%) aligned concordantly 0 times 8569 (0.10%) aligned concordantly exactly 1 time 13250 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 3636303 (44.03%) aligned concordantly 0 times 1724470 (20.88%) aligned concordantly exactly 1 time 2897947 (35.09%) aligned concordantly >1 times 55.97% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 3627596 (43.92%) aligned concordantly 0 times 1728663 (20.93%) aligned concordantly exactly 1 time 2902461 (35.14%) aligned concordantly >1 times 56.08% overall alignment rate 8258720 reads; of these: 8258720 (100.00%) were paired; of these: 8235789 (99.72%) aligned concordantly 0 times 8688 (0.11%) aligned concordantly exactly 1 time 14243 (0.17%) aligned concordantly >1 times 0.28% overall alignment rate Processed 8258720 sequences in total Successfully deleted the temporary files 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8258720 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224555975 Total methylated C's in CpG context: 3356155 Total methylated C's in CHG context: 212919 Total methylated C's in CHH context: 906781 Total methylated C's in Unknown context: 6133 Total unmethylated C's in CpG context: 32394649 Total unmethylated C's in CHG context: 38063701 Total unmethylated C's in CHH context: 149621770 Total unmethylated C's in Unknown context: 316037 C methylated in CpG context: 9.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 3629355 (43.95%) aligned concordantly 0 times 1727219 (20.91%) aligned concordantly exactly 1 time 2902145 (35.14%) aligned concordantly >1 times 56.05% overall alignment rate 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 3634760 (44.01%) aligned concordantly 0 times 1724509 (20.88%) aligned concordantly exactly 1 time 2899450 (35.11%) aligned concordantly >1 times 55.99% overall alignment rate 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 8237115 (99.74%) aligned concordantly 0 times 8596 (0.10%) aligned concordantly exactly 1 time 13008 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 8236318 (99.73%) aligned concordantly 0 times 8587 (0.10%) aligned concordantly exactly 1 time 13814 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate Processed 8258719 sequences in total Successfully deleted the temporary files 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8258719 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224440476 Total methylated C's in CpG context: 3361346 Total methylated C's in CHG context: 211312 Total methylated C's in CHH context: 896341 Total methylated C's in Unknown context: 6266 Total unmethylated C's in CpG context: 32371034 Total unmethylated C's in CHG context: 38030723 Total unmethylated C's in CHH context: 149569720 Total unmethylated C's in Unknown context: 316004 C methylated in CpG context: 9.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 3632410 (43.98%) aligned concordantly 0 times 1725383 (20.89%) aligned concordantly exactly 1 time 2900926 (35.13%) aligned concordantly >1 times 56.02% overall alignment rate 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 3628696 (43.94%) aligned concordantly 0 times 1727068 (20.91%) aligned concordantly exactly 1 time 2902955 (35.15%) aligned concordantly >1 times 56.06% overall alignment rate 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 8237000 (99.74%) aligned concordantly 0 times 8642 (0.10%) aligned concordantly exactly 1 time 13077 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 8258719 reads; of these: 8258719 (100.00%) were paired; of these: 8236063 (99.73%) aligned concordantly 0 times 8700 (0.11%) aligned concordantly exactly 1 time 13956 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate Processed 8258719 sequences in total Successfully deleted the temporary files 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8258719 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224507359 Total methylated C's in CpG context: 3364735 Total methylated C's in CHG context: 211879 Total methylated C's in CHH context: 905833 Total methylated C's in Unknown context: 6232 Total unmethylated C's in CpG context: 32379142 Total unmethylated C's in CHG context: 38041090 Total unmethylated C's in CHH context: 149604680 Total unmethylated C's in Unknown context: 315934 C methylated in CpG context: 9.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1H9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1H9_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1H9_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/1H9_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1H9_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/1H9_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H9_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: 41293598 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1122404978 Total methylated C's in CpG context: 16809650 Total methylated C's in CHG context: 1060210 Total methylated C's in CHH context: 4504280 Total methylated C's in Unknown context: 30901 Total unmethylated C's in CpG context: 161885039 Total unmethylated C's in CHG context: 190199487 Total unmethylated C's in CHH context: 747946312 Total unmethylated C's in Unknown context: 1581937 C methylated in CpG context: 9.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Deleting temporary report files... Bismark completed in 0d 5h 8m 27s ==================== Bismark run complete ====================