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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_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/1C9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8132087) Using the subset file >1C9_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/1C9_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/1C9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8132088) Using the subset file >1C9_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/1C9_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/1C9_R1_001.fastp-trim.fq.gz for PID: 20432 and offset 5 (sequences written out: 8132087) Using the subset file >1C9_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/1C9_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/1C9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8132088) Using the subset file >1C9_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/1C9_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/1C9_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8132087) Using the subset file >1C9_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/1C9_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/1C9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8132088) Using the subset file >1C9_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/1C9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz to 1C9_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/1C9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8132088) Using the subset file >1C9_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/1C9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz to 1C9_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/1C9_R2_001.fastp-trim.fq.gz for PID: 20432 and offset 5 (sequences written out: 8132087) Using the subset file >1C9_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/1C9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz to 1C9_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/1C9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8132087) Using the subset file >1C9_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/1C9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz to 1C9_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/1C9_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8132087) Using the subset file >1C9_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/1C9_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz to 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz (8132088 sequences in total) Writing a C -> T converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz to 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz (8132088 sequences in total) Writing a C -> T converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz to 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz (8132087 sequences in total) Writing a C -> T converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz to 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz (8132087 sequences in total) Writing a C -> T converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz to 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz (8132087 sequences in total) Writing a C -> T converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz to 1C9_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 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz (8132088 sequences in total) Input files are 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:49456:1056_1:N:0:TCCTCATG+AGGTGTAC/1 99 ntLink_6_CT_converted 9891496 0 44M11D81M = 9891483 -149 TGTAATATGGGTAGATATTTTTTTGTTAAGGGAGTTGGAGGATGTTAAGGTATTTGAAGGAATTAATATAGTTTAGGATTTTGTTGTTAATTTTGATTTTAGGTGTATTGGTTGTGGATTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-44 XS:i:-61 XN:i:0 XM:i:1 XO:i:1 XG:i:11 NM:i:12 MD:Z:44^ATAGGTTGTTT9G71 YS:i:-44 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49456:1056_2:N:0:TCCTCATG+AGGTGTAC/2 147 ntLink_6_CT_converted 9891483 0 57M11D68M = 9891496 149 AGGTATTTGTTTTTGTAATATGGGTAGATATTTTTTTGTTAAGGGAGTTGGAGGATGTTAAGGTATTTGAAGGAATTAATATAGTTTAGGATTTTGTTGTTAATTTTGATTTTAGGTGTATTGGT IIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-44 XS:i:-61 XN:i:0 XM:i:1 XO:i:1 XG:i:11 NM:i:12 MD:Z:57^ATAGGTTGTTT9G58 YS:i:-44 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:49456:1056_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TATAATATAAATAAATATTTTTTTATTAAAAAAATTAAAAAATATTAAAATATTTAAAAAAATTAATATAATTTAAAATTTTATTATTAATTTTAATTTTAAATATATTAATTATAAATTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49456:1056_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 ATTAATATATTTAAAATTAAAATTAATAATAAAATTTTAAATTATATTAATTTTTTTAAATATTTTAATATTTTTTAATTTTTTTAATAAAAAAATATTTATTTATATTATAAAAATAAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:49456:1056_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TATAATATAAATAAATATTTTTTTATTAAAAAAATTAAAAAATATTAAAATATTTAAAAAAATTAATATAATTTAAAATTTTATTATTAATTTTAATTTTAAATATATTAATTATAAATTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49456:1056_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 ATTAATATATTTAAAATTAAAATTAATAATAAAATTTTAAATTATATTAATTTTTTTAAATATTTTAATATTTTTTAATTTTTTTAATAAAAAAATATTTATTTATATTATAAAAATAAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:49456:1056_1:N:0:TCCTCATG+AGGTGTAC/1 83 ptg000018l_GA_converted 10448679 0 81M11D44M = 10448692 149 AAAAAAATCCACAACCAATACACCTAAAATCAAAATTAACAACAAAATCCTAAACTATATTAATTCCTTCAAATACCTTAACATCCTCCAACTCCCTTAACAAAAAAATATCTACCCATATTACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-68 XN:i:0 XM:i:3 XO:i:1 XG:i:11 NM:i:14 MD:Z:15T55C9^AAACAACCTAT13T30 YS:i:-56 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49456:1056_2:N:0:TCCTCATG+AGGTGTAC/2 163 ptg000018l_GA_converted 10448692 0 68M11D57M = 10448679 -149 ACCAATACACCTAAAATCAAAATTAACAACAAAATCCTAAACTATATTAATTCCTTCAAATACCTTAACATCCTCCAACTCCCTTAACAAAAAAATATCTACCCATATTACAAAAACAAATACCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIII AS:i:-56 XS:i:-62 XN:i:0 XM:i:3 XO:i:1 XG:i:11 NM:i:14 MD:Z:2T55C9^AAACAACCTAT13T43 YS:i:-56 YT:Z:CP >>> Writing bisulfite mapping results to 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz (8132088 sequences in total) Input files are 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44366:1070_1:N:0:TCCTCATG+AGGTGTAC/1 99 ptg000018l_CT_converted 4625737 2 125M = 4625877 278 TGATTATATTTGGATTTTTTGAGTAAAAGAAAAATTTTTTTGTTTTTAGTTTAAGTTATAAAATTTAAAATTTATTGTAGATTGTAAAAGGATTTTAATTGTAAGTAGTTATTTATAATAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-36 XS:i:-48 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:10A4A12T34A30G11T18 YS:i:-74 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44366:1070_2:N:0:TCCTCATG+AGGTGTAC/2 147 ptg000018l_CT_converted 4625877 2 48M13D77M = 4625737 -278 TTGGTTAAATTATTGTATTAAAGGTTGTAAAAAGTGTTTTTGTGTTTAATTAAGGTAGTTTTTGAGTTTTATATTGTTAGTTTATTGTTTGAGAATTATTTTTGGATTGTTAAAGTATGTTTATT IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-74 XS:i:-74 XN:i:0 XM:i:5 XO:i:1 XG:i:13 NM:i:18 MD:Z:14A18A7T6^ATTATTAATTTTT20G49T6 YS:i:-36 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44366:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TAATTATATTTAAATTTTTTAAATAAAAAAAAAATTTTTTTATTTTTAATTTAAATTATAAAATTTAAAATTTATTATAAATTATAAAAAAATTTTAATTATAAATAATTATTTATAATAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44366:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 AATAAATATATTTTAATAATTTAAAAATAATTTTTAAATAATAAATTAATAATATAAAATTTAAAAATTATTTTAATTAAATATAAAAATATTTTTTATAATTTTTAATATAATAATTTAATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44366:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TAATTATATTTAAATTTTTTAAATAAAAAAAAAATTTTTTTATTTTTAATTTAAATTATAAAATTTAAAATTTATTATAAATTATAAAAAAATTTTAATTATAAATAATTATTTATAATAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44366:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 AATAAATATATTTTAATAATTTAAAAATAATTTTTAAATAATAAATTAATAATATAAAATTTAAAAATTATTTTAATTAAATATAAAAATATTTTTTATAATTTTTAATATAATAATTTAATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44366:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TGATTATATTTGGATTTTTTGAGTAAAAGAAAAATTTTTTTGTTTTTAGTTTAAGTTATAAAATTTAAAATTTATTGTAGATTGTAAAAGGATTTTAATTGTAAGTAGTTATTTATAATAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44366:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 AATAAACATACTTTAACAATCCAAAAATAATTCTCAAACAATAAACTAACAATATAAAACTCAAAAACTACCTTAATTAAACACAAAAACACTTTTTACAACCTTTAATACAATAATTTAACCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP >>> Writing bisulfite mapping results to 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz (8132087 sequences in total) Input files are 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:48315:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TTTGATGATAAGGTGAGTTTGTAGTAGTAAAAATTTTATTATTTGTTTTTGTATGAAGTTTATTTGTGTTAAGTAAATGAAGGTATATTTTGTTTATTTTGTATAATGTGATTAATATGGAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48315:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 ATAAAAAAATTTACCTAAATCCAAAAAAACAAAAAAAAAAAAACAACACATAAAATTCAAAAAAAAAAAAATTTAAAAAACTAAAACTTTACATTAAATCATAATCACATATTTCCAATTATTCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9I999IIIIIIIIIIIIII9IIII-II9-I9IIII--II9III9-I9II9II-I--I9I-I-I9-IIII99-II-I9I9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:48315:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TTTAATAATAAAATAAATTTATAATAATAAAAATTTTATTATTTATTTTTATATAAAATTTATTTATATTAAATAAATAAAAATATATTTTATTTATTTTATATAATATAATTAATATAAAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48315:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 ATAAAAAAATTTATTTAAATTTAAAAAAATAAAAAAAAAAAAATAATATATAAAATTTAAAAAAAAAAAAATTTAAAAAATTAAAATTTTATATTAAATTATAATTATATATTTTTAATTATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9I999IIIIIIIIIIIIII9IIII-II9-I9IIII--II9III9-I9II9II-I--I9I-I-I9-IIII99-II-I9I9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:48315:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TTTAATAATAAAATAAATTTATAATAATAAAAATTTTATTATTTATTTTTATATAAAATTTATTTATATTAAATAAATAAAAATATATTTTATTTATTTTATATAATATAATTAATATAAAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48315:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 ATAAAAAAATTTATTTAAATTTAAAAAAATAAAAAAAAAAAAATAATATATAAAATTTAAAAAAAAAAAAATTTAAAAAATTAAAATTTTATATTAAATTATAATTATATATTTTTAATTATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9I999IIIIIIIIIIIIII9IIII-II9-I9IIII--II9III9-I9II9II-I--I9I-I-I9-IIII99-II-I9I9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:48315:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TTTGATGATAAGGTGAGTTTGTAGTAGTAAAAATTTTATTATTTGTTTTTGTATGAAGTTTATTTGTGTTAAGTAAATGAAGGTATATTTTGTTTATTTTGTATAATGTGATTAATATGGAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48315:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 ATAAAAAAATTTACCTAAATCCAAAAAAACAAAAAAAAAAAAACAACACATAAAATTCAAAAAAAAAAAAATTTAAAAAACTAAAACTTTACATTAAATCATAATCACATATTTCCAATTATTCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9I999IIIIIIIIIIIIII9IIII-II9-I9IIII--II9III9-I9II9II-I--I9I-I-I9-IIII99-II-I9I9 YT:Z:UP >>> Writing bisulfite mapping results to 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz Created C -> T as well as G -> A converted versions of the FastQ file 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz (8132087 sequences in total) Input files are 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:46017:1070_1:N:0:TCCTCATG+AGGTGTAC/1 99 ptg000004l_CT_converted 11907127 0 125M = 11907178 173 GTAGTTGTTTAATTTATATAAAATTAATTATTTATTGATTATGGTATTATATAATTGTGGTGGTAGTTGTTTAATTTATATAAAATTATTTATTTATTGATTATGGTATTATGGTATTATGGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-48 XS:i:-42 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:17T9A20G1G0G0T57G7G6 YS:i:-38 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:46017:1070_2:N:0:TCCTCATG+AGGTGTAC/2 147 ptg000004l_CT_converted 11907178 0 2M3I120M = 11907127 -173 ATATAATTGTGGTGGTAGTTGTTTAATTTATATAAAATTATTTATTTATTGATTATGGTATTATGGTATTATGGTAGTAGTTGTTTAATTTATATAAAATTATTTATTTATTGATTATGGTATTG IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-38 XS:i:-44 XN:i:0 XM:i:4 XO:i:1 XG:i:3 NM:i:7 MD:Z:0G58G7G27G26 YS:i:-48 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:46017:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 ATAATTATTTAATTTATATAAAATTAATTATTTATTAATTATAATATTATATAATTATAATAATAATTATTTAATTTATATAAAATTATTTATTTATTAATTATAATATTATAATATTATAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46017:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 TAATATTATAATTAATAAATAAATAATTTTATATAAATTAAATAATTATTATTATAATATTATAATATTATAATTAATAAATAAATAATTTTATATAAATTAAATAATTATTATTATAATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:46017:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 ATAATTATTTAATTTATATAAAATTAATTATTTATTAATTATAATATTATATAATTATAATAATAATTATTTAATTTATATAAAATTATTTATTTATTAATTATAATATTATAATATTATAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46017:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 TAATATTATAATTAATAAATAAATAATTTTATATAAATTAAATAATTATTATTATAATATTATAATATTATAATTAATAAATAAATAATTTTATATAAATTAAATAATTATTATTATAATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:46017:1070_1:N:0:TCCTCATG+AGGTGTAC/1 83 ptg000023l_GA_converted 36651039 0 125M = 36650991 -173 CTACCATAATACCATAATACCATAATCAATAAATAAATAATTTTATATAAATTAAACAACTACCACCACAATTATATAATACCATAATCAATAAATAATTAATTTTATATAAATTAAACAACTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-42 XS:i:-42 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:6C7C48T8A0C0C1C48 YS:i:-38 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:46017:1070_2:N:0:TCCTCATG+AGGTGTAC/2 163 ptg000023l_GA_converted 36650991 0 118M3I4M = 36651039 173 CAATACCATAATCAATAAATAAATAATTTTATATAAATTAAACAACTACTACCATAATACCATAATACCATAATCAATAAATAAATAATTTTATATAAATTAAACAACTACCACCACAATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII AS:i:-38 XS:i:-42 XN:i:0 XM:i:4 XO:i:1 XG:i:3 NM:i:7 MD:Z:54C7C48T9C0 YS:i:-42 YT:Z:CP >>> Writing bisulfite mapping results to 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz Created C -> T as well as G -> A converted versions of the FastQ file 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz (8132087 sequences in total) Input files are 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C9_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 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44658:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TGTATTGAGTATTATAAGGTATTTTATTTTTAGATGTATTTTTATATTATATAATTATAGGTAATAGTATGATTTGTAGTGGTATTTGATAATAATATTGTAAGTGATATTTTAAAATTGTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44658:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 CACTCACTACTTCATAACTCATAATATTTTAAACAATTTTAAAATATCACTTACAATATTATTATCAAATACCACTACAAATCATACTATTACCTATAATTATATAATATAAAAATACATCTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44658:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TATATTAAATATTATAAAATATTTTATTTTTAAATATATTTTTATATTATATAATTATAAATAATAATATAATTTATAATAATATTTAATAATAATATCATAAATAATATTTTAAAATTATTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44658:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 TATTTGTTATTTTGTAGTTTGTAATATTTTAAATAATTTTAAAATATTATTTATGATATTATTATTAAATATTATTATAAATTATATTATTATTTATAATTATATAATATAAAAATATATTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44658:1070_1:N:0:TCCTCATG+AGGTGTAC/1 77 * 0 0 * * 0 0 TATATTAAATATTATAAAATATTTTATTTTTAAATATATTTTTATATTATATAATTATAAATAATAATATAATTTATAATAATATTTAATAATAATATCATAAATAATATTTTAAAATTATTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44658:1070_2:N:0:TCCTCATG+AGGTGTAC/2 141 * 0 0 * * 0 0 TATTTGTTATTTTGTAGTTTGTAATATTTTAAATAATTTTAAAATATTATTTATGATATTATTATTAAATATTATTATAAATTATATTATTATTTATAATTATATAATATAAAAATATATTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C9_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: LH00526:197:22KFKVLT4:3:1101:44658:1070_1:N:0:TCCTCATG+AGGTGTAC/1 83 ptg000025l_GA_converted 16355496 42 125M = 16355468 -153 TTAAACAATTTTAAAATATCACTTACAATATTATTATCAAATACCACTACAAATCATACTATTACCTATAATTATATAATATAAAAATACATCTAAAAATAAAATACCTTATAATACTCAATACA III9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:44658:1070_2:N:0:TCCTCATG+AGGTGTAC/2 163 ptg000025l_GA_converted 16355468 42 125M = 16355496 153 CACTCACTACTTCATAACTCATAATATTTTAAACAATTTTAAAATATCACTTACAATATTATTATCAAATACCACTACAAATCATACTATTACCTATAATTATATAATATAAAAATACATCTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII 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 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1248:24856:15624_1:N:0:TCCTCATG+AGGTGTAC ptg000097l 1 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1303:40717:1868_1:N:0:TCCTCATG+AGGTGTAC ptg000101l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1288:20494:22922_1:N:0:TCCTCATG+AGGTGTAC ptg000054l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1296:40862:12094_1:N:0:TCCTCATG+AGGTGTAC ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1383:9829:25500_1:N:0:TCCTCATG+AGGTGTAC ptg000159l 21836 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1419:23610:6771_1:N:0:TCCTCATG+AGGTGTAC ptg000039l 1139394 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1460:40992:23749_1:N:0:TCCTCATG+AGGTGTAC ptg000114l 51140 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 LH00526:197:22KFKVLT4:3:2293:47870:6155_1:N:0:TCCTCATG+AGGTGTAC ptg000083l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2316:40466:3115_1:N:0:TCCTCATG+AGGTGTAC ptg000085l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2376:46414:21199_1:N:0:TCCTCATG+AGGTGTAC ptg000024l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2423:29153:15050_1:N:0:TCCTCATG+AGGTGTAC ptg000133l 2 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 LH00526:197:22KFKVLT4:4:1128:27559:29380_1:N:0:TCCTCATG+AGGTGTAC ptg000075l 54149 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1164:7425:8312_1:N:0:TCCTCATG+AGGTGTAC ptg000160l 32584 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1168:43468:14924_1:N:0:TCCTCATG+AGGTGTAC ptg000174l 27225 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1164:7417:8326_1:N:0:TCCTCATG+AGGTGTAC ptg000117l 29995 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1163:45103:25121_1:N:0:TCCTCATG+AGGTGTAC ptg000115l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1229:18495:28511_1:N:0:TCCTCATG+AGGTGTAC ptg000012l 20102961 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 LH00526:197:22KFKVLT4:4:1369:3743:27657_1:N:0:TCCTCATG+AGGTGTAC ptg000020l 17861296 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 LH00526:197:22KFKVLT4:4:2148:11601:6883_1:N:0:TCCTCATG+AGGTGTAC ptg000006l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2188:12887:21914_1:N:0:TCCTCATG+AGGTGTAC ptg000033l 2625611 Processed 7000000 sequence pairs so far 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 LH00526:197:22KFKVLT4:4:2357:11471:20611_1:N:0:TCCTCATG+AGGTGTAC ptg000048l 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 8112036 (99.75%) aligned concordantly 0 times 6629 (0.08%) aligned concordantly exactly 1 time 13422 (0.17%) aligned concordantly >1 times 0.25% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 8115592 (99.80%) aligned concordantly 0 times 6482 (0.08%) aligned concordantly exactly 1 time 10013 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 3657843 (44.98%) aligned concordantly 0 times 1790908 (22.02%) aligned concordantly exactly 1 time 2683336 (33.00%) aligned concordantly >1 times 55.02% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 3652102 (44.91%) aligned concordantly 0 times 1793567 (22.06%) aligned concordantly exactly 1 time 2686418 (33.03%) aligned concordantly >1 times 55.09% overall alignment rate Processed 8132087 sequences in total Successfully deleted the temporary files 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8132087 Final Cytosine Methylation Report ================================= Total number of C's analysed: 233607656 Total methylated C's in CpG context: 4406721 Total methylated C's in CHG context: 219136 Total methylated C's in CHH context: 968826 Total methylated C's in Unknown context: 7339 Total unmethylated C's in CpG context: 31778962 Total unmethylated C's in CHG context: 39517601 Total unmethylated C's in CHH context: 156716410 Total unmethylated C's in Unknown context: 325666 C methylated in CpG context: 12.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 3655739 (44.95%) aligned concordantly 0 times 1791339 (22.03%) aligned concordantly exactly 1 time 2685010 (33.02%) aligned concordantly >1 times 55.05% overall alignment rate 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 8112132 (99.75%) aligned concordantly 0 times 6543 (0.08%) aligned concordantly exactly 1 time 13413 (0.16%) aligned concordantly >1 times 0.25% overall alignment rate 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 8115368 (99.79%) aligned concordantly 0 times 6542 (0.08%) aligned concordantly exactly 1 time 10178 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 3658930 (44.99%) aligned concordantly 0 times 1791739 (22.03%) aligned concordantly exactly 1 time 2681419 (32.97%) aligned concordantly >1 times 55.01% overall alignment rate Processed 8132088 sequences in total Successfully deleted the temporary files 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8132088 Final Cytosine Methylation Report ================================= Total number of C's analysed: 233588655 Total methylated C's in CpG context: 4405418 Total methylated C's in CHG context: 218334 Total methylated C's in CHH context: 962720 Total methylated C's in Unknown context: 7249 Total unmethylated C's in CpG context: 31763223 Total unmethylated C's in CHG context: 39535123 Total unmethylated C's in CHH context: 156703837 Total unmethylated C's in Unknown context: 324856 C methylated in CpG context: 12.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 8115152 (99.79%) aligned concordantly 0 times 6641 (0.08%) aligned concordantly exactly 1 time 10294 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 3653032 (44.92%) aligned concordantly 0 times 1792624 (22.04%) aligned concordantly exactly 1 time 2686431 (33.03%) aligned concordantly >1 times 55.08% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 8111880 (99.75%) aligned concordantly 0 times 6657 (0.08%) aligned concordantly exactly 1 time 13550 (0.17%) aligned concordantly >1 times 0.25% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 3657888 (44.98%) aligned concordantly 0 times 1790348 (22.02%) aligned concordantly exactly 1 time 2683851 (33.00%) aligned concordantly >1 times 55.02% overall alignment rate Processed 8132087 sequences in total Successfully deleted the temporary files 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8132087 Final Cytosine Methylation Report ================================= Total number of C's analysed: 233560876 Total methylated C's in CpG context: 4401925 Total methylated C's in CHG context: 220018 Total methylated C's in CHH context: 975660 Total methylated C's in Unknown context: 7284 Total unmethylated C's in CpG context: 31768700 Total unmethylated C's in CHG context: 39504468 Total unmethylated C's in CHH context: 156690105 Total unmethylated C's in Unknown context: 324702 C methylated in CpG context: 12.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 8111772 (99.75%) aligned concordantly 0 times 6689 (0.08%) aligned concordantly exactly 1 time 13626 (0.17%) aligned concordantly >1 times 0.25% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 3656839 (44.97%) aligned concordantly 0 times 1791234 (22.03%) aligned concordantly exactly 1 time 2684014 (33.01%) aligned concordantly >1 times 55.03% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 8115110 (99.79%) aligned concordantly 0 times 6657 (0.08%) aligned concordantly exactly 1 time 10320 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 8132087 reads; of these: 8132087 (100.00%) were paired; of these: 3651643 (44.90%) aligned concordantly 0 times 1793082 (22.05%) aligned concordantly exactly 1 time 2687362 (33.05%) aligned concordantly >1 times 55.10% overall alignment rate Processed 8132087 sequences in total Successfully deleted the temporary files 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8132087 Final Cytosine Methylation Report ================================= Total number of C's analysed: 233720582 Total methylated C's in CpG context: 4412287 Total methylated C's in CHG context: 219854 Total methylated C's in CHH context: 977374 Total methylated C's in Unknown context: 7416 Total unmethylated C's in CpG context: 31779784 Total unmethylated C's in CHG context: 39538309 Total unmethylated C's in CHH context: 156792974 Total unmethylated C's in Unknown context: 324064 C methylated in CpG context: 12.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% Now waiting for all child processes to complete Processed 8000000 sequence pairs so far 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 8115444 (99.80%) aligned concordantly 0 times 6557 (0.08%) aligned concordantly exactly 1 time 10087 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 3660367 (45.01%) aligned concordantly 0 times 1789384 (22.00%) aligned concordantly exactly 1 time 2682337 (32.98%) aligned concordantly >1 times 54.99% overall alignment rate 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 8112120 (99.75%) aligned concordantly 0 times 6533 (0.08%) aligned concordantly exactly 1 time 13435 (0.17%) aligned concordantly >1 times 0.25% overall alignment rate 8132088 reads; of these: 8132088 (100.00%) were paired; of these: 3651550 (44.90%) aligned concordantly 0 times 1794664 (22.07%) aligned concordantly exactly 1 time 2685874 (33.03%) aligned concordantly >1 times 55.10% overall alignment rate Processed 8132088 sequences in total Successfully deleted the temporary files 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C9_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8132088 Final Cytosine Methylation Report ================================= Total number of C's analysed: 233644076 Total methylated C's in CpG context: 4413537 Total methylated C's in CHG context: 219346 Total methylated C's in CHH context: 962904 Total methylated C's in Unknown context: 7254 Total unmethylated C's in CpG context: 31769597 Total unmethylated C's in CHG context: 39526778 Total unmethylated C's in CHH context: 156751914 Total unmethylated C's in Unknown context: 325050 C methylated in CpG context: 12.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1C9_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1C9_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1C9_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/1C9_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1C9_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/1C9_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C9_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C9_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: 40660437 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1168121845 Total methylated C's in CpG context: 22039888 Total methylated C's in CHG context: 1096688 Total methylated C's in CHH context: 4847484 Total methylated C's in Unknown context: 36542 Total unmethylated C's in CpG context: 158860266 Total unmethylated C's in CHG context: 197622279 Total unmethylated C's in CHH context: 783655240 Total unmethylated C's in Unknown context: 1624338 C methylated in CpG context: 12.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% Deleting temporary report files... Bismark completed in 0d 5h 16m 8s ==================== Bismark run complete ====================