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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_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/2H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6420758) Using the subset file >2H3_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/2H3_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/2H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6420759) Using the subset file >2H3_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/2H3_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/2H3_R1_001.fastp-trim.fq.gz for PID: 74677 and offset 5 (sequences written out: 6420758) Using the subset file >2H3_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/2H3_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/2H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6420759) Using the subset file >2H3_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/2H3_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/2H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6420758) Using the subset file >2H3_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/2H3_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/2H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6420759) Using the subset file >2H3_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/2H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz to 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz to 2H3_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/2H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6420759) Using the subset file >2H3_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/2H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz to 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz to 2H3_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/2H3_R2_001.fastp-trim.fq.gz for PID: 74677 and offset 5 (sequences written out: 6420758) Using the subset file >2H3_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/2H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz to 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz to 2H3_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/2H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6420758) Using the subset file >2H3_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/2H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz to 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz to 2H3_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/2H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6420758) Using the subset file >2H3_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/2H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz to 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz to 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz (6420759 sequences in total) Writing a C -> T converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz to 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz to 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz (6420758 sequences in total) Writing a C -> T converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz to 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz to 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz (6420759 sequences in total) Writing a C -> T converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz to 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz to 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz (6420758 sequences in total) Writing a C -> T converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz to 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz to 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz (6420758 sequences in total) Writing a C -> T converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz to 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz to 2H3_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 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz (6420758 sequences in total) Input files are 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:32058:1098_1:N:0:GTCAGTCA+TAATGCCG/1 99 ptg000001l_CT_converted 4827990 27 125M = 4828101 236 ATTTTTTTTGTTAAAAAATTTTAATATTTTTGTTTAAGTTATGATTATTATTAAGATAGTTGGTATTATAGTATTGTGTATGTTATTAAATTAAATTAATTATTTTTTATATTTGAAAGAAAATA IIIIIIIIIIIIIIIIIIIIIIII9I9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-II-IIII-IIIII9-I-IIIIII9II9II9-I99-9I99I AS:i:-12 XS:i:-65 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:52G19T52 YS:i:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:32058:1098_2:N:0:GTCAGTCA+TAATGCCG/2 147 ptg000001l_CT_converted 4828101 27 125M = 4827990 -236 TTTGAAAGAAAATATTGAAAAAAAAAGATAAAGTTTATTGAAGTATTTTTGTTTGAAATTTTGATTGTGTTTTATGAATAATTTTAGTTTATTTTGTTATTTTTATATTGTTGTGGAAGTTAATA -IIIIII-IIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-74 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:95T29 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:32058:1098_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 ATTTTTTTTATTAAAAAATTTTAATATTTTTATTTAAATTATAATTATTATTAAAATAATTAATATTATAATATTATATATATTATTAAATTAAATTAATTATTTTTTATATTTAAAAAAAAATA IIIIIIIIIIIIIIIIIIIIIIII9I9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-II-IIII-IIIII9-I-IIIIII9II9II9-I99-9I99I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:32058:1098_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 TATTAATTTTTATAATAATATAAAAATAATAAAATAAATTAAAATTATTTATAAAATATAATTAAAATTTTAAATAAAAATATTTTAATAAATTTTATTTTTTTTTTTTAATATTTTTTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIII-IIIIII- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:32058:1098_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 ATTTTTTTTATTAAAAAATTTTAATATTTTTATTTAAATTATAATTATTATTAAAATAATTAATATTATAATATTATATATATTATTAAATTAAATTAATTATTTTTTATATTTAAAAAAAAATA IIIIIIIIIIIIIIIIIIIIIIII9I9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-II-IIII-IIIII9-I-IIIIII9II9II9-I99-9I99I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:32058:1098_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 TATTAATTTTTATAATAATATAAAAATAATAAAATAAATTAAAATTATTTATAAAATATAATTAAAATTTTAAATAAAAATATTTTAATAAATTTTATTTTTTTTTTTTAATATTTTTTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIII-IIIIII- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:32058:1098_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 ATTTTTTTTGTTAAAAAATTTTAATATTTTTGTTTAAGTTATGATTATTATTAAGATAGTTGGTATTATAGTATTGTGTATGTTATTAAATTAAATTAATTATTTTTTATATTTGAAAGAAAATA IIIIIIIIIIIIIIIIIIIIIIII9I9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIII-II-IIII-IIIII9-I-IIIIII9II9II9-I99-9I99I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:32058:1098_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 TATTAACTTCCACAACAATATAAAAATAACAAAATAAACTAAAATTATTCATAAAACACAATCAAAATTTCAAACAAAAATACTTCAATAAACTTTATCTTTTTTTTTCAATATTTTCTTTCAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIII-IIIIII- YT:Z:UP >>> Writing bisulfite mapping results to 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz Created C -> T as well as G -> A converted versions of the FastQ file 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz (6420759 sequences in total) Input files are 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:13895:1084_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 TTATTTTTTTTGTTATAATTTTTAATTTTGAATGTTAAATATTGATTTATATTATTTTTTTTGGTAGAGAATTAAATAATAGTGTTAAAAATTGTGTAAAATAGAAAGTAGAAATGTAGAGTTGA IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13895:1084_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 CTCAAAAAAACTAAAAAATAAAATATTCCACCTCCATCAAATCCTCATAAAAAATAATAAAAAAAAACACTTCTTTTCATTCAACATTCAAAAAAAAAAATTAAAAATAATTAACACCAACAAAA I9IIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9III-IIII9II9III-IIIIIIIIIIIIIIIIIII9I9IIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:13895:1084_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 TTATTTTTTTTATTATAATTTTTAATTTTAAATATTAAATATTAATTTATATTATTTTTTTTAATAAAAAATTAAATAATAATATTAAAAATTATATAAAATAAAAAATAAAAATATAAAATTAA IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13895:1084_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 TTTAAAAAAATTAAAAAATAAAATATTTTATTTTTATTAAATTTTTATAAAAAATAATAAAAAAAAATGTTTTTTTTTATTTAATATTTAAAAAAAAAAATTAAAAATAATTAATATTAATAAAA I9IIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9III-IIII9II9III-IIIIIIIIIIIIIIIIIII9I9IIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:13895:1084_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 TTATTTTTTTTATTATAATTTTTAATTTTAAATATTAAATATTAATTTATATTATTTTTTTTAATAAAAAATTAAATAATAATATTAAAAATTATATAAAATAAAAAATAAAAATATAAAATTAA IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13895:1084_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 TTTAAAAAAATTAAAAAATAAAATATTTTATTTTTATTAAATTTTTATAAAAAATAATAAAAAAAAATGTTTTTTTTTATTTAATATTTAAAAAAAAAAATTAAAAATAATTAATATTAATAAAA I9IIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9III-IIII9II9III-IIIIIIIIIIIIIIIIIII9I9IIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:13895:1084_1:N:0:GTCAGTCA+TAATGCCG/1 83 ptg000008l_GA_converted 1776186 0 20M4I4M6I91M = 1775979 -322 TCAACTCTACATTTCTACTTTCTATTTTACACAATTTTTAACACTATTATTTAATTCTCTACCAAAAAAAATAATATAAATCAATATTTAACATTCAAAATTAAAAATTATAACAAAAAAAATAA IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII AS:i:-52 XN:i:0 XM:i:2 XO:i:2 XG:i:10 NM:i:12 MD:Z:22C47C44 YS:i:-61 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:13895:1084_2:N:0:GTCAGTCA+TAATGCCG/2 163 ptg000008l_GA_converted 1775979 0 19M1D53M4D53M = 1776186 322 CTCAAAAAAACTAAAAAATAAAATATTCCACCTCCATCAAATCCTCATAAAAAATAATAAAAAAAAACACTTCTTTTCATTCAACATTCAAAAAAAAAAATTAAAAATAATTAACACCAACAAAA I9IIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9III-IIII9II9III-IIIIIIIIIIIIIIIIIII9I9IIIII9IIIIIIIIIIIIIIIII AS:i:-61 XN:i:0 XM:i:6 XO:i:2 XG:i:5 NM:i:11 MD:Z:19^A9A21C0C15T4^AAAA2C0C49 YS:i:-52 YT:Z:CP >>> Writing bisulfite mapping results to 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz (6420758 sequences in total) Input files are 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10231:1098_1:N:0:GTCAGTCA+TAATGCCG/1 99 ptg000061l_CT_converted 141170 2 125M = 141265 220 TAAATTGTTATTATTATTGGTATTTTGTTAGATGATATTTATGTTGGTTGTAAATAAGAATGTTTTGTTTGTTTTTTATAGTGTTTGTTATGTATTTTTTATAAATAAGGTAAGAAGTTTAGGGA IIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-30 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:95G7G5A15 YS:i:-36 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:10231:1098_2:N:0:GTCAGTCA+TAATGCCG/2 147 ptg000061l_CT_converted 141265 2 125M = 141170 -220 TTTTTATAAATAAGGTAAGAAGTTTAGGGAATAAAATGTTATGAAAAGTTATAATAGGATAAAAATATAGGAATGATGATTAGTTAGTGGGTTGTATGAAAAATGTTAATATTTTTAAATGTTTT IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII AS:i:-36 XS:i:-24 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:0G7G5A46T8A34G19 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10231:1098_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 TAAATTATTATTATTATTAATATTTTATTAAATAATATTTATATTAATTATAAATAAAAATATTTTATTTATTTTTTATAATATTTATTATATATTTTTTATAAATAAAATAAAAAATTTAAAAA IIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:10231:1098_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 AAAATATTTAAAAATATTAATATTTTTTATATAATTTATTAATTAATTATTATTTTTATATTTTTATTTTATTATAATTTTTTATAATATTTTATTTTTTAAATTTTTTATTTTATTTATAAAAA IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10231:1098_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 TAAATTATTATTATTATTAATATTTTATTAAATAATATTTATATTAATTATAAATAAAAATATTTTATTTATTTTTTATAATATTTATTATATATTTTTTATAAATAAAATAAAAAATTTAAAAA IIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:10231:1098_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 AAAATATTTAAAAATATTAATATTTTTTATATAATTTATTAATTAATTATTATTTTTATATTTTTATTTTATTATAATTTTTTATAATATTTTATTTTTTAAATTTTTTATTTTATTTATAAAAA IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10231:1098_1:N:0:GTCAGTCA+TAATGCCG/1 83 ptg000008l_GA_converted 36321176 6 125M = 36321081 -220 TCCCTAAACTTCTTACCTTATTTATAAAAAATACATAACAAACACTATAAAAAACAAACAAAACATTCTTATTTACAACCAACATAAATATCATCTAACAAAATACCAATAATAATAACAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIII 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:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:10231:1098_2:N:0:GTCAGTCA+TAATGCCG/2 163 ptg000008l_GA_converted 36321081 6 125M = 36321176 220 AAAACATTTAAAAATATTAACATTTTTCATACAACCCACTAACTAATCATCATTCCTATATTTTTATCCTATTATAACTTTTCATAACATTTTATTCCCTAAACTTCTTACCTTATTTATAAAAA IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII AS:i:0 XS:i:-12 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 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz (6420759 sequences in total) Input files are 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10352:1084_1:N:0:GTCAGTCA+TAATGCCG/1 99 ptg000027l_CT_converted 162861 0 125M = 162795 -191 GTTGTTTTTTGTAAAAAATTGTTTTAAAAAATATTAAATATTTGAGAAATGAGAGTATTTGGAAAATTGGTTATTATGTAAAGGTTATAGTTTATGTAAAATTTTTATTTTAGTTTAAAAATTAA IIIIIIIIIIIII9II9IIIIIIIIIIIII9IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-42 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:60T0T31G31 YS:i:-44 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:10352:1084_2:N:0:GTCAGTCA+TAATGCCG/2 147 ptg000027l_CT_converted 162795 0 91M1D34M = 162861 191 TTTATTTTGGTTTAAAAATTAAAATTTTAAAAAATAAGTTGAAATTTATTATATAAATTATTTATAGTTGTTTTTTGTAAAAGATTGTTTTAAAAATATTAAATATTTGAGAAATGAGAGTATTT III9II9II-IIIIII9I9IIII9I9IIIII99IIIIII99I9I9IIII-IIIIIIIIIIIIIII9II9IIII9IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-44 XS:i:-44 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:32T3T3A9T3T27A8^A34 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10352:1084_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 ATTATTTTTTATAAAAAATTATTTTAAAAAATATTAAATATTTAAAAAATAAAAATATTTAAAAAATTAATTATTATATAAAAATTATAATTTATATAAAATTTTTATTTTAATTTAAAAATTAA IIIIIIIIIIIII9II9IIIIIIIIIIIII9IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:10352:1084_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 AAATATTTTTATTTTTTAAATATTTAATATTTTTAAAATAATTTTTTATAAAAAATAATTATAAATAATTTATATAATAAATTTTAATTTATTTTTTAAAATTTTAATTTTTAAATTAAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIII9II9IIIIIIIIIIIIIII-IIII9I9I99IIIIII99IIIII9I9IIII9I9IIIIII-II9II9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10352:1084_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 ATTATTTTTTATAAAAAATTATTTTAAAAAATATTAAATATTTAAAAAATAAAAATATTTAAAAAATTAATTATTATATAAAAATTATAATTTATATAAAATTTTTATTTTAATTTAAAAATTAA IIIIIIIIIIIII9II9IIIIIIIIIIIII9IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:10352:1084_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 AAATATTTTTATTTTTTAAATATTTAATATTTTTAAAATAATTTTTTATAAAAAATAATTATAAATAATTTATATAATAAATTTTAATTTATTTTTTAAAATTTTAATTTTTAAATTAAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIII9II9IIIIIIIIIIIIIII-IIII9I9I99IIIIII99IIIII9I9IIII9I9IIIIII-II9II9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:10352:1084_1:N:0:GTCAGTCA+TAATGCCG/1 83 ptg000027l_GA_converted 7749644 0 125M = 7749371 -398 TTAATTTTTAAACTAAAATAAAAATTTTACATAAACTATAACCTTTACATAATAACCAATTTTCCAAATACTCTCATTTCTCAAATATTTAATATTTTTTAAAACAATTTTTTACAAAAAACAAC IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIII9IIIIIIIIIIIII9II9IIIIIIIIIIIII AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:64A51C8 YS:i:-44 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:10352:1084_2:N:0:GTCAGTCA+TAATGCCG/2 163 ptg000027l_GA_converted 7749371 0 29M1D96M = 7749644 398 AAATACTCTCATTTCTCAAATATTTAATATTTTTAAAACAATCTTTTACAAAAAACAACTATAAATAATTTATATAATAAATTTCAACTTATTTTTTAAAATTTTAATTTTTAAACCAAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIII9II9IIIIIIIIIIIIIII-IIII9I9I99IIIIII99IIIII9I9IIII9I9IIIIII-II9II9III AS:i:-44 XS:i:-44 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:29^T13T7C9C13A9T3A36 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz (6420758 sequences in total) Input files are 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2H3_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 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:19114:1098_1:N:0:GTCAGTCA+TAATGCCG/1 99 ntLink_6_CT_converted 20265073 6 67M = 20265048 -92 AAAAGTAGAATAGAGATAAAGGAAAGTATATATTTAGTTTGTTAGTTTTTGTTGTGTTATTATTGTA III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A59 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:19114:1098_2:N:0:GTCAGTCA+TAATGCCG/2 147 ntLink_6_CT_converted 20265048 6 67M = 20265073 92 GATTAATGTAGATATTGTTGTTTTGAAAAGTAAAATAGAGATAAAGGAAAGTATATATTTAGTTTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:67 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:19114:1098_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 AAAAATAAAATAAAAATAAAAAAAAATATATATTTAATTTATTAATTTTTATTATATTATTATTATA III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:19114:1098_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 ATAAATTAAATATATATTTTTTTTTATTTTTATTTTATTTTTTAAAATAATAATATTTATATTAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:19114:1098_1:N:0:GTCAGTCA+TAATGCCG/1 77 * 0 0 * * 0 0 AAAAATAAAATAAAAATAAAAAAAAATATATATTTAATTTATTAATTTTTATTATATTATTATTATA III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:19114:1098_2:N:0:GTCAGTCA+TAATGCCG/2 141 * 0 0 * * 0 0 ATAAATTAAATATATATTTTTTTTTATTTTTATTTTATTTTTTAAAATAATAATATTTATATTAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2H3_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: LH00652:104:22KG7JLT4:7:1101:19114:1098_1:N:0:GTCAGTCA+TAATGCCG/1 83 ptg000018l_GA_converted 12850093 12 67M = 12850118 92 TACAATAATAACACAACAAAAACTAACAAACTAAATATATACTTTCCTTTATCTCTATTCTACTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:59T7 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:19114:1098_2:N:0:GTCAGTCA+TAATGCCG/2 163 ptg000018l_GA_converted 12850118 12 67M = 12850093 -92 ACAAACTAAATATATACTTTCCTTTATCTCTATTTTACTTTTCAAAACAACAATATCTACATTAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:67 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2202:29679:2219_1:N:0:GTCAGTCA+TAATGCCG ptg000025l 21443081 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2317:39840:15839_1:N:0:GTCAGTCA+TAATGCCG ptg000006l 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1347:34080:7992_1:N:0:GTCAGTCA+TAATGCCG ptg000039l 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1454:10409:29515_1:N:0:GTCAGTCA+TAATGCCG ptg000177l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1454:10417:29529_1:N:0:GTCAGTCA+TAATGCCG ptg000177l 2 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2316:26799:3844_1:N:0:GTCAGTCA+TAATGCCG ntLink_1 163148 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 6407159 (99.79%) aligned concordantly 0 times 5664 (0.09%) aligned concordantly exactly 1 time 7935 (0.12%) aligned concordantly >1 times 0.21% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 3110259 (48.44%) aligned concordantly 0 times 1370805 (21.35%) aligned concordantly exactly 1 time 1939694 (30.21%) aligned concordantly >1 times 51.56% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 6406235 (99.77%) aligned concordantly 0 times 5633 (0.09%) aligned concordantly exactly 1 time 8890 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 3113592 (48.49%) aligned concordantly 0 times 1370644 (21.35%) aligned concordantly exactly 1 time 1936522 (30.16%) aligned concordantly >1 times 51.51% overall alignment rate Processed 6420758 sequences in total Successfully deleted the temporary files 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6420758 Final Cytosine Methylation Report ================================= Total number of C's analysed: 176867266 Total methylated C's in CpG context: 3470541 Total methylated C's in CHG context: 175756 Total methylated C's in CHH context: 757732 Total methylated C's in Unknown context: 5772 Total unmethylated C's in CpG context: 23590316 Total unmethylated C's in CHG context: 29746923 Total unmethylated C's in CHH context: 119125998 Total unmethylated C's in Unknown context: 264693 C methylated in CpG context: 12.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Now waiting for all child processes to complete Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 3113541 (48.49%) aligned concordantly 0 times 1370527 (21.35%) aligned concordantly exactly 1 time 1936690 (30.16%) aligned concordantly >1 times 51.51% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 6406234 (99.77%) aligned concordantly 0 times 5727 (0.09%) aligned concordantly exactly 1 time 8797 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 3107512 (48.40%) aligned concordantly 0 times 1371849 (21.37%) aligned concordantly exactly 1 time 1941397 (30.24%) aligned concordantly >1 times 51.60% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 6406987 (99.79%) aligned concordantly 0 times 5644 (0.09%) aligned concordantly exactly 1 time 8127 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate Processed 6420758 sequences in total Successfully deleted the temporary files 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6420758 Final Cytosine Methylation Report ================================= Total number of C's analysed: 176934326 Total methylated C's in CpG context: 3475335 Total methylated C's in CHG context: 175320 Total methylated C's in CHH context: 763780 Total methylated C's in Unknown context: 5829 Total unmethylated C's in CpG context: 23599014 Total unmethylated C's in CHG context: 29736038 Total unmethylated C's in CHH context: 119184839 Total unmethylated C's in Unknown context: 265224 C methylated in CpG context: 12.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 3109487 (48.43%) aligned concordantly 0 times 1370997 (21.35%) aligned concordantly exactly 1 time 1940274 (30.22%) aligned concordantly >1 times 51.57% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 3110087 (48.44%) aligned concordantly 0 times 1372733 (21.38%) aligned concordantly exactly 1 time 1937938 (30.18%) aligned concordantly >1 times 51.56% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 6406741 (99.78%) aligned concordantly 0 times 5686 (0.09%) aligned concordantly exactly 1 time 8331 (0.13%) aligned concordantly >1 times 0.22% overall alignment rate 6420758 reads; of these: 6420758 (100.00%) were paired; of these: 6406079 (99.77%) aligned concordantly 0 times 5607 (0.09%) aligned concordantly exactly 1 time 9072 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate Processed 6420758 sequences in total Successfully deleted the temporary files 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6420758 Final Cytosine Methylation Report ================================= Total number of C's analysed: 176938459 Total methylated C's in CpG context: 3470239 Total methylated C's in CHG context: 176332 Total methylated C's in CHH context: 766545 Total methylated C's in Unknown context: 5934 Total unmethylated C's in CpG context: 23591935 Total unmethylated C's in CHG context: 29750020 Total unmethylated C's in CHH context: 119183388 Total unmethylated C's in Unknown context: 265073 C methylated in CpG context: 12.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 3110341 (48.44%) aligned concordantly 0 times 1372256 (21.37%) aligned concordantly exactly 1 time 1938162 (30.19%) aligned concordantly >1 times 51.56% overall alignment rate 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 6406173 (99.77%) aligned concordantly 0 times 5588 (0.09%) aligned concordantly exactly 1 time 8998 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 6407096 (99.79%) aligned concordantly 0 times 5535 (0.09%) aligned concordantly exactly 1 time 8128 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 3110302 (48.44%) aligned concordantly 0 times 1370095 (21.34%) aligned concordantly exactly 1 time 1940362 (30.22%) aligned concordantly >1 times 51.56% overall alignment rate Processed 6420759 sequences in total Successfully deleted the temporary files 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6420759 Final Cytosine Methylation Report ================================= Total number of C's analysed: 176908220 Total methylated C's in CpG context: 3473937 Total methylated C's in CHG context: 174650 Total methylated C's in CHH context: 760329 Total methylated C's in Unknown context: 5930 Total unmethylated C's in CpG context: 23589970 Total unmethylated C's in CHG context: 29739065 Total unmethylated C's in CHH context: 119170269 Total unmethylated C's in Unknown context: 265489 C methylated in CpG context: 12.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 3108673 (48.42%) aligned concordantly 0 times 1370990 (21.35%) aligned concordantly exactly 1 time 1941096 (30.23%) aligned concordantly >1 times 51.58% overall alignment rate 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 3113097 (48.48%) aligned concordantly 0 times 1370165 (21.34%) aligned concordantly exactly 1 time 1937497 (30.18%) aligned concordantly >1 times 51.52% overall alignment rate 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 6406975 (99.79%) aligned concordantly 0 times 5567 (0.09%) aligned concordantly exactly 1 time 8217 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 6420759 reads; of these: 6420759 (100.00%) were paired; of these: 6406180 (99.77%) aligned concordantly 0 times 5548 (0.09%) aligned concordantly exactly 1 time 9031 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate Processed 6420759 sequences in total Successfully deleted the temporary files 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2H3_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6420759 Final Cytosine Methylation Report ================================= Total number of C's analysed: 176876034 Total methylated C's in CpG context: 3467067 Total methylated C's in CHG context: 175537 Total methylated C's in CHH context: 762376 Total methylated C's in Unknown context: 5881 Total unmethylated C's in CpG context: 23608928 Total unmethylated C's in CHG context: 29732445 Total unmethylated C's in CHH context: 119129681 Total unmethylated C's in Unknown context: 264966 C methylated in CpG context: 12.8% 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 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 2H3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 2H3_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 2H3_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/2H3_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 2H3_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/2H3_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 2H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 2H3_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: 32103792 Final Cytosine Methylation Report ================================= Total number of C's analysed: 884524305 Total methylated C's in CpG context: 17357119 Total methylated C's in CHG context: 877595 Total methylated C's in CHH context: 3810762 Total methylated C's in Unknown context: 29346 Total unmethylated C's in CpG context: 117980163 Total unmethylated C's in CHG context: 148704491 Total unmethylated C's in CHH context: 595794175 Total unmethylated C's in Unknown context: 1325445 C methylated in CpG context: 12.8% 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 40m 26s ==================== Bismark run complete ====================