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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_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/2A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_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/2A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6762726) Using the subset file >2A3_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/2A3_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/2A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_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/2A3_R1_001.fastp-trim.fq.gz for PID: 97664 and offset 5 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_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/2A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_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/2A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz to 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz to 2A3_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/2A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6762726) Using the subset file >2A3_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/2A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz to 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz to 2A3_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/2A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/2A3_R2_001.fastp-trim.fq.gz for PID: 97664 and offset 5 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz to 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz to 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz to 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz to 2A3_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/2A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6762725) Using the subset file >2A3_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/2A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz to 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz to 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz (6762725 sequences in total) Writing a C -> T converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz to 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz to 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz (6762726 sequences in total) Writing a C -> T converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz to 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz to 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz (6762725 sequences in total) Writing a C -> T converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz to 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz to 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz (6762725 sequences in total) Writing a C -> T converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz to 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz to 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz (6762725 sequences in total) Writing a C -> T converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz to 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz to 2A3_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 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz (6762725 sequences in total) Input files are 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:7480:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 ATATGAGTAAAAATGTAAGTATTTGTGAATTAGTAAATATAATTGATTTTTTAAGGTTTTTTAGTATAAAGGATAAAGTTGATATATTGTAAGTTATAGTGTTTGTATTATGTATAATTATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIII9IIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:7480:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 TACATAAAATTCATATTTTATACTATATCAAAAAATACTACCCCATTAAAAACTCATCTAACATAACAATCAATAACTAAATAAAAATTACATTAAATATTAAATACCATTATAATAATTATAAT IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:7480:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 ATATAAATAAAAATATAAATATTTATAAATTAATAAATATAATTAATTTTTTAAAATTTTTTAATATAAAAAATAAAATCAATATATTATAAATTATAATATTTATATTATATATAATTATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIII9IIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:7480:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 TATATAAAATTTATATTTTATATTATATTAAAAAATATTATTTTATTAAAAATTTATTTAATATAATAATTAATAATTAAATAAAAATTATATTAAATATTAAATATTATTATAATAATTATAAT IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:7480:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 ATATAAATAAAAATATAAATATTTATAAATTAATAAATATAATTAATTTTTTAAAATTTTTTAATATAAAAAATAAAATCAATATATTATAAATTATAATATTTATATTATATATAATTATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIII9IIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:7480:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 TATATAAAATTTATATTTTATATTATATTAAAAAATATTATTTTATTAAAAATTTATTTAATATAATAATTAATAATTAAATAAAAATTATATTAAATATTAAATATTATTATAATAATTATAAT IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:7480:1098_1:N:0:TCTACGCA+GGCTATTG/1 83 ptg000002l_GA_converted 11159407 42 125M = 11159280 -252 ATTTATAATTATACATAATACAAACACTATAACTTACAATATATCAACTTTATCCTTTATACTAAAAAACCTTAAAAAATCAATTATATTTACTAATTCACAAATACTTACATTTTTACTCATAT IIIIIIIIIIII9IIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:45T72T6 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:7480:1098_2:N:0:TCTACGCA+GGCTATTG/2 163 ptg000002l_GA_converted 11159280 42 125M = 11159407 252 TACATAAAATTCATATTTTATACTATATCAAAAAATACTACCCCATTAAAAACTCATCTAACATAACAATCAATAACTAAATAAAAATTACATTAAATATTAAATACCATTATAATAATTATAAT IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz Created C -> T as well as G -> A converted versions of the FastQ file 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz (6762726 sequences in total) Input files are 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:12828:1084_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TTTTTTAATTAATGAGAATTAAAATTAAAATTAATTGTATTATGTATGTGTGATTTTTTTTGTGTTTTGAGTGAGTTATATGTAATTGTTAGGTGATTGGTTTATTGTGTTGTTTGTTTTTGTTG II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII9-II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:12828:1084_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 ACTTACTTCTACTTATCCATTACTTAAAAACTACTAAACAAATAATCACACAACTTCAAATTACAACACAATTACTCCCACCAATCACAACAAAAACAAACAACACAATAAACCAATCACCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:12828:1084_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TTTTTTAATTAATAAAAATTAAAATTAAAATTAATTATATTATATATATATAATTTTTTTTATATTTTAAATAAATTATATATAATTATTAAATAATTAATTTATTATATTATTTATTTTTATTA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII9-II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:12828:1084_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 ATTTATTTTTATTTATTTATTATTTAAAAATTATTAAATAAATAATTATATAATTTTAAATTATAATATAATTATTTTTATTAATTATAATAAAAATAAATAATATAATAAATTAATTATTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:12828:1084_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TTTTTTAATTAATAAAAATTAAAATTAAAATTAATTATATTATATATATATAATTTTTTTTATATTTTAAATAAATTATATATAATTATTAAATAATTAATTTATTATATTATTTATTTTTATTA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII9-II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:12828:1084_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 ATTTATTTTTATTTATTTATTATTTAAAAATTATTAAATAAATAATTATATAATTTTAAATTATAATATAATTATTTTTATTAATTATAATAAAAATAAATAATATAATAAATTAATTATTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:12828:1084_1:N:0:TCTACGCA+GGCTATTG/1 83 ptg000008l_GA_converted 5399774 7 32M5D93M = 5399687 -217 CAACAAAAACAAACAACACAATAAACCAATCACCTAACAATTACATATAACTCACTCAAAACACAAAAAAAATCACACATACATAATACAATTAATTTTAATTTTAATTCTCATTAATTAAAAAA II-9IIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II AS:i:-20 XS:i:-26 XN:i:0 XM:i:0 XO:i:1 XG:i:5 NM:i:5 MD:Z:32^CAATT93 YS:i:-20 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:12828:1084_2:N:0:TCTACGCA+GGCTATTG/2 163 ptg000008l_GA_converted 5399687 7 119M5D6M = 5399774 217 ACTTACTTCTACTTATCCATTACTTAAAAACTACTAAACAAATAATCACACAACTTCAAATTACAACACAATTACTCCCACCAATCACAACAAAAACAAACAACACAATAAACCAATCACCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-20 XS:i:-32 XN:i:0 XM:i:0 XO:i:1 XG:i:5 NM:i:5 MD:Z:119^CAATT6 YS:i:-20 YT:Z:CP >>> Writing bisulfite mapping results to 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz (6762725 sequences in total) Input files are 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:2141:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TAAGGATATAAATTGAAAATAGTTTTATTAATTAATTTTTTAATAGAATGTTTTATTGTGATTGGGATTTTTGAAAATAATTTAGTTATTTTGAAAGGTTTTTGATAATTTTTTTAGATGTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2141:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 AAACTCATCCAAAAAACAATCAACTAACACAAATCTAAAACTTTACTCCACCTTCACCATTTTCACATAAAAAATTTAAATCTAATACATCTAAAAAAATTATCAAAAATCTTTCAAAATAACTA 9IIIIII-IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIII-III9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:2141:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TAAAAATATAAATTAAAAATAATTTTATTAATTAATTTTTTAATAAAATATTTTATTATAATTAAAATTTTTAAAAATAATTTAATTATTTTAAAAAATTTTTAATAATTTTTTTAAATATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2141:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 AAATTTATTTAAAAAATAATTAATTAATATAAATTTAAAATTTTATTTTATTTTTATTATTTTTATATAAAAAATTTAAATTTAATATATTTAAAAAAATTATTAAAAATTTTTTAAAATAATTA 9IIIIII-IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIII-III9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:2141:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TAAAAATATAAATTAAAAATAATTTTATTAATTAATTTTTTAATAAAATATTTTATTATAATTAAAATTTTTAAAAATAATTTAATTATTTTAAAAAATTTTTAATAATTTTTTTAAATATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2141:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 AAATTTATTTAAAAAATAATTAATTAATATAAATTTAAAATTTTATTTTATTTTTATTATTTTTATATAAAAAATTTAAATTTAATATATTTAAAAAAATTATTAAAAATTTTTTAAAATAATTA 9IIIIII-IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIII-III9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:2141:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TAAGGATATAAATTGAAAATAGTTTTATTAATTAATTTTTTAATAGAATGTTTTATTGTGATTGGGATTTTTGAAAATAATTTAGTTATTTTGAAAGGTTTTTGATAATTTTTTTAGATGTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2141:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 AAACTCATCCAAAAAACAATCAACTAACACAAATCTAAAACTTTACTCCACCTTCACCATTTTCACATAAAAAATTTAAATCTAATACATCTAAAAAAATTATCAAAAATCTTTCAAAATAACTA 9IIIIII-IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIII-I-IIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIII-III9IIIII YT:Z:UP >>> Writing bisulfite mapping results to 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz Created C -> T as well as G -> A converted versions of the FastQ file 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz (6762725 sequences in total) Input files are 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:1882:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TTGAGATTTGGTTGGTGTTGAGGAGGTGGTGTTTAGGGGTTATTGTATATAGTGTGTAATGTGAAAAAGGTAATTATTTTAGGGTGATTTGGAGATAAATGTTTTTATAGTGAGAGAAGTTATAA IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:1882:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 TCACCCTTTTCAACCATCTTCAAACACACTCCCCTTTTTATTAACATATAAAAATCACCTAATTATACAAATATTTCTTATAACCTCTCTCACTATAAAAACATTTATCTCCAAATCACCCTAAA IIIIIIIIIIIIIIII9IIIIII9II9III9III9I9IIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIII99I9-IIIII9IIIIIIIII9IIIIII9IIIIIIII9III9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:1882:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TTAAAATTTAATTAATATTAAAAAAATAATATTTAAAAATTATTATATATAATATATAATATAAAAAAAATAATTATTTTAAAATAATTTAAAAATAAATATTTTTATAATAAAAAAAATTATAA IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:1882:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 TTATTTTTTTTAATTATTTTTAAATATATTTTTTTTTTTATTAATATATAAAAATTATTTAATTATATAAATATTTTTTATAATTTTTTTTATTATAAAAATATTTATTTTTAAATTATTTTAAA IIIIIIIIIIIIIIII9IIIIII9II9III9III9I9IIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIII99I9-IIIII9IIIIIIIII9IIIIII9IIIIIIII9III9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:1882:1098_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TTAAAATTTAATTAATATTAAAAAAATAATATTTAAAAATTATTATATATAATATATAATATAAAAAAAATAATTATTTTAAAATAATTTAAAAATAAATATTTTTATAATAAAAAAAATTATAA IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:1882:1098_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 TTATTTTTTTTAATTATTTTTAAATATATTTTTTTTTTTATTAATATATAAAAATTATTTAATTATATAAATATTTTTTATAATTTTTTTTATTATAAAAATATTTATTTTTAAATTATTTTAAA IIIIIIIIIIIIIIII9IIIIII9II9III9III9I9IIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIII99I9-IIIII9IIIIIIIII9IIIIII9IIIIIIII9III9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:1882:1098_1:N:0:TCTACGCA+GGCTATTG/1 83 ptg000004l_GA_converted 6125997 42 125M = 6125920 -202 TTATAACTTCTCTCACTATAAAAACATTTATCTCCAAATCACCCTAAAATAATTACCTTTTTCACATTACACACTATATACAATAACCCCTAAACACCACCTCCTCAACACCAACCAAATCTCAA IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:1882:1098_2:N:0:TCTACGCA+GGCTATTG/2 163 ptg000004l_GA_converted 6125920 42 125M = 6125997 202 TCACCCTTTTCAACCATCTTCAAACACACTCCCCTTTTTATTAACATATAAAAATCACCTAATTATACAAATATTTCTTATAACCTCTCTCACTATAAAAACATTTATCTCCAAATCACCCTAAA IIIIIIIIIIIIIIII9IIIIII9II9III9III9I9IIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIII99I9-IIIII9IIIIIIIII9IIIIII9IIIIIIII9III9IIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:84T40 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz (6762725 sequences in total) Input files are 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2A3_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 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:18863:1084_1:N:0:TCTACGCA+GGCTATTG/1 99 ntLink_8_CT_converted 36408786 6 125M = 36408845 184 ATATATTTTTTTTAAAAAGTTGAGTGAAAATATTATATATTAAAATAGATGGGTTGAAATTTTTAGATATGAATTTATTATGTTTATTTGGTTATTTTAGTAAGGTTTTTAATAATTAGGAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:18863:1084_2:N:0:TCTACGCA+GGCTATTG/2 147 ntLink_8_CT_converted 36408845 6 125M = 36408786 -184 TTTTTAGATATGAATTTATTATGTTTATTTGGTTATTTTAGTAAGGTTTTTAATAATTAGGAATTAAGTGTAAAAATGAGGTTTATATATTAAGTAGAGTTTTTAGTGATTTATTGTATTGTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:18863:1084_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 ATATATTTTTTTTAAAAAATTAAATAAAAATATTATATATTAAAATAAATAAATTAAAATTTTTAAATATAAATTTATTATATTTATTTAATTATTTTAATAAAATTTTTAATAATTAAAAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:18863:1084_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 ATAATAATATAATAAATTATTAAAAATTTTATTTAATATATAAATTTTATTTTTATATTTAATTTTTAATTATTAAAAATTTTATTAAAATAATTAAATAAATATAATAAATTTATATTTAAAAA IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:18863:1084_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 ATATATTTTTTTTAAAAAATTAAATAAAAATATTATATATTAAAATAAATAAATTAAAATTTTTAAATATAAATTTATTATATTTATTTAATTATTTTAATAAAATTTTTAATAATTAAAAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:18863:1084_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 ATAATAATATAATAAATTATTAAAAATTTTATTTAATATATAAATTTTATTTTTATATTTAATTTTTAATTATTAAAAATTTTATTAAAATAATTAAATAAATATAATAAATTTATATTTAAAAA IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2A3_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: LH00652:104:22KG7JLT4:7:1101:18863:1084_1:N:0:TCTACGCA+GGCTATTG/1 83 ptg000001l_GA_converted 656930 1 125M = 656871 -184 TAATTCCTAATTATTAAAAACCTTACTAAAATAACCAAATAAACATAATAAATTCATATCTAAAAATTTCAACCCATCTATTTTAATATATAATATTTTCACTCAACTTTTTAAAAAAAATATAT IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:13C111 YS:i:-12 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:18863:1084_2:N:0:TCTACGCA+GGCTATTG/2 163 ptg000001l_GA_converted 656871 1 125M = 656930 184 ATAACAATACAATAAATCACTAAAAACTCTACTTAATATATAAACCTCATTTTTACACTTAATTCCTAATTATTAAAAACCTTACTAAAATAACCAAATAAACATAATAAATTCATATCTAAAAA IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:33A38C52 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1231:17544:18501_1:N:0:TCTACGCA+GGCTATTG ptg000093l 36762 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1279:9721:6913_1:N:0:TCTACGCA+GGCTATTG ptg000004l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1231:17560:18501_1:N:0:TCTACGCA+GGCTATTG ptg000093l 36762 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1242:8597:1575_1:N:0:TCTACGCA+GGCTATTG ptg000066l 66340 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 LH00652:104:22KG7JLT4:7:1279:9713:6927_1:N:0:TCTACGCA+GGCTATTG ptg000004l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1403:7415:5134_1:N:0:TCTACGCA+GGCTATTG ptg000006l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1429:16881:4349_1:N:0:TCTACGCA+GGCTATTG ptg000115l 42054 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1457:48682:8735_1:N:0:TCTACGCA+GGCTATTG ptg000092l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1336:27867:22173_1:N:0:TCTACGCA+GGCTATTG ptg000025l 21443081 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1457:48666:8735_1:N:0:TCTACGCA+GGCTATTG ptg000092l 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1334:23199:18459_1:N:0:TCTACGCA+GGCTATTG ptg000002l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2149:15376:19034_1:N:0:TCTACGCA+GGCTATTG ptg000024l 3 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 LH00652:104:22KG7JLT4:7:2244:13264:16554_1:N:0:TCTACGCA+GGCTATTG ptg000106l 40356 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2244:32203:9001_1:N:0:TCTACGCA+GGCTATTG ptg000075l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2368:28466:11888_1:N:0:TCTACGCA+GGCTATTG ptg000052l 52608 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2368:28482:11888_1:N:0:TCTACGCA+GGCTATTG ptg000052l 52608 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2244:13273:16540_1:N:0:TCTACGCA+GGCTATTG ptg000106l 40356 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1157:4163:10318_1:N:0:TCTACGCA+GGCTATTG ptg000116l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1157:4147:10318_1:N:0:TCTACGCA+GGCTATTG ptg000116l 1 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 LH00652:104:22KG7JLT4:8:1345:21063:2709_1:N:0:TCTACGCA+GGCTATTG ptg000129l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1345:21079:2709_1:N:0:TCTACGCA+GGCTATTG ptg000129l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2406:17568:15180_1:N:0:TCTACGCA+GGCTATTG ptg000006l 3 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2377:33465:14802_1:N:0:TCTACGCA+GGCTATTG ptg000006l 1 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1476:35277:14158_1:N:0:TCTACGCA+GGCTATTG ptg000004l 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2117:43934:28450_1:N:0:TCTACGCA+GGCTATTG ptg000046l 39578 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2117:43958:28492_1:N:0:TCTACGCA+GGCTATTG ptg000046l 39578 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2192:24057:4363_1:N:0:TCTACGCA+GGCTATTG ptg000006l 3 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2216:20092:22635_1:N:0:TCTACGCA+GGCTATTG ptg000181l 31369 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2216:20109:22635_1:N:0:TCTACGCA+GGCTATTG ptg000181l 31369 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6744507 (99.73%) aligned concordantly 0 times 5734 (0.08%) aligned concordantly exactly 1 time 12484 (0.18%) aligned concordantly >1 times 0.27% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6747584 (99.78%) aligned concordantly 0 times 5634 (0.08%) aligned concordantly exactly 1 time 9507 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3068569 (45.37%) aligned concordantly 0 times 1433649 (21.20%) aligned concordantly exactly 1 time 2260507 (33.43%) aligned concordantly >1 times 54.63% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3070199 (45.40%) aligned concordantly 0 times 1433645 (21.20%) aligned concordantly exactly 1 time 2258881 (33.40%) aligned concordantly >1 times 54.60% overall alignment rate Processed 6762725 sequences in total Successfully deleted the temporary files 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6762725 Final Cytosine Methylation Report ================================= Total number of C's analysed: 186150457 Total methylated C's in CpG context: 3312302 Total methylated C's in CHG context: 167248 Total methylated C's in CHH context: 778464 Total methylated C's in Unknown context: 6560 Total unmethylated C's in CpG context: 25085804 Total unmethylated C's in CHG context: 31354384 Total unmethylated C's in CHH context: 125452255 Total unmethylated C's in Unknown context: 276919 C methylated in CpG context: 11.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% Now waiting for all child processes to complete 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6747448 (99.77%) aligned concordantly 0 times 5668 (0.08%) aligned concordantly exactly 1 time 9609 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3069274 (45.39%) aligned concordantly 0 times 1433905 (21.20%) aligned concordantly exactly 1 time 2259546 (33.41%) aligned concordantly >1 times 54.61% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6744460 (99.73%) aligned concordantly 0 times 5742 (0.08%) aligned concordantly exactly 1 time 12523 (0.19%) aligned concordantly >1 times 0.27% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3067627 (45.36%) aligned concordantly 0 times 1432058 (21.18%) aligned concordantly exactly 1 time 2263040 (33.46%) aligned concordantly >1 times 54.64% overall alignment rate Processed 6762725 sequences in total Successfully deleted the temporary files 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6762725 Final Cytosine Methylation Report ================================= Total number of C's analysed: 186200228 Total methylated C's in CpG context: 3308566 Total methylated C's in CHG context: 167274 Total methylated C's in CHH context: 780324 Total methylated C's in Unknown context: 6638 Total unmethylated C's in CpG context: 25092562 Total unmethylated C's in CHG context: 31352891 Total unmethylated C's in CHH context: 125498611 Total unmethylated C's in Unknown context: 276750 C methylated in CpG context: 11.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% 6762726 reads; of these: 6762726 (100.00%) were paired; of these: 6744681 (99.73%) aligned concordantly 0 times 5762 (0.09%) aligned concordantly exactly 1 time 12283 (0.18%) aligned concordantly >1 times 0.27% overall alignment rate 6762726 reads; of these: 6762726 (100.00%) were paired; of these: 3072534 (45.43%) aligned concordantly 0 times 1431157 (21.16%) aligned concordantly exactly 1 time 2259035 (33.40%) aligned concordantly >1 times 54.57% overall alignment rate Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1407:4163:9898_1:N:0:TCTACGCA+GGCTATTG ptg000046l 39575 6762726 reads; of these: 6762726 (100.00%) were paired; of these: 3066776 (45.35%) aligned concordantly 0 times 1434999 (21.22%) aligned concordantly exactly 1 time 2260951 (33.43%) aligned concordantly >1 times 54.65% overall alignment rate 6762726 reads; of these: 6762726 (100.00%) were paired; of these: 6747597 (99.78%) aligned concordantly 0 times 5728 (0.08%) aligned concordantly exactly 1 time 9401 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate Processed 6762726 sequences in total Successfully deleted the temporary files 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6762726 Final Cytosine Methylation Report ================================= Total number of C's analysed: 186175487 Total methylated C's in CpG context: 3302844 Total methylated C's in CHG context: 167407 Total methylated C's in CHH context: 778389 Total methylated C's in Unknown context: 6585 Total unmethylated C's in CpG context: 25093544 Total unmethylated C's in CHG context: 31342198 Total unmethylated C's in CHH context: 125491105 Total unmethylated C's in Unknown context: 275676 C methylated in CpG context: 11.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2147:29339:17016_1:N:0:TCTACGCA+GGCTATTG ptg000025l 21443081 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2216:11032:17871_1:N:0:TCTACGCA+GGCTATTG ptg000012l 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2234:39605:3718_1:N:0:TCTACGCA+GGCTATTG ptg000075l 54138 Processed 6000000 sequence pairs so far 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6747402 (99.77%) aligned concordantly 0 times 5883 (0.09%) aligned concordantly exactly 1 time 9440 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3065835 (45.33%) aligned concordantly 0 times 1434672 (21.21%) aligned concordantly exactly 1 time 2262218 (33.45%) aligned concordantly >1 times 54.67% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3069390 (45.39%) aligned concordantly 0 times 1434297 (21.21%) aligned concordantly exactly 1 time 2259038 (33.40%) aligned concordantly >1 times 54.61% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6744883 (99.74%) aligned concordantly 0 times 5770 (0.09%) aligned concordantly exactly 1 time 12072 (0.18%) aligned concordantly >1 times 0.26% overall alignment rate Processed 6762725 sequences in total Successfully deleted the temporary files 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6762725 Final Cytosine Methylation Report ================================= Total number of C's analysed: 186190066 Total methylated C's in CpG context: 3314274 Total methylated C's in CHG context: 165954 Total methylated C's in CHH context: 785222 Total methylated C's in Unknown context: 6453 Total unmethylated C's in CpG context: 25074929 Total unmethylated C's in CHG context: 31364199 Total unmethylated C's in CHH context: 125485488 Total unmethylated C's in Unknown context: 275680 C methylated in CpG context: 11.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6744818 (99.74%) aligned concordantly 0 times 5765 (0.09%) aligned concordantly exactly 1 time 12142 (0.18%) aligned concordantly >1 times 0.26% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 6747588 (99.78%) aligned concordantly 0 times 5730 (0.08%) aligned concordantly exactly 1 time 9407 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3070692 (45.41%) aligned concordantly 0 times 1435247 (21.22%) aligned concordantly exactly 1 time 2256786 (33.37%) aligned concordantly >1 times 54.59% overall alignment rate 6762725 reads; of these: 6762725 (100.00%) were paired; of these: 3069040 (45.38%) aligned concordantly 0 times 1434365 (21.21%) aligned concordantly exactly 1 time 2259320 (33.41%) aligned concordantly >1 times 54.62% overall alignment rate Processed 6762725 sequences in total Successfully deleted the temporary files 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2A3_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6762725 Final Cytosine Methylation Report ================================= Total number of C's analysed: 186280202 Total methylated C's in CpG context: 3305627 Total methylated C's in CHG context: 166562 Total methylated C's in CHH context: 777564 Total methylated C's in Unknown context: 6645 Total unmethylated C's in CpG context: 25109717 Total unmethylated C's in CHG context: 31376083 Total unmethylated C's in CHH context: 125544649 Total unmethylated C's in Unknown context: 277136 C methylated in CpG context: 11.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 2A3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 2A3_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 2A3_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/2A3_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 2A3_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/2A3_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 2A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 2A3_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: 33813626 Final Cytosine Methylation Report ================================= Total number of C's analysed: 930996440 Total methylated C's in CpG context: 16543613 Total methylated C's in CHG context: 834445 Total methylated C's in CHH context: 3899963 Total methylated C's in Unknown context: 32881 Total unmethylated C's in CpG context: 125456556 Total unmethylated C's in CHG context: 156789755 Total unmethylated C's in CHH context: 627472108 Total unmethylated C's in Unknown context: 1382161 C methylated in CpG context: 11.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% Deleting temporary report files... Bismark completed in 0d 5h 50m 8s ==================== Bismark run complete ====================