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/1H6_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/1H6_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/1H6_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/1H6_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/1H6_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/1H6_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/1H6_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/1H6_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1H6_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/1H6_R2_001.fastp-trim.fq.gz The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1H6_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/1H6_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/1H6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_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/1H6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_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/1H6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_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/1H6_R1_001.fastp-trim.fq.gz for PID: 67633 and offset 5 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_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/1H6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_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/1H6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H6_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/1H6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H6_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/1H6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7778639) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1H6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_R2_001.fastp-trim.fq.gz<) Using the subset file >1H6_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/1H6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Input files are in FastQ format Writing a C -> T converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H6_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/1H6_R2_001.fastp-trim.fq.gz for PID: 67633 and offset 5 (sequences written out: 7778639) Using the subset file >1H6_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/1H6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H6_R1_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 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz (7778639 sequences in total) Writing a C -> T converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz (7778639 sequences in total) Writing a C -> T converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz (7778639 sequences in total) Writing a C -> T converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz (7778639 sequences in total) Writing a C -> T converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz (7778639 sequences in total) Writing a C -> T converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H6_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 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz (7778639 sequences in total) Input files are 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H6_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz (7778639 sequences in total) Input files are 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:38831:1070_1:N:0:CACGCAAT+ATGGAAGG/1 99 ptg000020l_CT_converted 10105059 0 125M = 10105069 135 TAAGGTTATTTTGAAAATTTGTTTTTAGGGAGGTAGGAAATTTGGGTTATGAATTTTTTATAAGTTTGAGAAATTGTGGATTTTGTTTTTATTTTTTATTATTAAGTAGGGTTTTTATAGATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-48 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:14G44T6A36T12G8 YS:i:-42 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:38831:1070_2:N:0:CACGCAAT+ATGGAAGG/2 147 ptg000020l_CT_converted 10105069 0 125M = 10105059 -135 TTGAAAATTTGTTTTTAGGGAGGTAGGAAATTTGGGTTATGAATTTTTTATAAGTTTGAGAAATTGTGGATTTTGTTTTTATTTTTTATTATTAAGTAGGGTTTTTATAGATAATTTTTGAATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-42 XS:i:-60 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:4G44T6A36T12G14G1G1 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:28044:1084_1:N:0:CACGCAAT+ATGGAAGG/1 99 ptg000027l_CT_converted 12834986 42 125M = 12835201 340 GATTAAAATTGTGTGTATATGAGTATTAAGATATAATTGAAAAATAATTAAAGTAATAAATAAGTAAGTAATGTAAGGATATAATGGGGTTATTTAAGTTTGGATGGTAAATTTTATTTTTTGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:0A1A79G42 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:28044:1084_2:N:0:CACGCAAT+ATGGAAGG/2 147 ptg000027l_CT_converted 12835201 42 125M = 12834986 -340 ATTATTAAAAATAAAAAATAAAAAAAAAAGTAAATTAAGATATTTTTTTATGAGTAGGGGTTATAAATGATGAGATTGTTTTAAAATAAGATTTGTAATTGTTAATTTATGAGAATATTAATTTA IIIII9IIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H6_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz (7778639 sequences in total) Input files are 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:42489:1070_1:N:0:CACGCAAT+ATGGAAGG/1 99 ptg000023l_CT_converted 16157845 17 125M = 16158007 287 AAGATTGTTATTATAAATGAAGTAAATAAATAAAGAAATGAAATAATATTAGATTTTAATTGATGGAATATATTAGTATAAGTTTATTGTGTTTTTATTTTGGTATTTTAAGGGAAGAAATTAAA IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIII-IIIIIII9III-I-IIIIIIIIIIIIII AS:i:-6 XS:i:-24 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:108A16 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:42489:1070_2:N:0:CACGCAAT+ATGGAAGG/2 147 ptg000023l_CT_converted 16158007 17 125M = 16157845 -287 TTTAAAAGTAATAATTTATTGAAGGTTTTAAAATTATAGAAAATTATATATTTTTTTTTTATTTGGTTGGTTTGGAAGTTATTTTATTGAGTGATTGTAAATATTTTTATGTATTAGTTATAGTA IIIIIIIIIIII-II9IIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-24 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:42489:1070_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 AAAATTATTATTATAAATAAAATAAATAAATAAAAAAATAAAATAATATTAAATTTTAATTAATAAAATATATTAATATAAATTTATTATATTTTTATTTTAATATTTCAAAAAAAAAAATTAAA IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIII-IIIIIII9III-I-IIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42489:1070_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 TATTATAATTAATATATAAAAATATTTATAATTATTTAATAAAATAATTTTTAAATTAATTAAATAAAAAAAAAATATATAATTTTTTATAATTTTAAAATTTTTAATAAATTATTATTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIII9II-IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:28044:1084_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 AATTAAAATTACACATATACAAATATTAAAATATAATTAAAAAATAATTAAAATAATAAATAAATAAATAATATAAAAATATAATAAAATTATTTAAATTTAAATAATAAATTTTATTTTTCATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28044:1084_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 TAAATTAATATTTTTATAAATTAATAATTATAAATTTTATTTTAAAATAATTTTATTATTTATAATTTTTATTTATAAAAAAATATTTTAATTTATTTTTTTTTTTATTTTTTATTTTTAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:38831:1070_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 TAAAATTATTTTAAAAATTTATTTTTAAAAAAATAAAAAATTTAAATTATAAATTTTTTATAAATTTAAAAAATTATAAATTTTATTTTTATTTTTTATTATTAAATAAAATTTTTATAAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38831:1070_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 TAATTTAAAAATTATTTATAAAAATTTTATTTAATAATAAAAAATAAAAATAAAATTTATAATTTTTTAAATTTATAAAAAATTTATAATTTAAATTTTTTATTTTTTTAAAAATAAATTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:38831:1070_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 TAAAATTATTTTAAAAATTTATTTTTAAAAAAATAAAAAATTTAAATTATAAATTTTTTATAAATTTAAAAAATTATAAATTTTATTTTTATTTTTTATTATTAAATAAAATTTTTATAAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38831:1070_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 TAATTTAAAAATTATTTATAAAAATTTTATTTAATAATAAAAAATAAAAATAAAATTTATAATTTTTTAAATTTATAAAAAATTTATAATTTAAATTTTTTATTTTTTTAAAAATAAATTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:42489:1070_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 AAAATTATTATTATAAATAAAATAAATAAATAAAAAAATAAAATAATATTAAATTTTAATTAATAAAATATATTAATATAAATTTATTATATTTTTATTTTAATATTTCAAAAAAAAAAATTAAA IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIII-IIIIIII9III-I-IIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42489:1070_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 TATTATAATTAATATATAAAAATATTTATAATTATTTAATAAAATAATTTTTAAATTAATTAAATAAAAAAAAAATATATAATTTTTTATAATTTTAAAATTTTTAATAAATTATTATTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIII9II-IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:28044:1084_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 AATTAAAATTACACATATACAAATATTAAAATATAATTAAAAAATAATTAAAATAATAAATAAATAAATAATATAAAAATATAATAAAATTATTTAAATTTAAATAATAAATTTTATTTTTCATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28044:1084_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 TAAATTAATATTTTTATAAATTAATAATTATAAATTTTATTTTAAAATAATTTTATTATTTATAATTTTTATTTATAAAAAAATATTTTAATTTATTTTTTTTTTTATTTTTTATTTTTAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:38831:1070_1:N:0:CACGCAAT+ATGGAAGG/1 83 ptg000036l_GA_converted 2203578 25 125M = 2203568 -135 ATTATCTATAAAAACCCTACTTAATAATAAAAAATAAAAACAAAATCCACAATTTCTCAAACTTATAAAAAATTCATAACCCAAATTTCCTACCTCCCTAAAAACAAATTTTCAAAATAACCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-36 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:38831:1070_2:N:0:CACGCAAT+ATGGAAGG/2 163 ptg000036l_GA_converted 2203568 25 125M = 2203578 135 CAATTCAAAAATTATCTATAAAAACCCTACTTAATAATAAAAAATAAAAACAAAATCCACAATTTCTCAAACTTATAAAAAATTCATAACCCAAATTTCCTACCTCCCTAAAAACAAATTTTCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-48 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1C123 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:28044:1084_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 GATTAAAATTGTGTGTATATGAGTATTAAGATATAATTGAAAAATAATTAAAGTAATAAATAAGTAAGTAATGTAAGGATATAATGGGGTTATTTAAGTTTGGATGGTAAATTTTATTTTTTGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28044:1084_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 TAAATTAATATTCTCATAAATTAACAATTACAAATCTTATTTTAAAACAATCTCATCATTTATAACCCCTACTCATAAAAAAATATCTTAATTTACTTTTTTTTTTATTTTTTATTTTTAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII-IIIII9IIIII YT:Z:UP >>> Writing bisulfite mapping results to 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:42489:1070_1:N:0:CACGCAAT+ATGGAAGG/1 83 ptg000015l_GA_converted 2361747 1 125M = 2361585 -287 TTTAATTTCTTCCCTTAAAATACCAAAATAAAAACACAATAAACTTATACTAATATATTCCATCAATTAAAATCTAATATTATTTCATTTCTTTATTTATTTACTTCATTTATAATAACAATCTT IIIIIIIIIIIIII-I-III9IIIIIII-IIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:15A0T108 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:42489:1070_2:N:0:CACGCAAT+ATGGAAGG/2 163 ptg000015l_GA_converted 2361585 1 125M = 2361747 287 TACTATAACTAATACATAAAAATATTTACAATCACTCAATAAAATAACTTCCAAACCAACCAAATAAAAAAAAAATATATAATTTTCTATAATTTTAAAACCTTCAATAAATTATTACTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIII9II-IIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:3C15T62C13T20A7 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz (7778639 sequences in total) Input files are 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H6_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz (7778639 sequences in total) Input files are 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H6_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 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31119:1084_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 TTAAGTAATTTTGTGTTTTTTATTTGTGGTTATGAGTGTTGTAAGTGAAGGTGGATAAATGTTGAATTGTTAAAAATAAAATTGTGAATTTTTTTTTGTGGAATATTTGTGAGTAAATGGATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31119:1084_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 ATAATATTATTAACAAATAAAACTTATACCAAACATCAAAATAACCATAATCAAAAATCTTTAAAAAATCTAAATTCCCTTACTCCACACTCCAAAATCCAACTAATCTCTATTTAACAAATCTT IIIIIIIIIIIIII9IIIIIIIIIIIIIIII9III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45661:1070_1:N:0:CACGCAAT+ATGGAAGG/1 99 ptg000034l_CT_converted 1244435 0 70M = 1244410 -95 GTGTTGGTTTTTTTTTTTTTTTGTGATTTAAGATAGGAGATGTTTTTTAATTTTGGTTTTTTTTTAATAA IIIIIIIIIIIIIIIIIII-9I9I-9-I-9I-I999II9I-99II-I----999-99-999999999--9 AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:19G8A16G1A16A5 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45661:1070_2:N:0:CACGCAAT+ATGGAAGG/2 147 ptg000034l_CT_converted 1244410 0 70M = 1244435 95 GATTATTAAGAGAGTAATTAAATGAGTGTTGGTTTTTTTTTTTTGTTGTGATTAAAGATAGGAGATGTTT IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45661:1070_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 ATATTAATTTTTTTTTTTTTTTATAATTCAAAATAAAAAATATTTTTCAACTTTAATTTTTTTTCAATAA IIIIIIIIIIIIIIIIIII-9I9I-9-I-9I-I999II9I-99II-I----999-99-999999999--9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45661:1070_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 AAATATTTTTTATTTTTAATTATAATAAAAAAAAAAAATTAATATTTATTTAATTATTTTTTTAATAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31119:1084_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 TTAAATAATTTTATATTTTTTATTTATAATTATAAATATTATAAATAAAAATAAATAAATATTAAATTATTAAAAATAAAATTATAAATTTTTTTTTATAAAATATTTATAAATAAATAAATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31119:1084_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 ATAATATTATTAATAAATAAAATTTATATTAAATATTAAAATAATTATAATTAAAAATTTTTAAAAAATTTAAATTTTTTTATTTTATATTTTAAAATTTAATTAATTTTTATTTAATAAATTTT IIIIIIIIIIIIII9IIIIIIIIIIIIIIII9III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45661:1070_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 ATATTAATTTTTTTTTTTTTTTATAATTCAAAATAAAAAATATTTTTCAACTTTAATTTTTTTTCAATAA IIIIIIIIIIIIIIIIIII-9I9I-9-I-9I-I999II9I-99II-I----999-99-999999999--9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45661:1070_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 AAATATTTTTTATTTTTAATTATAATAAAAAAAAAAAATTAATATTTATTTAATTATTTTTTTAATAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:31119:1084_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 TTAAATAATTTTATATTTTTTATTTATAATTATAAATATTATAAATAAAAATAAATAAATATTAAATTATTAAAAATAAAATTATAAATTTTTTTTTATAAAATATTTATAAATAAATAAATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31119:1084_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 ATAATATTATTAATAAATAAAATTTATATTAAATATTAAAATAATTATAATTAAAAATTTTTAAAAAATTTAAATTTTTTTATTTTATATTTTAAAATTTAATTAATTTTTATTTAATAAATTTT IIIIIIIIIIIIII9IIIIIIIIIIIIIIII9III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45661:1070_1:N:0:CACGCAAT+ATGGAAGG/1 83 ntLink_6_GA_converted 21353456 0 70M = 21353481 95 TTATTAAAAAAAAACCAAAATTAAAAAACATCTCCTATCTTAAATCACAAAAAAAAAAAAAAACCAACAC 9--999999999-99-999----I-II99-I9II999I-I9-I-9-I9I9-IIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:5T16T1C16T8C19 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45661:1070_2:N:0:CACGCAAT+ATGGAAGG/2 163 ntLink_6_GA_converted 21353481 0 70M = 21353456 -95 AAACATCTCCTATCTTTAATCACAACAAAAAAAAAAAACCAACACTCATTTAATTACTCTCTTAATAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YS:i:-30 YT:Z:CP >>> Writing bisulfite mapping results to 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:31119:1084_1:N:0:CACGCAAT+ATGGAAGG/1 77 * 0 0 * * 0 0 TTAAGTAATTTTGTGTTTTTTATTTGTGGTTATGAGTGTTGTAAGTGAAGGTGGATAAATGTTGAATTGTTAAAAATAAAATTGTGAATTTTTTTTTGTGGAATATTTGTGAGTAAATGGATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31119:1084_2:N:0:CACGCAAT+ATGGAAGG/2 141 * 0 0 * * 0 0 ATAATATTATTAACAAATAAAACTTATACCAAACATCAAAATAACCATAATCAAAAATCTTTAAAAAATCTAAATTCCCTTACTCCACACTCCAAAATCCAACTAATCTCTATTTAACAAATCTT IIIIIIIIIIIIII9IIIIIIIIIIIIIIII9III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII YT:Z:UP >>> Writing bisulfite mapping results to 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1121:31346:20807_1:N:0:CACGCAAT+ATGGAAGG ptg000125l 18882 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1147:9634:10483_1:N:0:CACGCAAT+ATGGAAGG ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1168:10897:17487_1:N:0:CACGCAAT+ATGGAAGG ptg000127l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1247:28700:14798_1:N:0:CACGCAAT+ATGGAAGG ptg000006l 1 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1361:13041:9881_1:N:0:CACGCAAT+ATGGAAGG ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1361:13049:9895_1:N:0:CACGCAAT+ATGGAAGG ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1413:1542:2975_1:N:0:CACGCAAT+ATGGAAGG ptg000007l 12295855 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1413:1534:2961_1:N:0:CACGCAAT+ATGGAAGG ptg000007l 12295855 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1437:32034:18944_1:N:0:CACGCAAT+ATGGAAGG ptg000094l 36804 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1438:51924:13509_1:N:0:CACGCAAT+ATGGAAGG ptg000052l 52609 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1440:44115:6687_1:N:0:CACGCAAT+ATGGAAGG ptg000122l 1 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2113:42902:15904_1:N:0:CACGCAAT+ATGGAAGG ptg000183l 26189 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2233:8226:5525_1:N:0:CACGCAAT+ATGGAAGG ptg000083l 1 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1130:46883:2457_1:N:0:CACGCAAT+ATGGAAGG ptg000025l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1130:46915:2457_1:N:0:CACGCAAT+ATGGAAGG ptg000025l 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1126:31168:3269_1:N:0:CACGCAAT+ATGGAAGG ptg000011l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1313:34728:13075_1:N:0:CACGCAAT+ATGGAAGG ptg000128l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1416:45095:14125_1:N:0:CACGCAAT+ATGGAAGG ptg000128l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1390:18390:22810_1:N:0:CACGCAAT+ATGGAAGG ptg000066l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1426:34235:17011_1:N:0:CACGCAAT+ATGGAAGG ptg000174l 27224 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2123:7660:16759_1:N:0:CACGCAAT+ATGGAAGG ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2123:7676:16759_1:N:0:CACGCAAT+ATGGAAGG ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2178:43816:23314_1:N:0:CACGCAAT+ATGGAAGG ptg000045l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2203:18236:1868_1:N:0:CACGCAAT+ATGGAAGG ptg000006l 1 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2353:31257:27405_1:N:0:CACGCAAT+ATGGAAGG ptg000025l 21443081 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2366:8469:13481_1:N:0:CACGCAAT+ATGGAAGG ptg000006l 3 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2445:19208:8928_1:N:0:CACGCAAT+ATGGAAGG ptg000006l 2 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3801533 (48.87%) aligned concordantly 0 times 1525019 (19.61%) aligned concordantly exactly 1 time 2452087 (31.52%) aligned concordantly >1 times 51.13% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3795875 (48.80%) aligned concordantly 0 times 1526912 (19.63%) aligned concordantly exactly 1 time 2455852 (31.57%) aligned concordantly >1 times 51.20% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7760550 (99.77%) aligned concordantly 0 times 6103 (0.08%) aligned concordantly exactly 1 time 11986 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7762832 (99.80%) aligned concordantly 0 times 6241 (0.08%) aligned concordantly exactly 1 time 9566 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate Processed 7778639 sequences in total Successfully deleted the temporary files 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7778639 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198483105 Total methylated C's in CpG context: 3758893 Total methylated C's in CHG context: 199134 Total methylated C's in CHH context: 860303 Total methylated C's in Unknown context: 6169 Total unmethylated C's in CpG context: 26856765 Total unmethylated C's in CHG context: 33232751 Total unmethylated C's in CHH context: 133575259 Total unmethylated C's in Unknown context: 275868 C methylated in CpG context: 12.3% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2475:7854:26312_1:N:0:CACGCAAT+ATGGAAGG ptg000160l 32581 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7762783 (99.80%) aligned concordantly 0 times 6230 (0.08%) aligned concordantly exactly 1 time 9626 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3793673 (48.77%) aligned concordantly 0 times 1525863 (19.62%) aligned concordantly exactly 1 time 2459103 (31.61%) aligned concordantly >1 times 51.23% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3801009 (48.86%) aligned concordantly 0 times 1523146 (19.58%) aligned concordantly exactly 1 time 2454484 (31.55%) aligned concordantly >1 times 51.14% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7760488 (99.77%) aligned concordantly 0 times 6150 (0.08%) aligned concordantly exactly 1 time 12001 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate Processed 7778639 sequences in total Successfully deleted the temporary files 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7778639 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198478742 Total methylated C's in CpG context: 3755263 Total methylated C's in CHG context: 198775 Total methylated C's in CHH context: 870927 Total methylated C's in Unknown context: 6236 Total unmethylated C's in CpG context: 26859745 Total unmethylated C's in CHG context: 33231293 Total unmethylated C's in CHH context: 133562739 Total unmethylated C's in Unknown context: 275785 C methylated in CpG context: 12.3% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3796675 (48.81%) aligned concordantly 0 times 1525719 (19.61%) aligned concordantly exactly 1 time 2456245 (31.58%) aligned concordantly >1 times 51.19% overall alignment rate Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2487:4909:8578_1:N:0:CACGCAAT+ATGGAAGG ptg000009l 19095988 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7760415 (99.77%) aligned concordantly 0 times 6117 (0.08%) aligned concordantly exactly 1 time 12107 (0.16%) aligned concordantly >1 times 0.23% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3802068 (48.88%) aligned concordantly 0 times 1522890 (19.58%) aligned concordantly exactly 1 time 2453681 (31.54%) aligned concordantly >1 times 51.12% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7762906 (99.80%) aligned concordantly 0 times 6056 (0.08%) aligned concordantly exactly 1 time 9677 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate Processed 7778639 sequences in total Successfully deleted the temporary files 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7778639 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198313513 Total methylated C's in CpG context: 3750545 Total methylated C's in CHG context: 197033 Total methylated C's in CHH context: 855057 Total methylated C's in Unknown context: 6103 Total unmethylated C's in CpG context: 26813033 Total unmethylated C's in CHG context: 33220092 Total unmethylated C's in CHH context: 133477753 Total unmethylated C's in Unknown context: 276840 C methylated in CpG context: 12.3% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7760596 (99.77%) aligned concordantly 0 times 6039 (0.08%) aligned concordantly exactly 1 time 12004 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7762972 (99.80%) aligned concordantly 0 times 6091 (0.08%) aligned concordantly exactly 1 time 9576 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3796297 (48.80%) aligned concordantly 0 times 1524634 (19.60%) aligned concordantly exactly 1 time 2457708 (31.60%) aligned concordantly >1 times 51.20% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3800918 (48.86%) aligned concordantly 0 times 1523815 (19.59%) aligned concordantly exactly 1 time 2453906 (31.55%) aligned concordantly >1 times 51.14% overall alignment rate Processed 7778639 sequences in total Successfully deleted the temporary files 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7778639 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198418016 Total methylated C's in CpG context: 3763489 Total methylated C's in CHG context: 196624 Total methylated C's in CHH context: 855515 Total methylated C's in Unknown context: 6076 Total unmethylated C's in CpG context: 26840965 Total unmethylated C's in CHG context: 33223775 Total unmethylated C's in CHH context: 133537648 Total unmethylated C's in Unknown context: 276549 C methylated in CpG context: 12.3% 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 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3795928 (48.80%) aligned concordantly 0 times 1526135 (19.62%) aligned concordantly exactly 1 time 2456576 (31.58%) aligned concordantly >1 times 51.20% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7760500 (99.77%) aligned concordantly 0 times 6144 (0.08%) aligned concordantly exactly 1 time 11995 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 7762964 (99.80%) aligned concordantly 0 times 6155 (0.08%) aligned concordantly exactly 1 time 9520 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 7778639 reads; of these: 7778639 (100.00%) were paired; of these: 3801380 (48.87%) aligned concordantly 0 times 1523438 (19.58%) aligned concordantly exactly 1 time 2453821 (31.55%) aligned concordantly >1 times 51.13% overall alignment rate Processed 7778639 sequences in total Successfully deleted the temporary files 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H6_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7778639 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198442604 Total methylated C's in CpG context: 3758806 Total methylated C's in CHG context: 198167 Total methylated C's in CHH context: 861737 Total methylated C's in Unknown context: 6105 Total unmethylated C's in CpG context: 26837121 Total unmethylated C's in CHG context: 33234891 Total unmethylated C's in CHH context: 133551882 Total unmethylated C's in Unknown context: 276421 C methylated in CpG context: 12.3% 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 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1H6_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1H6_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1H6_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/1H6_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1H6_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/1H6_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H6_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: 38893195 Final Cytosine Methylation Report ================================= Total number of C's analysed: 992135980 Total methylated C's in CpG context: 18786996 Total methylated C's in CHG context: 989733 Total methylated C's in CHH context: 4303539 Total methylated C's in Unknown context: 30689 Total unmethylated C's in CpG context: 134207629 Total unmethylated C's in CHG context: 166142802 Total unmethylated C's in CHH context: 667705281 Total unmethylated C's in Unknown context: 1381463 C methylated in CpG context: 12.3% 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 21m 31s ==================== Bismark run complete ====================