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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_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/1H11_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7594090) Using the subset file >1H11_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/1H11_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/1H11_R1_001.fastp-trim.fq.gz for PID: 46151 and offset 5 (sequences written out: 7594090) Using the subset file >1H11_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/1H11_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/1H11_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7594091) Using the subset file >1H11_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/1H11_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/1H11_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7594090) Using the subset file >1H11_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/1H11_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/1H11_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7594091) Using the subset file >1H11_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/1H11_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/1H11_R2_001.fastp-trim.fq.gz for PID: 46151 and offset 5 (sequences written out: 7594090) Using the subset file >1H11_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/1H11_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1H11_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7594090) Using the subset file >1H11_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/1H11_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H11_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/1H11_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7594091) Using the subset file >1H11_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/1H11_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H11_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/1H11_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7594090) Using the subset file >1H11_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/1H11_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H11_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/1H11_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7594091) Using the subset file >1H11_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/1H11_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz (7594091 sequences in total) Writing a C -> T converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz (7594091 sequences in total) Writing a C -> T converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz (7594090 sequences in total) Writing a C -> T converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz (7594090 sequences in total) Writing a C -> T converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz (7594090 sequences in total) Writing a C -> T converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H11_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 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz (7594090 sequences in total) Input files are 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H11_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 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz (7594091 sequences in total) Input files are 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H11_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 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz (7594091 sequences in total) Input files are 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:50379:1056_1:N:0:GATAGCCA+CTGTGTTG/1 99 ntLink_8_CT_converted 15152789 42 92M = 15152764 -117 ATTTGTTGGAAGTAGGTTTATATTGGAATTGAATATGGTGTGTTGTAAGAGATAAAATGTAGTAAGGTAATAATATAAAAAATTTAATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:92 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50379:1056_2:N:0:GATAGCCA+CTGTGTTG/2 147 ntLink_8_CT_converted 15152764 42 92M = 15152789 117 AATAATTTGTGAAAGAAGAAATAGTATTTGTTGGAAGTAGGTTTATATTGGAATTGAATATGGTGTGTTGTAAGAGATAAAATGTAGTAAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:92 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:46422:1070_1:N:0:GATAGCCA+CTGTGTTG/1 99 ptg000018l_CT_converted 7921624 2 125M = 7921727 228 GTAAAAGTATGATTTTTTAAGTTTATGTTGTTGGAGTTGTTTTTAAAGTGAAAGAGTATTAAATAGTTTTGGTTGTTTGTTTTTTGGGATGTATGATTTTTTTTTATTTATTTATATTGTATGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIII AS:i:-30 XS:i:-36 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:55T28A1A7T6G23 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:46422:1070_2:N:0:GATAGCCA+CTGTGTTG/2 147 ptg000018l_CT_converted 7921727 2 125M = 7921624 -228 TTATTTATTTATATTGTATGAGATAGTTTTTTTGTAGGTTATGTTTTTTTGGGTGATAAGTATATTATTTTTTTGTTTGTTTTATTAATTTTTTGATTATTTATTTATTAATTTATGGTTAAAAA 9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:23G69G7A17A5 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:51318:1056_1:N:0:GATAGCCA+CTGTGTTG/1 99 ptg000008l_CT_converted 16490279 2 125M = 16490343 189 AAATTATAAATTATGATTATTTTTAAATAAAATATTTTAATAGGTTAATAGATTAATTTTTTAGTAAATATTATAGGGTAATGTTAGATTTGGATGGTTTTAGAAAGGTAAGATATTTATGGATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:19G4T18A37A43 YS:i:-42 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51318:1056_2:N:0:GATAGCCA+CTGTGTTG/2 147 ptg000008l_CT_converted 16490343 2 125M = 16490279 -189 TAAATGTTATAGGGTAATGTTAGGTTTGGATGGTTTTAGAAAGGTAAGATATTTATGGATTAGAAAGAGAGTAATTAAATGAAGGTTGGTTTTTTTTTTTTGTTGTGATTAAGGTTAGGAGAAGT ---9I-9II9-II9IIII99III9I9IIIII999I9II9-III9-II-I99IIII-II-99I9II9IIIII-II-III9IIIIIIIII-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII AS:i:-42 XS:i:-48 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:5A11A5A38T49A1A7T2 YS:i:-24 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:50379:1056_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 ATTTATCAAAAATAAATTTATATTAAAATCAAATATAACATATTATAAAAAATAAAACATAATAAAATAATAATATAAAAAATTTAATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50379:1056_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 TTTTATTATGTTTTATTTTTTATAATATGTTATATTTGATTTTAATATAAATTTATTTTTGATAAATATTATTTTTTTTTTTGTAAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:46422:1070_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 ATAAAAATATAATTTTTTAAATTTATATTATTAAAATTATTTTTAAAATAAAAAAATATTAAATAATTTTAATTATTTATTTTTTAAAATATATAATTTTTTTTTATTTATTTATATTATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46422:1070_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 TTTTTAATTATAAATTAATAAATAAATAATTAAAAAATTAATAAAATAAATAAAAAAATAATATATTTATTATTTAAAAAAATATAATTTATAAAAAAATTATTTTATATAATATAAATAAATAA IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:51318:1056_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 AAATTATAAATTATAATTATTTTTAAATAAAATATTTTAATAAATTAATAAATTAATTTTTTAATAAATATTATAAAATAACATTAAATTTAAATAATTTTAAAAAAATAAAATATTTATAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51318:1056_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 ATTTTTTTTAATTTTAATTATAATAAAAAAAAAAAATTAATTTTTATTTAATTATTTTTTTTTTAATTTATAAATATTTTATTTTTTTAAAATTATTTAAATTTAATGTTATTTTATAATATTTA IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIII9III-II-IIIII9II9I99-II-IIII99I-II-9III-9II9I999IIIII9I9III99IIII9II-9II9-I9--- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:46422:1070_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 ATAAAAATATAATTTTTTAAATTTATATTATTAAAATTATTTTTAAAATAAAAAAATATTAAATAATTTTAATTATTTATTTTTTAAAATATATAATTTTTTTTTATTTATTTATATTATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46422:1070_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 TTTTTAATTATAAATTAATAAATAAATAATTAAAAAATTAATAAAATAAATAAAAAAATAATATATTTATTATTTAAAAAAATATAATTTATAAAAAAATTATTTTATATAATATAAATAAATAA IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:51318:1056_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 AAATTATAAATTATAATTATTTTTAAATAAAATATTTTAATAAATTAATAAATTAATTTTTTAATAAATATTATAAAATAACATTAAATTTAAATAATTTTAAAAAAATAAAATATTTATAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51318:1056_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 ATTTTTTTTAATTTTAATTATAATAAAAAAAAAAAATTAATTTTTATTTAATTATTTTTTTTTTAATTTATAAATATTTTATTTTTTTAAAATTATTTAAATTTAATGTTATTTTATAATATTTA IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIII9III-II-IIIII9II9I99-II-IIII99I-II-9III-9II9I999IIIII9I9III99IIII9II-9II9-I9--- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:50379:1056_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 ATTTATCAAAAATAAATTTATATTAAAATCAAATATAACATATTATAAAAAATAAAACATAATAAAATAATAATATAAAAAATTTAATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50379:1056_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 TTTTATTATGTTTTATTTTTTATAATATGTTATATTTGATTTTAATATAAATTTATTTTTGATAAATATTATTTTTTTTTTTGTAAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H11_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz (7594090 sequences in total) Input files are 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H11_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz (7594090 sequences in total) Input files are 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H11_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 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:46422:1070_1:N:0:GATAGCCA+CTGTGTTG/1 83 ptg000011l_GA_converted 4305282 6 125M = 4305179 -228 CTCATACAATATAAATAAATAAAAAAAAATCATACATCCCAAAAAACAAACAACCAAAACTATTTAATACTCTTTCACTTTAAAAACAACTCCAACAACATAAACTTAAAAAATCATACTTTTAC IIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:46422:1070_2:N:0:GATAGCCA+CTGTGTTG/2 163 ptg000011l_GA_converted 4305179 6 125M = 4305282 228 TTTTTAACCATAAATTAATAAATAAATAATCAAAAAATTAATAAAACAAACAAAAAAATAATATACTTATCACCCAAAAAAACATAACCTACAAAAAAACTATCTCATACAATATAAATAAATAA IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9 AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:102C22 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:50379:1056_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 ATTTGTTGGAAGTAGGTTTATATTGGAATTGAATATGGTGTGTTGTAAGAGATAAAATGTAGTAAGGTAATAATATAAAAAATTTAATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50379:1056_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 CCTTACTACATTTTATCTCTTACAACACACCATATTCAATTCCAATATAAACCTACTTCCAACAAATACTATTTCTTCTTTCACAAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:51318:1056_1:N:0:GATAGCCA+CTGTGTTG/1 83 ptg000033l_GA_converted 1404321 6 125M = 1404257 -189 AATCCATAAATATCTTACCTTTCTAAAACCATCCAAATCTAACATTACCCTATAATATTTACTAAAAAATTAATCTATTAACCTATTAAAATATTTTATTTAAAAATAATCATAATTTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51318:1056_2:N:0:GATAGCCA+CTGTGTTG/2 163 ptg000033l_GA_converted 1404257 6 125M = 1404321 189 ACTTCTCCTAACCTTAATCACAACAAAAAAAAAAAACCAACCTTCATTTAATTACTCTCTTTCTAATCCATAAATATCTTACCTTTCTAAAACCATCCAAACCTAACATTACCCTATAACATTTA IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIII9III-II-IIIII9II9I99-II-IIII99I-II-9III-9II9I999IIIII9I9III99IIII9II-9II9-I9--- AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:62A38T17T5 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:44431:1070_1:N:0:GATAGCCA+CTGTGTTG/1 99 ptg000020l_CT_converted 5166470 34 125M = 5166522 177 TTATTTTTTTTGTGTAAATTAGTTGTTTAGTGGTTAAGTAATGTTAGTATTTTAAGTAAATTATAAGTTTGATGATATTTATTGATAGTATTGATTATTATTTATAAGAGGAGATAAAATATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-26 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44431:1070_2:N:0:GATAGCCA+CTGTGTTG/2 147 ptg000020l_CT_converted 5166522 34 125M = 5166470 -177 TAAGTAAATTATAAGTTTGATGATATTTATTGATAGTATTGATTATTATTTATAAGAGGAGATAAAATATTTTTTTGTGAATTGATTATAGGTATTTTAGGTTTATGATTTAAAAGATTAGTTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-44 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 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:40870:1070_1:N:0:GATAGCCA+CTGTGTTG/1 99 ptg000048l_CT_converted 27093 1 125M = 27115 147 AAAAAAAATATTTTGTTAGGGTATGATTATGTATTTGGTGTTTGTTGTAGAATTTTTTTTAGAAGAAGAATGTTATTTTGTGGTTGATTTTTGTTTTTTGATTTTTGAAATAGTTGTTATTGTTG I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40870:1070_2:N:0:GATAGCCA+CTGTGTTG/2 147 ptg000048l_CT_converted 27115 1 125M = 27093 -147 ATGATTATGTATTTGGTGTTTGTTGTAGAATTTTTTTTAGAAGAAGAATGTTATTTTGTGGTTGATTTTTGTTTTTTGATTTTTGAAATAGTTGTTATTGTTGTTATTTTTGGTTTTGGTTTTTT II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H11_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)) Reading in the sequence files 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:44431:1070_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 TTATTTTTTTTATATAAATTAATTATTTAATAATTAAATAATATTAATATTTTAAATAAATTATAAATTTAATAATATTTATTAATAATATTAATTATTATTTATAAAAAAAAATAAAATATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44431:1070_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 ATAATTAATTTTTTAAATTATAAATTTAAAATATTTATAATTAATTTATAAAAAAATATTTTATTTTTTTTTATAAATAATAATTAATATTATTAATAAATATTATTAAATTTATAATTTATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:40870:1070_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 AAAAAAAATATTTTATTAAAATATAATTATATATTTAATATTTATTATAAAATTTTTTTTAAAAAAAAAATATTATTTTATAATTAATTTTTATTTTTTAATTTTTAAAATAATTATTATTATTA I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40870:1070_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 AAAAAATTAAAATTAAAAATAATAATAATAATAATTATTTTAAAAATTAAAAAATAAAAATTAATTATAAAATAATATTTTTTTTTTAAAAAAAATTTTATAATAAATATTAAATATATAATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:44431:1070_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 TTATTTTTTTTATATAAATTAATTATTTAATAATTAAATAATATTAATATTTTAAATAAATTATAAATTTAATAATATTTATTAATAATATTAATTATTATTTATAAAAAAAAATAAAATATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44431:1070_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 ATAATTAATTTTTTAAATTATAAATTTAAAATATTTATAATTAATTTATAAAAAAATATTTTATTTTTTTTTATAAATAATAATTAATATTATTAATAAATATTATTAAATTTATAATTTATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:40870:1070_1:N:0:GATAGCCA+CTGTGTTG/1 77 * 0 0 * * 0 0 AAAAAAAATATTTTATTAAAATATAATTATATATTTAATATTTATTATAAAATTTTTTTTAAAAAAAAAATATTATTTTATAATTAATTTTTATTTTTTAATTTTTAAAATAATTATTATTATTA I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40870:1070_2:N:0:GATAGCCA+CTGTGTTG/2 141 * 0 0 * * 0 0 AAAAAATTAAAATTAAAAATAATAATAATAATAATTATTTTAAAAATTAAAAAATAAAAATTAATTATAAAATAATATTTTTTTTTTAAAAAAAATTTTATAATAAATATTAAATATATAATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H11_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: LH00526:197:22KFKVLT4:3:1101:44431:1070_1:N:0:GATAGCCA+CTGTGTTG/1 83 ptg000020l_GA_converted 7137806 0 125M = 7137754 -177 AAAATATTTTATCTCCTCTTATAAATAATAATCAATACTATCAATAAATATCATCAAACTTATAATTTACTTAAAATACTAACATTACTTAACCACTAAACAACTAATTTACACAAAAAAAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-36 XS:i:-48 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:14A43T24C19A0C16T3 YS:i:-36 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44431:1070_2:N:0:GATAGCCA+CTGTGTTG/2 163 ptg000020l_GA_converted 7137754 0 125M = 7137806 177 ACAACTAATCTTTTAAATCATAAACCTAAAATACCTATAATCAATTCACAAAAAAATATTTTATCTCCTCTTATAAATAATAATCAATACTATCAATAAATATCATCAAACTTATAATTTACTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-36 XS:i:-54 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:25T19C1C3T14A43T14 YS:i:-36 YT:Z:CP >>> Writing bisulfite mapping results to 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:40870:1070_1:N:0:GATAGCCA+CTGTGTTG/1 83 ptg000053l_GA_converted 1347 1 125M = 1325 -147 CAACAATAACAACTATTTCAAAAATCAAAAAACAAAAATCAACCACAAAATAACATTCTTCTTCTAAAAAAAATTCTACAACAAACACCAAATACATAATCATACCCTAACAAAATATTTTTTTT IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40870:1070_2:N:0:GATAGCCA+CTGTGTTG/2 163 ptg000053l_GA_converted 1325 1 125M = 1347 147 AAAAAACCAAAACCAAAAATAACAACAATAACAACTATTTCAAAAATCAAAAAACAAAAATCAACCACAAAATAACATTCTTCTTCTAAAAAAAATTCTACAACAAACACCAAATACATAATCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1227:35934:15498_1:N:0:GATAGCCA+CTGTGTTG ptg000066l 66366 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 LH00526:197:22KFKVLT4:3:1316:47393:11688_1:N:0:GATAGCCA+CTGTGTTG ptg000015l 14997092 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1365:42667:5609_1:N:0:GATAGCCA+CTGTGTTG ptg000083l 2 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 LH00526:197:22KFKVLT4:3:2163:33806:17361_1:N:0:GATAGCCA+CTGTGTTG ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2163:33822:17361_1:N:0:GATAGCCA+CTGTGTTG ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2163:33798:17375_1:N:0:GATAGCCA+CTGTGTTG ptg000066l 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2317:4561:29016_1:N:0:GATAGCCA+CTGTGTTG ptg000007l 12295855 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2352:19345:25360_1:N:0:GATAGCCA+CTGTGTTG ptg000057l 39949 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1119:36501:26312_1:N:0:GATAGCCA+CTGTGTTG ptg000066l 66374 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 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 Processed 5000000 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 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 3576719 (47.10%) aligned concordantly 0 times 1406025 (18.51%) aligned concordantly exactly 1 time 2611346 (34.39%) aligned concordantly >1 times 52.90% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 7570039 (99.68%) aligned concordantly 0 times 8589 (0.11%) aligned concordantly exactly 1 time 15462 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 3579520 (47.14%) aligned concordantly 0 times 1405524 (18.51%) aligned concordantly exactly 1 time 2609046 (34.36%) aligned concordantly >1 times 52.86% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 7570856 (99.69%) aligned concordantly 0 times 8650 (0.11%) aligned concordantly exactly 1 time 14584 (0.19%) aligned concordantly >1 times 0.31% overall alignment rate Processed 7594090 sequences in total Successfully deleted the temporary files 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7594090 Final Cytosine Methylation Report ================================= Total number of C's analysed: 185394552 Total methylated C's in CpG context: 2485955 Total methylated C's in CHG context: 181055 Total methylated C's in CHH context: 778751 Total methylated C's in Unknown context: 5229 Total unmethylated C's in CpG context: 28022067 Total unmethylated C's in CHG context: 31978115 Total unmethylated C's in CHH context: 121948609 Total unmethylated C's in Unknown context: 253225 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2411:11949:12977_1:N:0:GATAGCCA+CTGTGTTG ptg000066l 66348 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 7569883 (99.68%) aligned concordantly 0 times 8666 (0.11%) aligned concordantly exactly 1 time 15542 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 3581855 (47.17%) aligned concordantly 0 times 1406674 (18.52%) aligned concordantly exactly 1 time 2605562 (34.31%) aligned concordantly >1 times 52.83% overall alignment rate 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 3580568 (47.15%) aligned concordantly 0 times 1405886 (18.51%) aligned concordantly exactly 1 time 2607637 (34.34%) aligned concordantly >1 times 52.85% overall alignment rate 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 7570721 (99.69%) aligned concordantly 0 times 8665 (0.11%) aligned concordantly exactly 1 time 14705 (0.19%) aligned concordantly >1 times 0.31% overall alignment rate Processed 7594091 sequences in total Successfully deleted the temporary files 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7594091 Final Cytosine Methylation Report ================================= Total number of C's analysed: 185506290 Total methylated C's in CpG context: 2481682 Total methylated C's in CHG context: 180533 Total methylated C's in CHH context: 778245 Total methylated C's in Unknown context: 5328 Total unmethylated C's in CpG context: 28040617 Total unmethylated C's in CHG context: 31991999 Total unmethylated C's in CHH context: 122033214 Total unmethylated C's in Unknown context: 252988 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2403:26790:18104_1:N:0:GATAGCCA+CTGTGTTG ptg000033l 2625597 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2444:45847:17977_1:N:0:GATAGCCA+CTGTGTTG ptg000033l 2625625 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 7570863 (99.69%) aligned concordantly 0 times 8530 (0.11%) aligned concordantly exactly 1 time 14697 (0.19%) aligned concordantly >1 times 0.31% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 3580002 (47.14%) aligned concordantly 0 times 1405585 (18.51%) aligned concordantly exactly 1 time 2608503 (34.35%) aligned concordantly >1 times 52.86% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 7569996 (99.68%) aligned concordantly 0 times 8603 (0.11%) aligned concordantly exactly 1 time 15491 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 3575825 (47.09%) aligned concordantly 0 times 1407206 (18.53%) aligned concordantly exactly 1 time 2611059 (34.38%) aligned concordantly >1 times 52.91% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 7570852 (99.69%) aligned concordantly 0 times 8612 (0.11%) aligned concordantly exactly 1 time 14626 (0.19%) aligned concordantly >1 times 0.31% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 3581501 (47.16%) aligned concordantly 0 times 1405027 (18.50%) aligned concordantly exactly 1 time 2607562 (34.34%) aligned concordantly >1 times 52.84% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 3577818 (47.11%) aligned concordantly 0 times 1405391 (18.51%) aligned concordantly exactly 1 time 2610881 (34.38%) aligned concordantly >1 times 52.89% overall alignment rate 7594090 reads; of these: 7594090 (100.00%) were paired; of these: 7569665 (99.68%) aligned concordantly 0 times 8833 (0.12%) aligned concordantly exactly 1 time 15592 (0.21%) aligned concordantly >1 times 0.32% overall alignment rate Processed 7594090 sequences in total Successfully deleted the temporary files 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7594090 Final Cytosine Methylation Report ================================= Total number of C's analysed: 185324229 Total methylated C's in CpG context: 2494830 Total methylated C's in CHG context: 180897 Total methylated C's in CHH context: 776437 Total methylated C's in Unknown context: 5286 Total unmethylated C's in CpG context: 27992249 Total unmethylated C's in CHG context: 31960222 Total unmethylated C's in CHH context: 121919594 Total unmethylated C's in Unknown context: 254080 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 7594090 sequences in total Successfully deleted the temporary files 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7594090 Final Cytosine Methylation Report ================================= Total number of C's analysed: 185465133 Total methylated C's in CpG context: 2491114 Total methylated C's in CHG context: 179697 Total methylated C's in CHH context: 773915 Total methylated C's in Unknown context: 5167 Total unmethylated C's in CpG context: 28029127 Total unmethylated C's in CHG context: 31991132 Total unmethylated C's in CHH context: 122000148 Total unmethylated C's in Unknown context: 253428 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Now waiting for all child processes to complete 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 7569973 (99.68%) aligned concordantly 0 times 8628 (0.11%) aligned concordantly exactly 1 time 15490 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 3577749 (47.11%) aligned concordantly 0 times 1406910 (18.53%) aligned concordantly exactly 1 time 2609432 (34.36%) aligned concordantly >1 times 52.89% overall alignment rate 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 7570906 (99.69%) aligned concordantly 0 times 8474 (0.11%) aligned concordantly exactly 1 time 14711 (0.19%) aligned concordantly >1 times 0.31% overall alignment rate 7594091 reads; of these: 7594091 (100.00%) were paired; of these: 3581537 (47.16%) aligned concordantly 0 times 1405557 (18.51%) aligned concordantly exactly 1 time 2606997 (34.33%) aligned concordantly >1 times 52.84% overall alignment rate Processed 7594091 sequences in total Successfully deleted the temporary files 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H11_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7594091 Final Cytosine Methylation Report ================================= Total number of C's analysed: 185431326 Total methylated C's in CpG context: 2486913 Total methylated C's in CHG context: 179505 Total methylated C's in CHH context: 776697 Total methylated C's in Unknown context: 5045 Total unmethylated C's in CpG context: 28024681 Total unmethylated C's in CHG context: 31988700 Total unmethylated C's in CHH context: 121974830 Total unmethylated C's in Unknown context: 253138 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1H11_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1H11_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1H11_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/1H11_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1H11_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/1H11_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H11_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H11_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: 37970452 Final Cytosine Methylation Report ================================= Total number of C's analysed: 927121530 Total methylated C's in CpG context: 12440494 Total methylated C's in CHG context: 901687 Total methylated C's in CHH context: 3884045 Total methylated C's in Unknown context: 26055 Total unmethylated C's in CpG context: 140108741 Total unmethylated C's in CHG context: 159910168 Total unmethylated C's in CHH context: 609876395 Total unmethylated C's in Unknown context: 1266859 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Deleting temporary report files... Bismark completed in 0d 5h 1m 11s ==================== Bismark run complete ====================