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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_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/1H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7846449) Using the subset file >1H3_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/1H3_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/1H3_R1_001.fastp-trim.fq.gz for PID: 47579 and offset 5 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_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/1H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_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/1H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_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/1H3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_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/1H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H3_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/1H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7846449) Using the subset file >1H3_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/1H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H3_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/1H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H3_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/1H3_R2_001.fastp-trim.fq.gz for PID: 47579 and offset 5 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H3_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/1H3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7846448) Using the subset file >1H3_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/1H3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz (7846448 sequences in total) Writing a C -> T converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz (7846448 sequences in total) Writing a C -> T converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz (7846449 sequences in total) Writing a C -> T converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz (7846448 sequences in total) Writing a C -> T converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz (7846448 sequences in total) Writing a C -> T converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H3_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 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz (7846448 sequences in total) Input files are 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H3_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz (7846449 sequences in total) Input files are 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H3_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 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz (7846448 sequences in total) Input files are 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:40514:1070_1:N:0:GGTTGAAC+AACGTGGA/1 99 ptg000002l_CT_converted 8436008 6 125M = 8436208 324 ATTATAAAATGTTTATGGAAAATTTTTTTTATTTAAAATGTGTAGTTTTGATTTTTTGTTGGTTTGAAATAAGTATTTAATATTTAATAATTAGATTTGTAGTTTAGTTTTTTGGGTTATGGGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIII9IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIII--IIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:25G99 YS:i:-14 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40514:1070_2:N:0:GGTTGAAC+AACGTGGA/2 147 ptg000002l_CT_converted 8436208 6 12M1I112M = 8436008 -324 TATTATTTAATTAAGTTGGATAGAAAAAAGTAATAATAAATTTAGTTAAAAAAAATATTTATGTGGGAATAAAATAAAATAAATAGGTTTATAAAATTGGTAAATTTTGTTGTTTGATGATTGTT II9IIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:61T62 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:50023:1056_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 TTAATTGATGGATGGTTGTAATTGATGTATTTGTTAGTAATAAATATTTTTTGTAATTATTATTATATATTTTAAGTGTAATTTTGTAAATATGAAGGTTAAATGAGATGTGGAATTTGTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50023:1056_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TAACACTTAACACTCATCAAACACTAAAAAATCTTTCTCTTTCTTAAATTTCAATATCTATAAACAATCTTCAATTTTCATACCAAAATAATAACAAAAAAACAAAAC IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:42813:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 AGAATTTAATAGAAGGAGGAATGAGTTTTTGGTGGATTATATTTATTTTTGGGATGTTATAGATTGTATTAATTTGTTATATTGAAATTAAATAGGTAATTGTTATTATGTTGATGTTATATAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42813:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TTTCTTTCACTACCAACTCTATTTTTTCTTTACTAAAATCTAAAAACAACACAATAAAACCTTAAAAAAATACCAACCTTATATAACATCAACATAATAACAATTACCTATTTAATTTCAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:42813:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 AAAATTTAATAAAAAAAAAAATAAATTTTTAATAAATTATATTTATTTTTAAAATATTATAAATTATATTAATTTATTATATTAAAATTAAATAAATAATTATTATTATATTAATATTATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42813:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TTTTTTTTATTATTAATTTTATTTTTTTTTTATTAAAATTTAAAAATAATATAATAAAATTTTAAAAAAATATTAATTTTATATAATATTAATATAATAATAATTATTTATTTAATTTTAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:50023:1056_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 TTAATTAATAAATAATTATAATTAATATATTTATTAATAATAAATATTTTTTATAATTATTATTATATATTTTAAATATAATTTTATAAATATAAAAATTAAATAAAATATAAAATTTATTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50023:1056_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TAATATTTAATATTTATTAAATATTAAAAAATTTTTTTTTTTTTTAAATTTTAATATTTATAAATAATTTTTAATTTTTATATTAAAATAATAATAAAAAAATAAAAT IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:40514:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 ATTATAAAATATTTATAAAAAATTTTTTTTATTTAAAATATATAATTTTAATTTTTTATTAATTTAAAATAAATATTTAATATTTAATAATTAAATTTATAATTTAATTTTTTAAATTATAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIII9IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIII--IIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40514:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 AATAATTATTAAATAATAAAATTTATTAATTTTATAAATTTATTTATTTTATTTTATTTTTATATAAATATTTTTTTTAATTAAATTTATTATTATTTTTTTTTATTTAATTTAATTAAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:50023:1056_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 TTAATTAATAAATAATTATAATTAATATATTTATTAATAATAAATATTTTTTATAATTATTATTATATATTTTAAATATAATTTTATAAATATAAAAATTAAATAAAATATAAAATTTATTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50023:1056_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TAATATTTAATATTTATTAAATATTAAAAAATTTTTTTTTTTTTTAAATTTTAATATTTATAAATAATTTTTAATTTTTATATTAAAATAATAATAAAAAAATAAAAT IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:42813:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 AAAATTTAATAAAAAAAAAAATAAATTTTTAATAAATTATATTTATTTTTAAAATATTATAAATTATATTAATTTATTATATTAAAATTAAATAAATAATTATTATTATATTAATATTATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42813:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TTTTTTTTATTATTAATTTTATTTTTTTTTTATTAAAATTTAAAAATAATATAATAAAATTTTAAAAAAATATTAATTTTATATAATATTAATATAATAATAATTATTTATTTAATTTTAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:40514:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 ATTATAAAATATTTATAAAAAATTTTTTTTATTTAAAATATATAATTTTAATTTTTTATTAATTTAAAATAAATATTTAATATTTAATAATTAAATTTATAATTTAATTTTTTAAATTATAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIII9IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIII--IIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40514:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 AATAATTATTAAATAATAAAATTTATTAATTTTATAAATTTATTTATTTTATTTTATTTTTATATAAATATTTTTTTTAATTAAATTTATTATTATTTTTTTTTATTTAATTTAATTAAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H3_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz (7846448 sequences in total) Input files are 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:42813:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 AGAATTTAATAGAAGGAGGAATGAGTTTTTGGTGGATTATATTTATTTTTGGGATGTTATAGATTGTATTAATTTGTTATATTGAAATTAAATAGGTAATTGTTATTATGTTGATGTTATATAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:42813:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TTTCTTTCACTACCAACTCTATTTTTTCTTTACTAAAATCTAAAAACAACACAATAAAACCTTAAAAAAATACCAACCTTATATAACATCAACATAATAACAATTACCTATTTAATTTCAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP >>> Writing bisulfite mapping results to 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:50023:1056_1:N:0:GGTTGAAC+AACGTGGA/1 83 ptg000016l_GA_converted 3837807 42 125M = 3837584 -348 AAATAACAAATTCCACATCTCATTTAACCTTCATATTTACAAAATTACACTTAAAATATATAATAATAATTACAAAAAATATTTATTACTAACAAATACATCAATTACAACCATCCATCAATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50023:1056_2:N:0:GGTTGAAC+AACGTGGA/2 163 ptg000016l_GA_converted 3837584 42 108M = 3837807 348 TAACACTTAACACTCATCAAACACTAAAAAATCTTTCTCTTTCTTAAATTTCAATATCTATAAACAATCTTCAATTTTCATACCAAAATAATAACAAAAAAACAAAAC IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:108 YS:i:0 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:40514:1070_1:N:0:GGTTGAAC+AACGTGGA/1 83 ptg000002l_GA_converted 8879438 42 125M = 8879238 -325 ACCCCATAACCCAAAAAACTAAACTACAAATCTAATTATTAAATATTAAATACTTATTTCAAACCAACAAAAAATCAAAACTACACATTTTAAATAAAAAAAATTTTCCATAAACATTTTATAAT IIIII--IIII9IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIII9IIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40514:1070_2:N:0:GGTTGAAC+AACGTGGA/2 163 ptg000002l_GA_converted 8879238 42 125M = 8879438 325 AACAATCATCAAACAACAAAATTTACCAATTTTATAAACCTATTTATTTTATTTTATTCCCACATAAATATTTTTTTTAACTAAATTTATTATTACTTTTTTCTATCCAACTTAATTAAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIII9II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Created C -> T as well as G -> A converted versions of the FastQ file 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz (7846448 sequences in total) Input files are 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H3_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 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:50711:1070_1:N:0:GGTTGAAC+AACGTGGA/1 99 ptg000047l_CT_converted 1453645 2 70M3I52M = 1453896 388 AGAAGAAGATTTTTGTTTTGTTAGTGTTATAGAGTATAGAGATTATATTATTGTAGAGTATTAAGAGTATTAGTATTGTTATTATTGTTATTATGTATATAGTATAAATAATATTAGTATTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9III-II9I9IIIIIIII-IIIII9999IIII9-II-I9I9I9IIIIIIIIII9IIIIII AS:i:-50 XS:i:-50 XN:i:0 XM:i:6 XO:i:1 XG:i:3 NM:i:9 MD:Z:58A3G3A13G2A12G25 YS:i:-59 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50711:1070_2:N:0:GGTTGAAC+AACGTGGA/2 147 ptg000047l_CT_converted 1453896 2 99M12D26M = 1453645 -388 TATATTATTATTTTTATTATTATTATGATTATTAAATAAAGTAAATTTAAATGGAAAGTAAGTTAATTGTTTGGTTTTTTAAAAAATTGAAAATAGGTTTGAGGTTATTGTTTGGAAATATTGAA I-II9I9IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII-IIIIII9IIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIII AS:i:-59 XS:i:-65 XN:i:0 XM:i:3 XO:i:1 XG:i:12 NM:i:15 MD:Z:82T0T15^TTTGAGAGGATA22A3 YS:i:-50 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H3_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)) Reading in the sequence files 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:40531:1070_1:N:0:GGTTGAAC+AACGTGGA/1 99 ptg000002l_CT_converted 8436008 6 125M = 8436208 324 ATTATAAATTGTTTATGGAAAATTTTTTTTATTTAAAATGTGTAGTTTTGATTTTTTGTTGGTTTGAAATAAGTATTTAATATTTAATAATTAGATTTGTAGTTTAGTTTTTTGGGTTATGGGGT IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIII9IIIIII99II9IIIIIIIIIIIIIIIIIIIII-I9IIIII9I9IIIIIIIIIIIIII9II9IIIII AS:i:-12 XS:i:-18 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:8A16G99 YS:i:-20 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40531:1070_2:N:0:GGTTGAAC+AACGTGGA/2 147 ptg000002l_CT_converted 8436208 6 12M1I112M = 8436008 -324 TATTATTTAATTAAGTTGGAGAGAAAAAAGTAATAATAAATTTAGTTAAAAAAAATATTTATGTGGGAATAAAATAAAATAAATAGGTTTATAAAATTGGTAAATTTTGTTGTTTGATGATTGTT II9IIIIIIIIIII99IIII-IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II AS:i:-20 XS:i:-20 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:19T41T62 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:50711:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 AAAAAAAAATTTTTATTTTATTAATATTATAAAATATAAAAATTATATTATTATAAAATATTAAAAATATTAATATTATTATTATTATTATTATATATATAATATAAATAATATTAATATTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9III-II9I9IIIIIIII-IIIII9999IIII9-II-I9I9I9IIIIIIIIII9IIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50711:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TTTGATATTTTTAAATAATAATTTTAAATTTATTTTTAATTTTTTAAAAAATTAAATAATTAATTTATTTTTTATTTAAATTTATTTTATTTAATAATTATAATAATAATAAAAATAATAATATA IIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9IIIIII-IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9I9II-I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:50711:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 AAAAAAAAATTTTTATTTTATTAATATTATAAAATATAAAAATTATATTATTATAAAATATTAAAAATATTAATATTATTATTATTATTATTATATATATAATATAAATAATATTAATATTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9III-II9I9IIIIIIII-IIIII9999IIII9-II-I9I9I9IIIIIIIIII9IIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50711:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 TTTGATATTTTTAAATAATAATTTTAAATTTATTTTTAATTTTTTAAAAAATTAAATAATTAATTTATTTTTTATTTAAATTTATTTTATTTAATAATTATAATAATAATAAAAATAATAATATA IIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9IIIIII-IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9I9II-I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:40531:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 ATTATAAACTATTTATAAAAAATTTTTTTTATTTAAAATATATAATTTTAATTTTTTATTAATTTAAAATAAATATTTAATATTTAATAATTAAATTTATAATTTAATTTTTTAAATTATAAAAT IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIII9IIIIII99II9IIIIIIIIIIIIIIIIIIIII-I9IIIII9I9IIIIIIIIIIIIII9II9IIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40531:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 AATAATTATTAAATAATAAAATTTATTAATTTTATAAATTTATTTATTTTATTTTATTTTTATATAAATATTTTTTTTAATTAAATTTATTATTATTTTTTTTTTTTTAATTTAATTAAATAATA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII-IIII99IIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H3_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: LH00526:197:22KFKVLT4:3:1101:50711:1070_1:N:0:GGTTGAAC+AACGTGGA/1 83 ptg000009l_GA_converted 13927694 2 36M3I86M = 13927428 -388 AAATAATACTAATATTATTTATACTATATACATAATAACAATAATAACAATACTAATACTCTTAATACTCTACAATAATATAATCTCTATACTCTATAACACTAACAAAACAAAAATCTTCTTCT IIIIII9IIIIIIIIII9I9I9I-II-9IIII9999IIIII-IIIIIIII9I9II-III9-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-50 XN:i:0 XM:i:7 XO:i:1 XG:i:3 NM:i:10 MD:Z:25C15C2T4A5T3C3T58 YS:i:-59 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50711:1070_2:N:0:GGTTGAAC+AACGTGGA/2 163 ptg000009l_GA_converted 13927428 2 25M12D100M = 13927694 388 TTCAATATTTCCAAACAATAACCTCAAACCTATTTTCAATTTTTTAAAAAACCAAACAATTAACTTACTTTCCATTTAAATTTACTTTATTTAATAATCATAATAATAATAAAAATAATAATATA IIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9IIIIII-IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9I9II-I AS:i:-59 XS:i:-71 XN:i:0 XM:i:3 XO:i:1 XG:i:12 NM:i:15 MD:Z:3T21^ATATCCTCTCAA16A0A82 YS:i:-56 YT:Z:CP >>> Writing bisulfite mapping results to 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:40531:1070_1:N:0:GGTTGAAC+AACGTGGA/1 77 * 0 0 * * 0 0 ATTATAAACTATTTATAAAAAATTTTTTTTATTTAAAATATATAATTTTAATTTTTTATTAATTTAAAATAAATATTTAATATTTAATAATTAAATTTATAATTTAATTTTTTAAATTATAAAAT IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIII9IIIIII99II9IIIIIIIIIIIIIIIIIIIII-I9IIIII9I9IIIIIIIIIIIIII9II9IIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40531:1070_2:N:0:GGTTGAAC+AACGTGGA/2 141 * 0 0 * * 0 0 AATAATTATTAAATAATAAAATTTATTAATTTTATAAATTTATTTATTTTATTTTATTTTTATATAAATATTTTTTTTAATTAAATTTATTATTATTTTTTTTTTTTTAATTTAATTAAATAATA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII-IIII99IIIIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H3_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)) Reading in the sequence files 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:40531:1070_1:N:0:GGTTGAAC+AACGTGGA/1 83 ptg000002l_GA_converted 8879438 42 125M = 8879238 -325 ACCCCATAACCCAAAAAACTAAACTACAAATCTAATTATTAAATATTAAATACTTATTTCAAACCAACAAAAAATCAAAACTACACATTTTAAATAAAAAAAATTTTCCATAAACAATTTATAAT IIIII9II9IIIIIIIIIIIIII9I9IIIII9I-IIIIIIIIIIIIIIIIIIIII9II99IIIIII9IIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:116T8 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40531:1070_2:N:0:GGTTGAAC+AACGTGGA/2 163 ptg000002l_GA_converted 8879238 42 125M = 8879438 325 AACAATCATCAAACAACAAAATTTACCAATTTTATAAACCTATTTATTTTATTTTATTCCCACATAAATATTTTTTTTAACTAAATTTATTATTACTTTTTTCTCTCCAACTTAATTAAATAATA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII-IIII99IIIIIIIIIII9II AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:104A20 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1129:49707:29142_1:N:0:GGTTGAAC+AACGTGGA ptg000118l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1129:42853:5903_1:N:0:GGTTGAAC+AACGTGGA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1129:42861:5917_1:N:0:GGTTGAAC+AACGTGGA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1129:49691:29142_1:N:0:GGTTGAAC+AACGTGGA ptg000118l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1152:22266:19854_1:N:0:GGTTGAAC+AACGTGGA ptg000098l 55074 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1182:33102:17207_1:N:0:GGTTGAAC+AACGTGGA ptg000025l 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 LH00526:197:22KFKVLT4:3:1414:25981:3003_1:N:0:GGTTGAAC+AACGTGGA ptg000007l 12295855 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 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2346:33320:19406_1:N:0:GGTTGAAC+AACGTGGA ptg000066l 66374 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2177:20599:7135_1:N:0:GGTTGAAC+AACGTGGA ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2248:37512:13187_1:N:0:GGTTGAAC+AACGTGGA ptg000002l 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1192:44528:18047_1:N:0:GGTTGAAC+AACGTGGA ntLink_4 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2390:3913:14896_1:N:0:GGTTGAAC+AACGTGGA ptg000009l 19095993 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1285:36760:25808_1:N:0:GGTTGAAC+AACGTGGA ptg000083l 2 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1183:51779:28693_1:N:0:GGTTGAAC+AACGTGGA ptg000065l 49673 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2120:11115:24813_1:N:0:GGTTGAAC+AACGTGGA ptg000054l 36035 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1340:2165:19126_1:N:0:GGTTGAAC+AACGTGGA ptg000183l 26189 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1183:51787:28707_1:N:0:GGTTGAAC+AACGTGGA ptg000065l 49673 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1268:33693:23945_1:N:0:GGTTGAAC+AACGTGGA ptg000048l 1 Processed 7000000 sequence pairs so far Processed 5000000 sequence pairs so far 7846449 reads; of these: 7846449 (100.00%) were paired; of these: 3444006 (43.89%) aligned concordantly 0 times 1734228 (22.10%) aligned concordantly exactly 1 time 2668215 (34.01%) aligned concordantly >1 times 56.11% overall alignment rate 7846449 reads; of these: 7846449 (100.00%) were paired; of these: 3447233 (43.93%) aligned concordantly 0 times 1734241 (22.10%) aligned concordantly exactly 1 time 2664975 (33.96%) aligned concordantly >1 times 56.07% overall alignment rate 7846449 reads; of these: 7846449 (100.00%) were paired; of these: 7825669 (99.74%) aligned concordantly 0 times 7394 (0.09%) aligned concordantly exactly 1 time 13386 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 7846449 reads; of these: 7846449 (100.00%) were paired; of these: 7827998 (99.76%) aligned concordantly 0 times 7321 (0.09%) aligned concordantly exactly 1 time 11130 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate Processed 7846449 sequences in total Successfully deleted the temporary files 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7846449 Final Cytosine Methylation Report ================================= Total number of C's analysed: 226068428 Total methylated C's in CpG context: 3588682 Total methylated C's in CHG context: 216856 Total methylated C's in CHH context: 961923 Total methylated C's in Unknown context: 7226 Total unmethylated C's in CpG context: 31446077 Total unmethylated C's in CHG context: 38003448 Total unmethylated C's in CHH context: 151851442 Total unmethylated C's in Unknown context: 326401 C methylated in CpG context: 10.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3445708 (43.91%) aligned concordantly 0 times 1734962 (22.11%) aligned concordantly exactly 1 time 2665778 (33.97%) aligned concordantly >1 times 56.09% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7825710 (99.74%) aligned concordantly 0 times 7185 (0.09%) aligned concordantly exactly 1 time 13553 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7827782 (99.76%) aligned concordantly 0 times 7417 (0.09%) aligned concordantly exactly 1 time 11249 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3443324 (43.88%) aligned concordantly 0 times 1734632 (22.11%) aligned concordantly exactly 1 time 2668492 (34.01%) aligned concordantly >1 times 56.12% overall alignment rate Processed 7846448 sequences in total Successfully deleted the temporary files 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7846448 Final Cytosine Methylation Report ================================= Total number of C's analysed: 226121604 Total methylated C's in CpG context: 3590498 Total methylated C's in CHG context: 217875 Total methylated C's in CHH context: 962697 Total methylated C's in Unknown context: 7071 Total unmethylated C's in CpG context: 31476931 Total unmethylated C's in CHG context: 38021476 Total unmethylated C's in CHH context: 151852127 Total unmethylated C's in Unknown context: 326348 C methylated in CpG context: 10.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7828049 (99.77%) aligned concordantly 0 times 7300 (0.09%) aligned concordantly exactly 1 time 11099 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3448169 (43.95%) aligned concordantly 0 times 1732053 (22.07%) aligned concordantly exactly 1 time 2666226 (33.98%) aligned concordantly >1 times 56.05% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3442056 (43.87%) aligned concordantly 0 times 1736220 (22.13%) aligned concordantly exactly 1 time 2668172 (34.00%) aligned concordantly >1 times 56.13% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7825776 (99.74%) aligned concordantly 0 times 7290 (0.09%) aligned concordantly exactly 1 time 13382 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate Processed 7846448 sequences in total Successfully deleted the temporary files 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7846448 Final Cytosine Methylation Report ================================= Total number of C's analysed: 226017557 Total methylated C's in CpG context: 3585414 Total methylated C's in CHG context: 216501 Total methylated C's in CHH context: 957561 Total methylated C's in Unknown context: 6778 Total unmethylated C's in CpG context: 31457383 Total unmethylated C's in CHG context: 38018724 Total unmethylated C's in CHH context: 151781974 Total unmethylated C's in Unknown context: 326563 C methylated in CpG context: 10.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3442714 (43.88%) aligned concordantly 0 times 1733859 (22.10%) aligned concordantly exactly 1 time 2669875 (34.03%) aligned concordantly >1 times 56.12% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7825879 (99.74%) aligned concordantly 0 times 7228 (0.09%) aligned concordantly exactly 1 time 13341 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3445907 (43.92%) aligned concordantly 0 times 1733995 (22.10%) aligned concordantly exactly 1 time 2666546 (33.98%) aligned concordantly >1 times 56.08% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7827958 (99.76%) aligned concordantly 0 times 7337 (0.09%) aligned concordantly exactly 1 time 11153 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate Processed 7846448 sequences in total Successfully deleted the temporary files 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7846448 Final Cytosine Methylation Report ================================= Total number of C's analysed: 226097727 Total methylated C's in CpG context: 3586990 Total methylated C's in CHG context: 217388 Total methylated C's in CHH context: 958934 Total methylated C's in Unknown context: 7005 Total unmethylated C's in CpG context: 31451790 Total unmethylated C's in CHG context: 37998356 Total unmethylated C's in CHH context: 151884269 Total unmethylated C's in Unknown context: 325763 C methylated in CpG context: 10.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2102:42206:2485_1:N:0:GGTTGAAC+AACGTGGA ptg000101l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2120:11099:24813_1:N:0:GGTTGAAC+AACGTGGA ptg000054l 36035 Processed 7000000 sequence pairs so far 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7826019 (99.74%) aligned concordantly 0 times 7257 (0.09%) aligned concordantly exactly 1 time 13172 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 7828200 (99.77%) aligned concordantly 0 times 7298 (0.09%) aligned concordantly exactly 1 time 10950 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3443218 (43.88%) aligned concordantly 0 times 1734845 (22.11%) aligned concordantly exactly 1 time 2668385 (34.01%) aligned concordantly >1 times 56.12% overall alignment rate 7846448 reads; of these: 7846448 (100.00%) were paired; of these: 3448280 (43.95%) aligned concordantly 0 times 1733599 (22.09%) aligned concordantly exactly 1 time 2664569 (33.96%) aligned concordantly >1 times 56.05% overall alignment rate Processed 7846448 sequences in total Successfully deleted the temporary files 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H3_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7846448 Final Cytosine Methylation Report ================================= Total number of C's analysed: 226153400 Total methylated C's in CpG context: 3584585 Total methylated C's in CHG context: 217203 Total methylated C's in CHH context: 963021 Total methylated C's in Unknown context: 7013 Total unmethylated C's in CpG context: 31487471 Total unmethylated C's in CHG context: 38023666 Total unmethylated C's in CHH context: 151877454 Total unmethylated C's in Unknown context: 326504 C methylated in CpG context: 10.2% 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 Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1H3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1H3_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1H3_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/1H3_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1H3_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/1H3_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H3_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: 39232241 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1130458716 Total methylated C's in CpG context: 17936169 Total methylated C's in CHG context: 1085823 Total methylated C's in CHH context: 4804136 Total methylated C's in Unknown context: 35093 Total unmethylated C's in CpG context: 157319652 Total unmethylated C's in CHG context: 190065670 Total unmethylated C's in CHH context: 759247266 Total unmethylated C's in Unknown context: 1631579 C methylated in CpG context: 10.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Deleting temporary report files... Bismark completed in 0d 4h 39m 18s ==================== Bismark run complete ====================