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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_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/2D1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7630157) Using the subset file >2D1_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/2D1_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/2D1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7630156) Using the subset file >2D1_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/2D1_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/2D1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7630157) Using the subset file >2D1_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/2D1_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/2D1_R1_001.fastp-trim.fq.gz for PID: 97999 and offset 5 (sequences written out: 7630156) Using the subset file >2D1_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/2D1_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/2D1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7630157) Using the subset file >2D1_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/2D1_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/2D1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7630157) Using the subset file >2D1_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/2D1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz to 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz to 2D1_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/2D1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7630157) Using the subset file >2D1_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/2D1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz to 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz to 2D1_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/2D1_R2_001.fastp-trim.fq.gz for PID: 97999 and offset 5 (sequences written out: 7630156) Using the subset file >2D1_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/2D1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz to 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz to 2D1_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/2D1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7630157) Using the subset file >2D1_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/2D1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz to 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz to 2D1_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/2D1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7630156) Using the subset file >2D1_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/2D1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz to 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz to 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz (7630156 sequences in total) Writing a C -> T converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz to 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz to 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz (7630157 sequences in total) Writing a C -> T converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz to 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz to 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz (7630157 sequences in total) Writing a C -> T converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz to 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz to 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz (7630156 sequences in total) Writing a C -> T converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz to 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz to 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz (7630157 sequences in total) Writing a C -> T converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz to 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz to 2D1_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 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz (7630157 sequences in total) Input files are 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D1_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 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz (7630156 sequences in total) Input files are 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:21727:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 99 ptg000026l_CT_converted 8643319 32 125M = 8643316 -128 TTAATTATTTGTAATTAATTTAGTGGTATGTAAATTAATTTAGTTGTAGTGTATTTTGTTAATATTATAGAATGTGAATAAGATGAGATAATTGTAAATTGTGTAAGTGTTTATTTTTAAGTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII-9I9II-II9IIIIIIIII9II9IIIIIIIIIIII9IIIIIIIIIIIIIIII-9III99IIIII9 AS:i:0 XS:i:-24 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:21727:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 147 ptg000026l_CT_converted 8643316 32 125M = 8643319 128 TTTTTAATTATTTGTAATTAATTTAGTGGTATGTAAATTAATTTAGTTGTAGTGTATTTTGTTAATATTATAGAATGTGAATAAGATGAGATAATTGTAAATTGTGTAAGTGTTTATTTTTAAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-24 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:2869:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 99 ptg000034l_CT_converted 642727 6 125M = 642811 209 TGGTAGTTTGGATGAAATATTATTATAATTAGGTTTTAATAGGATTAAAAATATTTTAAGAAATTTAGTTTTAAATTAGAATAATTTATTGGTAATATTATGATTTTTATGTAATGGAGAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:23G101 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:2869:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 147 ptg000034l_CT_converted 642811 6 125M = 642727 -209 TTTATTGGTAATATTATGATTTTTATGTAATGGAGAATTTAAAAAAATTATATGTTGTTGAAAAATTTATTGTAGTTAATAGTTTTTTTTATGTTAAATTTAGGATAATGTATTTTAGGTAAAAG 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz (7630156 sequences in total) Input files are 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D1_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 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz (7630157 sequences in total) Input files are 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:2869:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TAATAATTTAAATAAAATATTATTATAATTAAATTTTAATAAAATTAAAAATATTTTAAAAAATTTAATTTTAAATTAAAATAATTTATTAATAATATTATAATTTTTATATAATAAAAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2869:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 TTTTTATTTAAAATATATTATTTTAAATTTAATATAAAAAAAATTATTAATTATAATAAATTTTTTAATAATATATAATTTTTTTAAATTTTTTATTATATAAAAATTATAATATTATTAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:21727:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TTAATTATTTATAATTAATTTAATAATATATAAATTAATTTAATTATAATATATTTTATTAATATTATAAAATATAAATAAAATAAAATAATTATAAATTATATAAATATTTATTTTTAAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII-9I9II-II9IIIIIIIII9II9IIIIIIIIIIII9IIIIIIIIIIIIIIII-9III99IIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:21727:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 ATTTAAAAATAAATATTTATATAATTTATAATTATTTTATTTTATTTATATTTTATAATATTAATAAAATATATTATAATTAAATTAATTTATATATTATTAAATTAATTATAAATAATTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:19332:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 99 ptg000023l_CT_converted 9322463 6 90M = 9322447 -106 TATTAGAGGATGTTGTATATTAGAATATGTGGTTTATAATGTTTTTTTTTTATTTTTGAAGTATAGTATAGTTTTTTTTTTTTTTAAGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-I-I9II AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:83G6 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:19332:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 147 ptg000023l_CT_converted 9322447 6 92M = 9322463 106 AAATTATTGTTATTATTATTAGAGGATGTTGTATATTAGAATATGTGGTTTATAATGTTTTTTTTTTATTTTTGAAGTATAGTATAGTTTTT IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:92 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:2869:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TAATAATTTAAATAAAATATTATTATAATTAAATTTTAATAAAATTAAAAATATTTTAAAAAATTTAATTTTAAATTAAAATAATTTATTAATAATATTATAATTTTTATATAATAAAAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2869:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 TTTTTATTTAAAATATATTATTTTAAATTTAATATAAAAAAAATTATTAATTATAATAAATTTTTTAATAATATATAATTTTTTTAAATTTTTTATTATATAAAAATTATAATATTATTAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:10700:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 99 ptg000055l_CT_converted 19499 1 125M = 19696 322 AAATTTGAAATAGTTTGAAAAATTAAAATTTGGTTTTGTAGATATGATGATGAAGTTTTAAGTGATTTGATGGAATTTAGTGTGTTTAATAATGATGAAATTTGAGGTTTTTTATGGTGTTGTTG IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9II-IIIIIIIIIIIIIIIIIIIII9 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:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:10700:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 147 ptg000055l_CT_converted 19696 1 125M = 19499 -322 TTGTTGGATAGTTAGTTGTAATTTTTGTTGGAGGATTTGGTGTAATTTTTTAATAATTTAATAATTAATGGATAGGAAATAGTGAGAAAAGAAAGAGATAATTTTATTTTGTGGAATATATTTTA III9IIIIIIIII-I9IIIIIIIII99IIII-IIIIIIIII9IIII9IIIIIII9IIIIII-IIIII-IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:34G90 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:21727:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TTAATTATTTATAATTAATTTAATAATATATAAATTAATTTAATTATAATATATTTTATTAATATTATAAAATATAAATAAAATAAAATAATTATAAATTATATAAATATTTATTTTTAAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII-9I9II-II9IIIIIIIII9II9IIIIIIIIIIII9IIIIIIIIIIIIIIII-9III99IIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:21727:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 ATTTAAAAATAAATATTTATATAATTTATAATTATTTTATTTTATTTATATTTTATAATATTAATAAAATATATTATAATTAAATTAATTTATATATTATTAAATTAATTATAAATAATTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D1_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 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz (7630157 sequences in total) Input files are 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:10700:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 AAATTTAAAATAATTTAAAAAATTAAAATTTAATTTTATAAATATAATAATAAAATTTTAAATAATTTAATAAAATTTAATATATTTAATAATAATAAAATTTAAAATTTTTTATAATATTATTA IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9II-IIIIIIIIIIIIIIIIIIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:10700:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 TAAAATATATTTTATAAAATAAAATTATTTTTTTTTTTTTTTATTATTTTTTATTTATTAATTATTAAATTATTAAAAAATTATATTAAATTTTTTAATAAAAATTATAATTAATTATTTAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII-IIIIII9IIIIIII9IIII9IIIIIIIII-IIII99IIIIIIIII9I-IIIIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:2869:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 83 ptg000012l_GA_converted 7735024 30 125M = 7734940 -209 TAAATTCTCCATTACATAAAAATCATAATATTACCAATAAATTATTCTAATTTAAAACTAAATTTCTTAAAATATTTTTAATCCTATTAAAACCTAATTATAATAATATTTCATCCAAACTACCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-18 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:2869:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 163 ptg000012l_GA_converted 7734940 30 125M = 7735024 209 CTTTTACCTAAAATACATTATCCTAAATTTAACATAAAAAAAACTATTAACTACAATAAATTTTTCAACAACATATAATTTTTTTAAATTCTCCATTACATAAAAATCATAATATTACCAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 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 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:21727:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TTAATTATTTGTAATTAATTTAGTGGTATGTAAATTAATTTAGTTGTAGTGTATTTTGTTAATATTATAGAATGTGAATAAGATGAGATAATTGTAAATTGTGTAAGTGTTTATTTTTAAGTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII-9I9II-II9IIIIIIIII9II9IIIIIIIIIIII9IIIIIIIIIIIIIIII-9III99IIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:21727:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 ACTTAAAAATAAACACTTACACAATTTACAATTATCTCATCTTATTCACATTCTATAATATTAACAAAATACACTACAACTAAATTAATTTACATACCACTAAATTAATTACAAATAATTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:19332:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TATTAAAAAATATTATATATTAAAATATATAATTTATAATATTTTTTTTTTATTTTTAAAATATAATATAATTTTTTTTTTTTTTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-I-I9II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:19332:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 AAAAATTATATTATATTTTAAAAATAAAAAAAAAATATTATAAATTATATATTTTAATATATAATATTTTTTAATAATAATAATAATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:2286:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 99 ntLink_6_CT_converted 5794240 42 125M = 5794280 165 TTGGTGTATGGAAATAATTAATTATTGTGATAATGTTAGTATATTATTATTGTAATAATTTTTTTTTTATTTTTTTGTTTTAGTGAGTTTAAAGGATTTATGTTTTAGTAGTTTAAGGATTGGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIII9IIIIII 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 LH00652:104:22KG7JLT4:7:1101:2286:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 147 ntLink_6_CT_converted 5794280 42 125M = 5794240 -165 ATATTATTATTGTAATAATTTTTTTTTTATTTTTTTGTTTTAGTGAGTTTAAAGGATTTATGTTTTAGTAGTTTAAGGATTGGAGGTTTTTTTTTATGTTTGTATTAAAATTAAATATATAGAAG IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 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 Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2D1_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 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00652:104:22KG7JLT4:7:1101:19332:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TATTAAAAAATATTATATATTAAAATATATAATTTATAATATTTTTTTTTTATTTTTAAAATATAATATAATTTTTTTTTTTTTTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-I-I9II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:19332:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 AAAAATTATATTATATTTTAAAAATAAAAAAAAAATATTATAAATTATATATTTTAATATATAATATTTTTTAATAATAATAATAATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:10700:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 AAATTTAAAATAATTTAAAAAATTAAAATTTAATTTTATAAATATAATAATAAAATTTTAAATAATTTAATAAAATTTAATATATTTAATAATAATAAAATTTAAAATTTTTTATAATATTATTA IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9II-IIIIIIIIIIIIIIIIIIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:10700:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 TAAAATATATTTTATAAAATAAAATTATTTTTTTTTTTTTTTATTATTTTTTATTTATTAATTATTAAATTATTAAAAAATTATATTAAATTTTTTAATAAAAATTATAATTAATTATTTAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII-IIIIII9IIIIIII9IIII9IIIIIIIII-IIII99IIIIIIIII9I-IIIIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:2286:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TTAATATATAAAAATAATTAATTATTATAATAATATTAATATATTATTATCATAATAATTTTTTTTTTATTTTTTTATTTTAATAAATTTAAAAAATTTATATTTTAATAATTTAAAAATTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIII9IIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2286:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 TTTTTATATATTTAATTTTAATATAAATATAAAAAAAAATTTTTAATTTTTAAATTATTAAAATATAAATTTTTTAAATTTATTAAAATAAAAAAATAAAAAAAAAATTATTATGATAATAATAT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2D1_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)) Reading in the sequence files 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00652:104:22KG7JLT4:7:1101:19332:1084_1:N:0:GTCGTTAC+GCTTAGCT/1 83 ptg000020l_GA_converted 13718287 1 90M = 13718301 106 CCCTTAAAAAAAAAAAAAACTATACTATACTTCAAAAATAAAAAAAAAACATTATAAACCACATATTCTAATATACAACATCCTCTAATA II9I-I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6C83 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:19332:1084_2:N:0:GTCGTTAC+GCTTAGCT/2 163 ptg000020l_GA_converted 13718301 1 92M = 13718287 -106 AAAAACTATACTATACTTCAAAAATAAAAAAAAAACATTATAAACCACATATTCTAATATACAACATCCTCTAATAATAATAACAATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:92 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:2286:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TTAATATATAAAAATAATTAATTATTATAATAATATTAATATATTATTATCATAATAATTTTTTTTTTATTTTTTTATTTTAATAAATTTAAAAAATTTATATTTTAATAATTTAAAAATTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIII9IIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2286:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 TTTTTATATATTTAATTTTAATATAAATATAAAAAAAAATTTTTAATTTTTAAATTATTAAAATATAAATTTTTTAAATTTATTAAAATAAAAAAATAAAAAAAAAATTATTATGATAATAATAT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:10700:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 83 ptg000102l_GA_converted 58314 1 125M = 58117 -322 CAACAACACCATAAAAAACCTCAAATTTCATCATTATTAAACACACTAAATTCCATCAAATCACTTAAAACTTCATCATCATATCTACAAAACCAAATTTTAATTTTTCAAACTATTTCAAATTT 9IIIIIIIIIIIIIIIIIIIII-II9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII 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:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:10700:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 163 ptg000102l_GA_converted 58117 1 125M = 58314 322 TAAAATATATTCCACAAAATAAAATTATCTCTTTCTTTTCTCACTATTTCCTATCCATTAATTATTAAATTATTAAAAAATTACACCAAATCCTCCAACAAAAATTACAACTAACTATCCAACAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII-IIIIII9IIIIIII9IIII9IIIIIIIII-IIII99IIIIIIIII9I-IIIIIIIII9III AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:90C34 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz Found first alignment: LH00652:104:22KG7JLT4:7:1101:2286:1098_1:N:0:GTCGTTAC+GCTTAGCT/1 77 * 0 0 * * 0 0 TTGGTGTATGGAAATAATTAATTATTGTGATAATGTTAGTATATTATTATTGTAATAATTTTTTTTTTATTTTTTTGTTTTAGTGAGTTTAAAGGATTTATGTTTTAGTAGTTTAAGGATTGGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIII9IIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:2286:1098_2:N:0:GTCGTTAC+GCTTAGCT/2 141 * 0 0 * * 0 0 CTTCTATATATTTAATTTTAATACAAACATAAAAAAAAACCTCCAATCCTTAAACTACTAAAACATAAATCCTTTAAACTCACTAAAACAAAAAAATAAAAAAAAAATTATTACAATAATAATAT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far 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 LH00652:104:22KG7JLT4:7:2294:39921:10066_1:N:0:GTCGTTAC+GCTTAGCT ptg000015l 14997091 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2415:3556:22999_1:N:0:GTCGTTAC+GCTTAGCT ptg000048l 76432 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 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2324:21549:20477_1:N:0:GTCGTTAC+GCTTAGCT ptg000160l 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 7605267 (99.67%) aligned concordantly 0 times 9629 (0.13%) aligned concordantly exactly 1 time 15261 (0.20%) aligned concordantly >1 times 0.33% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 3153749 (41.33%) aligned concordantly 0 times 1650699 (21.63%) aligned concordantly exactly 1 time 2825709 (37.03%) aligned concordantly >1 times 58.67% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 3148903 (41.27%) aligned concordantly 0 times 1650857 (21.64%) aligned concordantly exactly 1 time 2830397 (37.09%) aligned concordantly >1 times 58.73% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 7604062 (99.66%) aligned concordantly 0 times 9465 (0.12%) aligned concordantly exactly 1 time 16630 (0.22%) aligned concordantly >1 times 0.34% overall alignment rate Processed 7630157 sequences in total Successfully deleted the temporary files 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7630157 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215940204 Total methylated C's in CpG context: 3471811 Total methylated C's in CHG context: 208148 Total methylated C's in CHH context: 957705 Total methylated C's in Unknown context: 6822 Total unmethylated C's in CpG context: 31254905 Total unmethylated C's in CHG context: 36695654 Total unmethylated C's in CHH context: 143351981 Total unmethylated C's in Unknown context: 298996 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 7603814 (99.65%) aligned concordantly 0 times 9687 (0.13%) aligned concordantly exactly 1 time 16655 (0.22%) aligned concordantly >1 times 0.35% overall alignment rate 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 3147296 (41.25%) aligned concordantly 0 times 1652917 (21.66%) aligned concordantly exactly 1 time 2829943 (37.09%) aligned concordantly >1 times 58.75% overall alignment rate 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 7605316 (99.67%) aligned concordantly 0 times 9522 (0.12%) aligned concordantly exactly 1 time 15318 (0.20%) aligned concordantly >1 times 0.33% overall alignment rate 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 3153382 (41.33%) aligned concordantly 0 times 1651337 (21.64%) aligned concordantly exactly 1 time 2825437 (37.03%) aligned concordantly >1 times 58.67% overall alignment rate Processed 7630156 sequences in total Successfully deleted the temporary files 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7630156 Final Cytosine Methylation Report ================================= Total number of C's analysed: 216004324 Total methylated C's in CpG context: 3467170 Total methylated C's in CHG context: 207283 Total methylated C's in CHH context: 951412 Total methylated C's in Unknown context: 6917 Total unmethylated C's in CpG context: 31268946 Total unmethylated C's in CHG context: 36699390 Total unmethylated C's in CHH context: 143410123 Total unmethylated C's in Unknown context: 298069 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Now waiting for all child processes to complete Processed 7000000 sequence pairs so far 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 7603920 (99.66%) aligned concordantly 0 times 9734 (0.13%) aligned concordantly exactly 1 time 16502 (0.22%) aligned concordantly >1 times 0.34% overall alignment rate 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 7605407 (99.68%) aligned concordantly 0 times 9638 (0.13%) aligned concordantly exactly 1 time 15111 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 3150304 (41.29%) aligned concordantly 0 times 1650913 (21.64%) aligned concordantly exactly 1 time 2828939 (37.08%) aligned concordantly >1 times 58.71% overall alignment rate 7630156 reads; of these: 7630156 (100.00%) were paired; of these: 3154486 (41.34%) aligned concordantly 0 times 1651026 (21.64%) aligned concordantly exactly 1 time 2824644 (37.02%) aligned concordantly >1 times 58.66% overall alignment rate Processed 7630156 sequences in total Successfully deleted the temporary files 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7630156 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215888216 Total methylated C's in CpG context: 3466731 Total methylated C's in CHG context: 208831 Total methylated C's in CHH context: 951439 Total methylated C's in Unknown context: 6726 Total unmethylated C's in CpG context: 31243367 Total unmethylated C's in CHG context: 36672574 Total unmethylated C's in CHH context: 143345274 Total unmethylated C's in Unknown context: 298798 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Processed 7000000 sequence pairs so far 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 3153265 (41.33%) aligned concordantly 0 times 1649674 (21.62%) aligned concordantly exactly 1 time 2827218 (37.05%) aligned concordantly >1 times 58.67% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 3149635 (41.28%) aligned concordantly 0 times 1650972 (21.64%) aligned concordantly exactly 1 time 2829550 (37.08%) aligned concordantly >1 times 58.72% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 7605418 (99.68%) aligned concordantly 0 times 9521 (0.12%) aligned concordantly exactly 1 time 15218 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 7604181 (99.66%) aligned concordantly 0 times 9578 (0.13%) aligned concordantly exactly 1 time 16398 (0.21%) aligned concordantly >1 times 0.34% overall alignment rate Processed 7630157 sequences in total Successfully deleted the temporary files 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7630157 Final Cytosine Methylation Report ================================= Total number of C's analysed: 216003218 Total methylated C's in CpG context: 3462777 Total methylated C's in CHG context: 206711 Total methylated C's in CHH context: 944557 Total methylated C's in Unknown context: 6675 Total unmethylated C's in CpG context: 31268385 Total unmethylated C's in CHG context: 36694195 Total unmethylated C's in CHH context: 143426593 Total unmethylated C's in Unknown context: 298622 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 7605483 (99.68%) aligned concordantly 0 times 9462 (0.12%) aligned concordantly exactly 1 time 15212 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 3152264 (41.31%) aligned concordantly 0 times 1651050 (21.64%) aligned concordantly exactly 1 time 2826843 (37.05%) aligned concordantly >1 times 58.69% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 3148549 (41.26%) aligned concordantly 0 times 1649701 (21.62%) aligned concordantly exactly 1 time 2831907 (37.11%) aligned concordantly >1 times 58.74% overall alignment rate 7630157 reads; of these: 7630157 (100.00%) were paired; of these: 7603975 (99.66%) aligned concordantly 0 times 9657 (0.13%) aligned concordantly exactly 1 time 16525 (0.22%) aligned concordantly >1 times 0.34% overall alignment rate Processed 7630157 sequences in total Successfully deleted the temporary files 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D1_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7630157 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215912238 Total methylated C's in CpG context: 3469982 Total methylated C's in CHG context: 207031 Total methylated C's in CHH context: 945977 Total methylated C's in Unknown context: 6603 Total unmethylated C's in CpG context: 31270013 Total unmethylated C's in CHG context: 36668756 Total unmethylated C's in CHH context: 143350479 Total unmethylated C's in Unknown context: 299085 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 2D1_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 2D1_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 2D1_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/2D1_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 2D1_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/2D1_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D1_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: 38150783 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1079748200 Total methylated C's in CpG context: 17338471 Total methylated C's in CHG context: 1038004 Total methylated C's in CHH context: 4751090 Total methylated C's in Unknown context: 33743 Total unmethylated C's in CpG context: 156305616 Total unmethylated C's in CHG context: 183430569 Total unmethylated C's in CHH context: 716884450 Total unmethylated C's in Unknown context: 1493570 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Deleting temporary report files... Bismark completed in 0d 5h 10m 37s ==================== Bismark run complete ====================