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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_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/1D3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_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/1D3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_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/1D3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_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/1D3_R1_001.fastp-trim.fq.gz for PID: 70204 and offset 5 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_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/1D3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_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/1D3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1D3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D3_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/1D3_R2_001.fastp-trim.fq.gz for PID: 70204 and offset 5 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D3_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/1D3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D3_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/1D3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7867154) Using the subset file >1D3_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/1D3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz (7867154 sequences in total) Writing a C -> T converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz (7867154 sequences in total) Writing a C -> T converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz (7867154 sequences in total) Writing a C -> T converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz (7867154 sequences in total) Writing a C -> T converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz (7867154 sequences in total) Writing a C -> T converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D3_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 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz (7867154 sequences in total) Created C -> T as well as G -> A converted versions of the FastQ file 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz (7867154 sequences in total) Input files are 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D3_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)) Input files are 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D3_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 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz (7867154 sequences in total) Input files are 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D3_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 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz (7867154 sequences in total) Input files are 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:41469:1070_1:N:0:TCCACGTT+GTTCAACC/1 99 ptg000004l_CT_converted 9779641 6 94M3D20M = 9779677 151 TGTAGGGTTATTATAAAAAATATTTTTTGTTTTTTTGTGTATTTTTAAATGTTGGTGTTGATTTAAATTTTTTATAAAAAAGTTATTTTTTTTTTGGTTTTATTTAGAGATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XS:i:-14 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:94^TTA20 YS:i:-14 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41469:1070_2:N:0:TCCACGTT+GTTCAACC/2 147 ptg000004l_CT_converted 9779677 6 58M3D54M = 9779641 -151 GTGTATTTTTAAATGTTGGTGTTGATTTAAATTTTTTATAAAAAAGTTATTTTTTTTTTGGTTTTATTTAGAGATAAATTTTGTTTTTTGGTGAAAGTATTTTTAGTTTAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:58^TTA54 YS:i:-14 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:51649:1070_1:N:0:TCCACGTT+GTTCAACC/1 99 ptg000002l_CT_converted 8303274 42 125M = 8303297 148 TTTTTGTTTTAAAAGTTTAATGAATTAATAATAAATAGTTAGTATTTATAATTTTTTGTAGTTAAAAGGATATTTTATAATTTTAAGATTTTATTAAGAGTTAGTTAAATAAGTGATTAAATGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII-IIIIIIIIIII-IIII9IIIIIII 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 LH00526:197:22KFKVLT4:3:1101:51649:1070_2:N:0:TCCACGTT+GTTCAACC/2 147 ptg000002l_CT_converted 8303297 42 125M = 8303274 -148 ATTAATAATAAATAGTTAGTATTTATAATTTTTTGTAGTTAAAAGGATATTTTATAATTTTAAGATTTTATTAAGAGTTAGTTAAATAAGTGATTAAATGTAATAGAATTATAGATAATTTGAGG 99IIIIII9IIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII 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 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:38637:1070_1:N:0:TCCACGTT+GTTCAACC/1 99 ptg000007l_CT_converted 2557100 0 60M = 2557075 -85 ATTTTTTGGTAAAATTGTGATTTTTTAATTAATTTTTGTTGTTTTATAGAGTTTTTGGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-36 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:9A8A8G32 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:38637:1070_2:N:0:TCCACGTT+GTTCAACC/2 147 ptg000007l_CT_converted 2557075 0 60M = 2557100 85 TTGGTTAAAATTGTTTATTTTGAGTATTTTTTGGTAAAATTGTGATTTTTTAATTAATTT IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2A12A18A8A8G7 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:45402:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTAATTTAGATTATTGTTAGTTGTGGTTTTATTTTGGTAGGTTTTGGTTGTATGTATGGAATTAATTGTTATGATGTTTTGAAATGATTTTAATTTGTATTAAAATAGTTGAATATAAATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45402:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 TAATATACAAACCAATAAATACATATCTTTCAATATAACCTAATATTTATATTCAACTATTTTAATACAAATTAAAATCATTTCAAAACATCATAACAATTAATTCCATACATACAACCAAAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:51649:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTTTATTTTAAAAATTTAATAAATTAATAATAAATAATTAATATTTATAATTTTTTATAATTAAAAAAATATTTTATAATTTTAAAATTTTATTAAAAATTAATTAAATAAATAATTAAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII-IIIIIIIIIII-IIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51649:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 TTTTAAATTATTTATAATTTTATTATATTTAATTATTTATTTAATTAATTTTTAATAAAATTTTAAAATTATAAAATATTTTTTTAATTATAAAAAATTATAAATATTAATTATTTATTATTAAT IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIII99 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:38637:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 ATTTTTTAATAAAATTATAATTTTTTAATTAATTTTTATTATTTTATAAAATTTTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38637:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 AAATTAATTAAAAAATTATAATTTTATTAAAAAATATTTAAAATAAATAATTTTAATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:45402:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTAATTTAAATTATTATTAATTATAATTTTATTTTAATAAATTTTAATTATATATACAAAATTAATTATTATAATATTTCAAAACAATTTTAATTTATATTAAAATAATTAAATATAAATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45402:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 TAATATATGAATTGATAAATATATATTTTTTAATATAATTTAATATTTATATTTAATTATTTTAATATAAATTAAAATTGTTTTGAAATATTATAATAATTAATTTTGTATATATAATTAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:41469:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TATAAAATTATTATAAAAAATATTTTTTATTTTTTTATATATTTTTAAATATTAATATTAATTTAAATTTTTTATAAAAAAATTATTTTTTTTTTAATTTTATTTAAAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41469:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 ATTAAATTAAAAATATTTTTATTAAAAAATAAAATTTATTTTTAAATAAAATTAAAAAAAAAATAATTTTTTTATAAAAAATTTAAATTAATATTAATATTTAAAAATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:45402:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTAATTTAAATTATTATTAATTATAATTTTATTTTAATAAATTTTAATTATATATACAAAATTAATTATTATAATATTTCAAAACAATTTTAATTTATATTAAAATAATTAAATATAAATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45402:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 TAATATATGAATTGATAAATATATATTTTTTAATATAATTTAATATTTATATTTAATTATTTTAATATAAATTAAAATTGTTTTGAAATATTATAATAATTAATTTTGTATATATAATTAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:51649:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTTTATTTTAAAAATTTAATAAATTAATAATAAATAATTAATATTTATAATTTTTTATAATTAAAAAAATATTTTATAATTTTAAAATTTTATTAAAAATTAATTAAATAAATAATTAAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII-IIIIIIIIIII-IIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51649:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 TTTTAAATTATTTATAATTTTATTATATTTAATTATTTATTTAATTAATTTTTAATAAAATTTTAAAATTATAAAATATTTTTTTAATTATAAAAAATTATAAATATTAATTATTTATTATTAAT IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIII99 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:41469:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TATAAAATTATTATAAAAAATATTTTTTATTTTTTTATATATTTTTAAATATTAATATTAATTTAAATTTTTTATAAAAAAATTATTTTTTTTTTAATTTTATTTAAAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41469:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 ATTAAATTAAAAATATTTTTATTAAAAAATAAAATTTATTTTTAAATAAAATTAAAAAAAAAATAATTTTTTTATAAAAAATTTAAATTAATATTAATATTTAAAAATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:38637:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 ATTTTTTAATAAAATTATAATTTTTTAATTAATTTTTATTATTTTATAAAATTTTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38637:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 AAATTAATTAAAAAATTATAATTTTATTAAAAAATATTTAAAATAAATAATTTTAATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:41469:1070_1:N:0:TCCACGTT+GTTCAACC/1 83 ptg000023l_GA_converted 3951170 6 19M3D95M = 3951136 -151 TTTATCTCTAAATAAAACCAAAAAAAAAATAACTTTTTTATAAAAAATTTAAATCAACACCAACATTTAAAAATACACAAAAAAACAAAAAATATTTTTTATAATAACCCTACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XS:i:-17 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:19^AAA95 YS:i:-14 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41469:1070_2:N:0:TCCACGTT+GTTCAACC/2 163 ptg000023l_GA_converted 3951136 6 53M3D59M = 3951170 151 ACTAAACTAAAAATACTTTCACCAAAAAACAAAATTTATCTCTAAATAAAACCAAAAAAAAAATAACTTTTTTATAAAAAATTTAAATCAACACCAACATTTAAAAATACAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XS:i:-17 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:53^AAA59 YS:i:-14 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:38637:1070_1:N:0:TCCACGTT+GTTCAACC/1 83 ptg000011l_GA_converted 3924165 1 60M = 3924190 85 TACCAAAAACTCTATAAAACAACAAAAATTAATTAAAAAATCACAATTTTACCAAAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:60 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:38637:1070_2:N:0:TCCACGTT+GTTCAACC/2 163 ptg000011l_GA_converted 3924190 1 60M = 3924165 -85 AAATTAATTAAAAAATCACAATTTTACCAAAAAATACTCAAAATAAACAATTTTAACCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:60 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:51649:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTTTGTTTTAAAAGTTTAATGAATTAATAATAAATAGTTAGTATTTATAATTTTTTGTAGTTAAAAGGATATTTTATAATTTTAAGATTTTATTAAGAGTTAGTTAAATAAGTGATTAAATGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII-IIIIIIIIIII-IIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51649:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 CCTCAAATTATCTATAATTCTATTACATTTAATCACTTATTTAACTAACTCTTAATAAAATCTTAAAATTATAAAATATCCTTTTAACTACAAAAAATTATAAATACTAACTATTTATTATTAAT IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIII99 YT:Z:UP >>> Writing bisulfite mapping results to 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:45402:1070_1:N:0:TCCACGTT+GTTCAACC/1 83 ntLink_6_GA_converted 2447923 42 125M = 2447883 -165 TAATATTTATATTCAACTATTTTAATACAAATTAAAATCATTTCAAAACATCATAACAATTAATTCCATACATACAACCAAAACCTACCAAAATAAAACCACAACTAACAATAATCTAAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:45402:1070_2:N:0:TCCACGTT+GTTCAACC/2 163 ntLink_6_GA_converted 2447883 42 125M = 2447923 165 TAATATACAAACCAATAAATACATATCTTTCAATATAACCTAATATTTATATTCAACTATTTTAATACAAATTAAAATCATTTCAAAACATCATAACAATTAATTCCATACATACAACCAAAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-- 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 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz (7867154 sequences in total) Input files are 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D3_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 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:43848:1070_1:N:0:TCCACGTT+GTTCAACC/1 99 ptg000026l_CT_converted 14146436 42 125M = 14146529 218 TTTTTATAATTGTAATTTTGGTAATTTTATGTTATTGTAGAGGATGGTATGGAATTGTTTTAAAGTGTGTGTTGTATGTGTAGTAATTTTATTTTTGTGTTATTTAATTAATGAAGGTTTTAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9I9I9IIIII-IIIII-II9II9IIII9I9999I9IIIIII-III 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 LH00526:197:22KFKVLT4:3:1101:43848:1070_2:N:0:TCCACGTT+GTTCAACC/2 147 ptg000026l_CT_converted 14146529 42 125M = 14146436 -218 TTTGTGTTATTTAATTAATGAAGGTTTTAATTTGTAGTTTTGTTGATATTAAAGTTTTTTAATGAATTGTTTTTTGGTGTTATGTGGTTTTTGGGGTTTTGTAAGTTGGTGTTTTTTTTTTGTTT IIII999IIIIIII-II9II9I-II9II-IIIIIIIIIIII-IIIIII--IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIII 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 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:43848:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTTTATAATTATAATTTTAATAATTTTATATTATTATAAAAAATAATATAAAATTATTTTAAAATATATATTATATATATAATAATTTTATTTTTATATTATTTAATTAATAAAAATTTTAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9I9I9IIIII-IIIII-II9II9IIII9I9999I9IIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43848:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 AAATAAAAAAAAAATATTAATTTATAAAATTTTAAAAATTATATAATATTAAAAAATAATTTATTAAAAAATTTTAATATTAATAAAATTATAAATTAAAATTTTTATTAATTAAATAATATAAA IIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII--IIIIII-IIIIIIIIIIII-II9II-I9II9II-IIIIIII999IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D3_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: LH00526:197:22KFKVLT4:3:1101:43848:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTTTATAATTATAATTTTAATAATTTTATATTATTATAAAAAATAATATAAAATTATTTTAAAATATATATTATATATATAATAATTTTATTTTTATATTATTTAATTAATAAAAATTTTAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9I9I9IIIII-IIIII-II9II9IIII9I9999I9IIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43848:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 AAATAAAAAAAAAATATTAATTTATAAAATTTTAAAAATTATATAATATTAAAAAATAATTTATTAAAAAATTTTAATATTAATAAAATTATAAATTAAAATTTTTATTAATTAAATAATATAAA IIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII--IIIIII-IIIIIIIIIIII-II9II-I9II9II-IIIIIII999IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43848:1070_1:N:0:TCCACGTT+GTTCAACC/1 77 * 0 0 * * 0 0 TTTTTATAATTGTAATTTTGGTAATTTTATGTTATTGTAGAGGATGGTATGGAATTGTTTTAAAGTGTGTGTTGTATGTGTAGTAATTTTATTTTTGTGTTATTTAATTAATGAAGGTTTTAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9I9I9IIIII-IIIII-II9II9IIII9I9999I9IIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43848:1070_2:N:0:TCCACGTT+GTTCAACC/2 141 * 0 0 * * 0 0 AAACAAAAAAAAAACACCAACTTACAAAACCCCAAAAACCACATAACACCAAAAAACAATTCATTAAAAAACTTTAATATCAACAAAACTACAAATTAAAACCTTCATTAATTAAATAACACAAA IIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII--IIIIII-IIIIIIIIIIII-II9II-I9II9II-IIIIIII999IIII YT:Z:UP >>> Writing bisulfite mapping results to 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1159:19094:27167_1:N:0:TCCACGTT+GTTCAACC ptg000066l 66346 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1201:33458:16927_1:N:0:TCCACGTT+GTTCAACC ptg000006l 3 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2172:14773:4418_1:N:0:TCCACGTT+GTTCAACC ptg000006l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2211:38629:9993_1:N:0:TCCACGTT+GTTCAACC ptg000007l 12295855 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2310:31645:4320_1:N:0:TCCACGTT+GTTCAACC ptg000060c 1 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2354:47652:18692_1:N:0:TCCACGTT+GTTCAACC ptg000007l 12295855 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2389:46559:25514_1:N:0:TCCACGTT+GTTCAACC ptg000015l 14997108 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1162:35683:26242_1:N:0:TCCACGTT+GTTCAACC ptg000083l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1172:11900:18804_1:N:0:TCCACGTT+GTTCAACC ptg000006l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1361:14490:8046_1:N:0:TCCACGTT+GTTCAACC ptg000006l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1446:8752:12318_1:N:0:TCCACGTT+GTTCAACC ptg000039l 1 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2133:32908:18692_1:N:0:TCCACGTT+GTTCAACC ptg000066l 66354 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1423:36541:12066_1:N:0:TCCACGTT+GTTCAACC ptg000006l 1 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2371:33231:9139_1:N:0:TCCACGTT+GTTCAACC ptg000054l 1 Processed 7000000 sequence pairs so far 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3177071 (40.38%) aligned concordantly 0 times 1727835 (21.96%) aligned concordantly exactly 1 time 2962248 (37.65%) aligned concordantly >1 times 59.62% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7836722 (99.61%) aligned concordantly 0 times 11563 (0.15%) aligned concordantly exactly 1 time 18869 (0.24%) aligned concordantly >1 times 0.39% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7838870 (99.64%) aligned concordantly 0 times 11531 (0.15%) aligned concordantly exactly 1 time 16753 (0.21%) aligned concordantly >1 times 0.36% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3174265 (40.35%) aligned concordantly 0 times 1727873 (21.96%) aligned concordantly exactly 1 time 2965016 (37.69%) aligned concordantly >1 times 59.65% overall alignment rate Processed 7867154 sequences in total Successfully deleted the temporary files 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7867154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225682155 Total methylated C's in CpG context: 4076991 Total methylated C's in CHG context: 228324 Total methylated C's in CHH context: 1040240 Total methylated C's in Unknown context: 7658 Total unmethylated C's in CpG context: 31343955 Total unmethylated C's in CHG context: 38144237 Total unmethylated C's in CHH context: 150848408 Total unmethylated C's in Unknown context: 321086 C methylated in CpG context: 11.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7836438 (99.61%) aligned concordantly 0 times 11649 (0.15%) aligned concordantly exactly 1 time 19067 (0.24%) aligned concordantly >1 times 0.39% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7838831 (99.64%) aligned concordantly 0 times 11463 (0.15%) aligned concordantly exactly 1 time 16860 (0.21%) aligned concordantly >1 times 0.36% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3178831 (40.41%) aligned concordantly 0 times 1726943 (21.95%) aligned concordantly exactly 1 time 2961380 (37.64%) aligned concordantly >1 times 59.59% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3173036 (40.33%) aligned concordantly 0 times 1726880 (21.95%) aligned concordantly exactly 1 time 2967238 (37.72%) aligned concordantly >1 times 59.67% overall alignment rate Processed 7867154 sequences in total Successfully deleted the temporary files 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7867154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225810550 Total methylated C's in CpG context: 4065719 Total methylated C's in CHG context: 230229 Total methylated C's in CHH context: 1046813 Total methylated C's in Unknown context: 7714 Total unmethylated C's in CpG context: 31395205 Total unmethylated C's in CHG context: 38169704 Total unmethylated C's in CHH context: 150902880 Total unmethylated C's in Unknown context: 322582 C methylated in CpG context: 11.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Processed 7000000 sequence pairs so far 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3170507 (40.30%) aligned concordantly 0 times 1729982 (21.99%) aligned concordantly exactly 1 time 2966665 (37.71%) aligned concordantly >1 times 59.70% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7838503 (99.64%) aligned concordantly 0 times 11471 (0.15%) aligned concordantly exactly 1 time 17180 (0.22%) aligned concordantly >1 times 0.36% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3178352 (40.40%) aligned concordantly 0 times 1725441 (21.93%) aligned concordantly exactly 1 time 2963361 (37.67%) aligned concordantly >1 times 59.60% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7836344 (99.61%) aligned concordantly 0 times 11513 (0.15%) aligned concordantly exactly 1 time 19297 (0.25%) aligned concordantly >1 times 0.39% overall alignment rate Processed 7867154 sequences in total Successfully deleted the temporary files 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7867154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225719241 Total methylated C's in CpG context: 4071782 Total methylated C's in CHG context: 231468 Total methylated C's in CHH context: 1052884 Total methylated C's in Unknown context: 7879 Total unmethylated C's in CpG context: 31365107 Total unmethylated C's in CHG context: 38148587 Total unmethylated C's in CHH context: 150849413 Total unmethylated C's in Unknown context: 320157 C methylated in CpG context: 11.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.4% 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3172658 (40.33%) aligned concordantly 0 times 1728224 (21.97%) aligned concordantly exactly 1 time 2966272 (37.70%) aligned concordantly >1 times 59.67% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7836732 (99.61%) aligned concordantly 0 times 11498 (0.15%) aligned concordantly exactly 1 time 18924 (0.24%) aligned concordantly >1 times 0.39% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7838912 (99.64%) aligned concordantly 0 times 11534 (0.15%) aligned concordantly exactly 1 time 16708 (0.21%) aligned concordantly >1 times 0.36% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3179445 (40.41%) aligned concordantly 0 times 1724461 (21.92%) aligned concordantly exactly 1 time 2963248 (37.67%) aligned concordantly >1 times 59.59% overall alignment rate Processed 7867154 sequences in total Successfully deleted the temporary files 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7867154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225679699 Total methylated C's in CpG context: 4065623 Total methylated C's in CHG context: 230437 Total methylated C's in CHH context: 1041535 Total methylated C's in Unknown context: 7651 Total unmethylated C's in CpG context: 31365829 Total unmethylated C's in CHG context: 38141562 Total unmethylated C's in CHH context: 150834713 Total unmethylated C's in Unknown context: 320659 C methylated in CpG context: 11.5% 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 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7836823 (99.61%) aligned concordantly 0 times 11567 (0.15%) aligned concordantly exactly 1 time 18764 (0.24%) aligned concordantly >1 times 0.39% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 7839111 (99.64%) aligned concordantly 0 times 11360 (0.14%) aligned concordantly exactly 1 time 16683 (0.21%) aligned concordantly >1 times 0.36% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3175374 (40.36%) aligned concordantly 0 times 1727578 (21.96%) aligned concordantly exactly 1 time 2964202 (37.68%) aligned concordantly >1 times 59.64% overall alignment rate 7867154 reads; of these: 7867154 (100.00%) were paired; of these: 3180229 (40.42%) aligned concordantly 0 times 1726116 (21.94%) aligned concordantly exactly 1 time 2960809 (37.64%) aligned concordantly >1 times 59.58% overall alignment rate Processed 7867154 sequences in total Successfully deleted the temporary files 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D3_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7867154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 225694603 Total methylated C's in CpG context: 4058528 Total methylated C's in CHG context: 230335 Total methylated C's in CHH context: 1040590 Total methylated C's in Unknown context: 7619 Total unmethylated C's in CpG context: 31352508 Total unmethylated C's in CHG context: 38148460 Total unmethylated C's in CHH context: 150864182 Total unmethylated C's in Unknown context: 321301 C methylated in CpG context: 11.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1D3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1D3_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1D3_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/1D3_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1D3_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/1D3_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D3_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: 39335770 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1128586248 Total methylated C's in CpG context: 20338643 Total methylated C's in CHG context: 1150793 Total methylated C's in CHH context: 5222062 Total methylated C's in Unknown context: 38521 Total unmethylated C's in CpG context: 156822604 Total unmethylated C's in CHG context: 190752550 Total unmethylated C's in CHH context: 754299596 Total unmethylated C's in Unknown context: 1605785 C methylated in CpG context: 11.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Deleting temporary report files... Bismark completed in 0d 4h 47m 21s ==================== Bismark run complete ====================