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/1B4_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/1B4_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/1B4_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/1B4_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/1B4_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/1B4_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/1B4_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/1B4_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B4_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/1B4_R2_001.fastp-trim.fq.gz The provided filenames for paired-end alignments are /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B4_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/1B4_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/1B4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_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/1B4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_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/1B4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_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/1B4_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_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/1B4_R1_001.fastp-trim.fq.gz for PID: 37059 and offset 5 (sequences written out: 9048752) Using the subset file >1B4_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/1B4_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/1B4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B4_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/1B4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B4_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/1B4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B4_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/1B4_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9048753) Using the subset file >1B4_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/1B4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B4_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/1B4_R2_001.fastp-trim.fq.gz for PID: 37059 and offset 5 (sequences written out: 9048752) Using the subset file >1B4_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/1B4_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz (9048753 sequences in total) Writing a C -> T converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz (9048752 sequences in total) Writing a C -> T converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz (9048753 sequences in total) Writing a C -> T converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz (9048753 sequences in total) Writing a C -> T converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz (9048753 sequences in total) Writing a C -> T converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B4_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B4_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 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz (9048753 sequences in total) Input files are 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:49165:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 99 ntLink_6_CT_converted 18624975 21 125M = 18625133 283 TATATGTTTGTTTATAAAGTTTTTGATATTAAGAATTTGTTTGTTTTTGTAGTTTGTGTGTGGTTGTTTTTTTTTTATTTTGGTATTTTGTATTAATTTGTGTTTGTATGTTTTTTTATTGGTTG IIIIIII-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I-IIII9II9I-IIII9IIIIII9-II-99II9-999I99 AS:i:-12 XS:i:-56 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:109A2A12 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49165:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 147 ntLink_6_CT_converted 18625133 21 125M = 18624975 -283 TTGAAGTGAGAAAATGTATTTTTAGTTTATTTAGTTGTTTGTGTTTTTTAGTGTTAGATGTGTTATTGTTGGTTAATTTTTTATTGGTGAATGGTATATTTATGTATGTTATGGTAGTAGTGATT IIIIIIIII-I9IIIII9IIIII9IIII-III9IIIIIIIII-IIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-24 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:42A82 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B4_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz (9048752 sequences in total) Input files are 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B4_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 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz (9048753 sequences in total) Input files are 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:41421:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATTTGGGTTGGTTAGAGGTAAGGATAATAGTAGAAGTGTGGAGGGGTTATTGTATGTTGAAGTTTTTATATATTGGTAGTAGTTTGTGAGTTTTTTTATATAATTGGTTTAGGGTTAGTGTGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41421:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AAACTCAAAAAACCAAAATCACATCTCTTCTTACAACTCTCAAACTTCTCTCATACTTAACAACCTCCCATATACTCCATAACTCAACAAACACACACTAACCCTAAACCAATTAT IIIIII9IIIIIIIIIIIIIIIII9III9IIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:50848:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TGTGTTTTATTGTTTTTTTGTTTGTTTATTGTTTGAATTTATAAATATATAAATTAATAAGTAAATAATAGTGAAGATGTATGGATGTTATATGGATTTTTATTTAGTTAGTTTGGGGTGTTGAA I99IIIIIIII99I9III99III9I-I--9III9I-9-III-II-9-II-9II9-99--I-9-IIII9-III9-III-II9I99I-9-99999-I-I9I99-9I99--9-99-9-9-9I--999- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50848:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 TAAATAACATTCAACACCCCAAACTAACTAAATAAAAATCCACATAACATCCATACATCTTCACTATTATTTACTTATTTATTTATTTATTTATAAATTCAAACAATATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9--IIIIIIIII9I-IIII9II99III9I-III9IIIIIIII99IIIIIIIIIIIIIIII9IIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:49165:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATACATTTATTTATAAAATTTTTAATATTAAAAATTTATTTATTTTTATAATTTACATATAATTATTTTTTTTTTATTTTAATATTTTATATTAATTCATATTCATATATTCTTTTATTAATTA IIIIIII-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I-IIII9II9I-IIII9IIIIII9-II-99II9-999I99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49165:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AATTATTATTATTATAATATATGTAAATATATTGTTTATTGATAAAAAATTAATTAATAATAATATATTTAATATTAAAAAATATAAATAATTAAATAAATTAAAAATATATTTTTTTGTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIIIIIIIIIIIIIII-IIIIIIIII9III-IIII9IIIII9IIIII9I-IIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B4_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz (9048753 sequences in total) Input files are 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:41421:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATTTAAATTAATTAAAAATAAAAATAATAATAAAAATATAAAAAAATTATTATATATTAAAATTTTTATATATTAATAATAATTTATAAATTTTTTTATATAATTAATTTAAAATTAATATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41421:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AAATTTAAAAAATTAAAATTATATTTTTTTTTATAATTTTTAAATTTTTTTTATATTTAATAATTTTTTGTATATTTTATAATTTAATAAATATATATTAATTTTAAATTAATTAT IIIIII9IIIIIIIIIIIIIIIII9III9IIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:50848:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATATTTTATTATTTTTTTATTTATCTATTATTTAAATTTATAAATACATAAATCAATAAATAAATAATAATAAAAATATATAAATATTATATAAATTTTTATTTAATTAATTTAAAATATTAAA I99IIIIIIII99I9III99III9I-I--9III9I-9-III-II-9-II-9II9-99--I-9-IIII9-III9-III-II9I99I-9-99999-I-I9I99-9I99--9-99-9-9-9I--999- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50848:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 TAAATAATATTTAATATTTTAAATTAATTAAATAAAAATTTATATAATATTTATATATTTTTATTATTATTTATTTATTTATTTATTTATTTATAAATTTAAATAATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9--IIIIIIIII9I-IIII9II99III9I-III9IIIIIIII99IIIIIIIIIIIIIIII9IIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:49165:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATACATTTATTTATAAAATTTTTAATATTAAAAATTTATTTATTTTTATAATTTACATATAATTATTTTTTTTTTATTTTAATATTTTATATTAATTCATATTCATATATTCTTTTATTAATTA IIIIIII-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I-IIII9II9I-IIII9IIIIII9-II-99II9-999I99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49165:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AATTATTATTATTATAATATATGTAAATATATTGTTTATTGATAAAAAATTAATTAATAATAATATATTTAATATTAAAAAATATAAATAATTAAATAAATTAAAAATATATTTTTTTGTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIIIIIIIIIIIIIII-IIIIIIIII9III-IIII9IIIII9IIIII9I-IIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:50848:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATATTTTATTATTTTTTTATTTATCTATTATTTAAATTTATAAATACATAAATCAATAAATAAATAATAATAAAAATATATAAATATTATATAAATTTTTATTTAATTAATTTAAAATATTAAA I99IIIIIIII99I9III99III9I-I--9III9I-9-III-II-9-II-9II9-99--I-9-IIII9-III9-III-II9I99I-9-99999-I-I9I99-9I99--9-99-9-9-9I--999- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50848:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 TAAATAATATTTAATATTTTAAATTAATTAAATAAAAATTTATATAATATTTATATATTTTTATTATTATTTATTTATTTATTTATTTATTTATAAATTTAAATAATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9--IIIIIIIII9I-IIII9II99III9I-III9IIIIIIII99IIIIIIIIIIIIIIII9IIII-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:39835:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 99 ptg000020l_CT_converted 14595090 2 94M2D31M = 14595151 187 AAAAATTGTTTTTAGTTTTTTAATGTTTATTATTTTAAAAGGATTATGGTTTTTTAAGTTGAGGGGGTTATGAAATAAAATAAAATTAGGTAAAAAAAGTAAATTAAATAATTTTTTTATTATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-23 XS:i:-29 XN:i:0 XM:i:2 XO:i:1 XG:i:2 NM:i:4 MD:Z:66T17G9^AT31 YS:i:-31 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39835:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 147 ptg000020l_CT_converted 14595151 2 33M2D82M1I9M = 14595090 -187 AGGGGGTTATGAAATAAAATAAAATTAGGTAAAAAAAGTAAATTAAATAATTTTTTTATTATTGATGATGTTTTTTGTTTTTTTATAATATTTATTTTAGATGTAATAATATTAATTTTGAAATT IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-31 XS:i:-35 XN:i:0 XM:i:2 XO:i:2 XG:i:3 NM:i:5 MD:Z:5T17G9^AT91 YS:i:-23 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:41421:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATTTAAATTAATTAAAAATAAAAATAATAATAAAAATATAAAAAAATTATTATATATTAAAATTTTTATATATTAATAATAATTTATAAATTTTTTTATATAATTAATTTAAAATTAATATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41421:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AAATTTAAAAAATTAAAATTATATTTTTTTTTATAATTTTTAAATTTTTTTTATATTTAATAATTTTTTGTATATTTTATAATTTAATAAATATATATTAATTTTAAATTAATTAT IIIIII9IIIIIIIIIIIIIIIII9III9IIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:50848:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TGTGTTTTATTGTTTTTTTGTTTGTTTATTGTTTGAATTTATAAATATATAAATTAATAAGTAAATAATAGTGAAGATGTATGGATGTTATATGGATTTTTATTTAGTTAGTTTGGGGTGTTGAA I99IIIIIIII99I9III99III9I-I--9III9I-9-III-II-9-II-9II9-99--I-9-IIII9-III9-III-II9I99I-9-99999-I-I9I99-9I99--9-99-9-9-9I--999- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50848:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 TAAATAACATTCAACACCCCAAACTAACTAAATAAAAATCCACATAACATCCATACATCTTCACTATTATTTACTTATTTATTTATTTATTTATAAATTCAAACAATATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9--IIIIIIIII9I-IIII9II99III9I-III9IIIIIIII99IIIIIIIIIIIIIIII9IIII-IIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:49165:1056_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 TATATGTTTGTTTATAAAGTTTTTGATATTAAGAATTTGTTTGTTTTTGTAGTTTGTGTGTGGTTGTTTTTTTTTTATTTTGGTATTTTGTATTAATTTGTGTTTGTATGTTTTTTTATTGGTTG IIIIIII-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I-IIII9II9I-IIII9IIIIII9-II-99II9-999I99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49165:1056_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AATCACTACTACCATAACATACATAAATATACCATTCACCAATAAAAAATTAACCAACAATAACACATCTAACACTAAAAAACACAAACAACTAAATAAACTAAAAATACATTTTCTCACTTCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIIIIIIIIIIIIIII-IIIIIIIII9III-IIII9IIIII9IIIII9I-IIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:39835:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 AAAAATTATTTTTAATTTTTTAATATTTATTATTTTAAAAAAATTATAATTTTTTAAATTAAAAAAATTATAAAATAAAATAAAATTAAATAAAAAAAATAAATTAAATAATTTTTTTATTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39835:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AATTTTAAAATTAATATTATTATATTTAAAATAAATATTATAAAAAAATAAAAAATATTATTAATAATAAAAAAATTATTTAATTTATTTTTTTTATTTAATTTTATTTTATTTTATAATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:41421:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 83 ntLink_8_GA_converted 6744058 42 125M = 6743967 -216 CACACACTAACCCTAAACCAATTATATAAAAAAACTCACAAACTACTACCAATATATAAAAACTTCAACATACAATAACCCCTCCACACTTCTACTATTATCCTTACCTCTAACCAACCCAAATA 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 LH00526:197:22KFKVLT4:3:1101:41421:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 163 ntLink_8_GA_converted 6743967 42 116M = 6744058 216 AAACTCAAAAAACCAAAATCACATCTCTTCTTACAACTCTCAAACTTCTCTCATACTTAACAACCTCCCATATACTCCATAACTCAACAAACACACACTAACCCTAAACCAATTAT IIIIII9IIIIIIIIIIIIIIIII9III9IIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:116 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:39835:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 AAAAATTATTTTTAATTTTTTAATATTTATTATTTTAAAAAAATTATAATTTTTTAAATTAAAAAAATTATAAAATAAAATAAAATTAAATAAAAAAAATAAATTAAATAATTTTTTTATTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39835:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 AATTTTAAAATTAATATTATTATATTTAAAATAAATATTATAAAAAAATAAAAAATATTATTAATAATAAAAAAATTATTTAATTTATTTTTTTTATTTAATTTTATTTTATTTTATAATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:39835:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 83 ptg000012l_GA_converted 1413293 1 27M2D98M = 1413232 -188 CAATAATAAAAAAATTATTTAATTTACTTTTTTTACCTAATTTTATTTTATTTCATAACCCCCTCAACTTAAAAAACCATAATCCTTTTAAAATAATAAACATTAAAAAACTAAAAACAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-29 XS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:2 NM:i:5 MD:Z:27^TT13C52C16T14 YS:i:-17 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39835:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 163 ptg000012l_GA_converted 1413232 1 88M2D37M = 1413293 188 AATTTCAAAATTAATATTATTACATCTAAAATAAATATTATAAAAAAACAAAAAACATCATCAATAATAAAAAAATTATTTAATTTACTTTTTTTACCTAATTTTATTTTATTTCATAACCCCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII AS:i:-17 XS:i:-20 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:88^TT13C23 YS:i:-29 YT:Z:CP >>> Writing bisulfite mapping results to 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 1B4_R2_001.fastp-trim.fq.gz.temp.4.gz (9048753 sequences in total) Input files are 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B4_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 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:41016:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 AATTAAAATTAAGATTAAATAATATTAGAATTGTTATGAATTTATTTTTAAATAATTATTTGGGAAAAATGTGGTGATTTTTATTTAAGTTAAAAAATTTTTATAGAAAAGTTAGGTAGAAAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41016:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 ACTTTTCTATAAAAATTTTTTAACTTAAATAAAAATCACCACATTTTTCCCAAATAATTATTTAAAAATAAATTCATAACAATTCTAATATTATTTAATCTTAATTTTAATTAACTACCAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:41016:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 AATTAAAATTAAAATTAAATAATATTAAAATTATTATAAATTTATTTTTAAATAATTATTTAAAAAAAATATAATAATTTTTATTTAAATTAAAAAATTTTTATAAAAAAATTAAATAAAAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41016:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 ATTTTTTTATAAAAATTTTTTAATTTAAATAAAAATTATTATATTTTTTTTAAATAATTATTTAAAAATAAATTTATAATAATTTTAATATTATTTAATTTTAATTTTAATTAATTATTAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:41016:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 77 * 0 0 * * 0 0 AATTAAAATTAAAATTAAATAATATTAAAATTATTATAAATTTATTTTTAAATAATTATTTAAAAAAAATATAATAATTTTTATTTAAATTAAAAAATTTTTATAAAAAAATTAAATAAAAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41016:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 141 * 0 0 * * 0 0 ATTTTTTTATAAAAATTTTTTAATTTAAATAAAAATTATTATATTTTTTTTAAATAATTATTTAAAAATAAATTTATAATAATTTTAATATTATTTAATTTTAATTTTAATTAATTATTAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B4_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: LH00526:197:22KFKVLT4:3:1101:41016:1070_1:N:0:GGAAGAGA+TTCTCTCG/1 83 ptg000031l_GA_converted 12028974 42 125M = 12028987 138 ACCTTTCTACCTAACTTTTCTATAAAAATTTTTTAACTTAAATAAAAATCACCACATTTTTCCCAAATAATTATTTAAAAATAAATTCATAACAATTCTAATATTATTTAATCTTAATTTTAATT IIIIIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:41016:1070_2:N:0:GGAAGAGA+TTCTCTCG/2 163 ptg000031l_GA_converted 12028987 42 125M = 12028974 -138 ACTTTTCTATAAAAATTTTTTAACTTAAATAAAAATCACCACATTTTTCCCAAATAATTATTTAAAAATAAATTCATAACAATTCTAATATTATTTAATCTTAATTTTAATTAACTACCAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.4.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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1243:18503:17039_1:N:0:GGAAGAGA+TTCTCTCG ptg000029c 1802547 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 LH00526:197:22KFKVLT4:3:1467:14304:22740_1:N:0:GGAAGAGA+TTCTCTCG ptg000066l 66350 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2110:6891:6659_1:N:0:GGAAGAGA+TTCTCTCG ptg000007l 12295855 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1494:36323:7205_1:N:0:GGAAGAGA+TTCTCTCG ptg000185l 34486 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2103:33806:28707_1:N:0:GGAAGAGA+TTCTCTCG ptg000029c 1802547 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2197:42165:21970_1:N:0:GGAAGAGA+TTCTCTCG ptg000015l 14997131 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2220:40126:27909_1:N:0:GGAAGAGA+TTCTCTCG ptg000006l 1 Processed 3000000 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 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1115:8947:21003_1:N:0:GGAAGAGA+TTCTCTCG ptg000007l 12295855 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1161:6050:13103_1:N:0:GGAAGAGA+TTCTCTCG ptg000141l 1 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1443:10460:26116_1:N:0:GGAAGAGA+TTCTCTCG ptg000039l 1 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2196:42214:20149_1:N:0:GGAAGAGA+TTCTCTCG ptg000033l 2625626 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1372:29808:13075_1:N:0:GGAAGAGA+TTCTCTCG ptg000025l 21443081 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2393:51690:13383_1:N:0:GGAAGAGA+TTCTCTCG ptg000083l 1 Processed 9000000 sequence pairs so far Processed 7000000 sequence pairs so far 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3724284 (41.16%) aligned concordantly 0 times 2042271 (22.57%) aligned concordantly exactly 1 time 3282198 (36.27%) aligned concordantly >1 times 58.84% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9014822 (99.63%) aligned concordantly 0 times 13736 (0.15%) aligned concordantly exactly 1 time 20195 (0.22%) aligned concordantly >1 times 0.37% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3731297 (41.24%) aligned concordantly 0 times 2037200 (22.51%) aligned concordantly exactly 1 time 3280256 (36.25%) aligned concordantly >1 times 58.76% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9014167 (99.62%) aligned concordantly 0 times 13597 (0.15%) aligned concordantly exactly 1 time 20989 (0.23%) aligned concordantly >1 times 0.38% overall alignment rate Processed 9048753 sequences in total Successfully deleted the temporary files 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1B4_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9048753 Final Cytosine Methylation Report ================================= Total number of C's analysed: 264966320 Total methylated C's in CpG context: 4996149 Total methylated C's in CHG context: 314800 Total methylated C's in CHH context: 1349585 Total methylated C's in Unknown context: 8447 Total unmethylated C's in CpG context: 37290329 Total unmethylated C's in CHG context: 45171918 Total unmethylated C's in CHH context: 175843539 Total unmethylated C's in Unknown context: 369506 C methylated in CpG context: 11.8% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.2% Processed 9000000 sequence pairs so far 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3727327 (41.19%) aligned concordantly 0 times 2038763 (22.53%) aligned concordantly exactly 1 time 3282663 (36.28%) aligned concordantly >1 times 58.81% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3729792 (41.22%) aligned concordantly 0 times 2040014 (22.54%) aligned concordantly exactly 1 time 3278947 (36.24%) aligned concordantly >1 times 58.78% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9014763 (99.62%) aligned concordantly 0 times 13799 (0.15%) aligned concordantly exactly 1 time 20191 (0.22%) aligned concordantly >1 times 0.38% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9014285 (99.62%) aligned concordantly 0 times 13551 (0.15%) aligned concordantly exactly 1 time 20917 (0.23%) aligned concordantly >1 times 0.38% overall alignment rate Processed 9048753 sequences in total Successfully deleted the temporary files 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9048753 Final Cytosine Methylation Report ================================= Total number of C's analysed: 265007745 Total methylated C's in CpG context: 5004455 Total methylated C's in CHG context: 312890 Total methylated C's in CHH context: 1339771 Total methylated C's in Unknown context: 8713 Total unmethylated C's in CpG context: 37284358 Total unmethylated C's in CHG context: 45175617 Total unmethylated C's in CHH context: 175890654 Total unmethylated C's in Unknown context: 369185 C methylated in CpG context: 11.8% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.3% Processed 9000000 sequence pairs so far 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3728709 (41.21%) aligned concordantly 0 times 2040354 (22.55%) aligned concordantly exactly 1 time 3279690 (36.24%) aligned concordantly >1 times 58.79% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3726864 (41.19%) aligned concordantly 0 times 2039433 (22.54%) aligned concordantly exactly 1 time 3282456 (36.28%) aligned concordantly >1 times 58.81% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9015032 (99.63%) aligned concordantly 0 times 13701 (0.15%) aligned concordantly exactly 1 time 20020 (0.22%) aligned concordantly >1 times 0.37% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9014327 (99.62%) aligned concordantly 0 times 13837 (0.15%) aligned concordantly exactly 1 time 20589 (0.23%) aligned concordantly >1 times 0.38% overall alignment rate Processed 9048753 sequences in total Successfully deleted the temporary files 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9048753 Final Cytosine Methylation Report ================================= Total number of C's analysed: 265220313 Total methylated C's in CpG context: 5004722 Total methylated C's in CHG context: 313173 Total methylated C's in CHH context: 1346741 Total methylated C's in Unknown context: 8508 Total unmethylated C's in CpG context: 37332996 Total unmethylated C's in CHG context: 45223749 Total unmethylated C's in CHH context: 175998932 Total unmethylated C's in Unknown context: 370390 C methylated in CpG context: 11.8% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.2% Processed 9000000 sequence pairs so far 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3730838 (41.23%) aligned concordantly 0 times 2038528 (22.53%) aligned concordantly exactly 1 time 3279387 (36.24%) aligned concordantly >1 times 58.77% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 3726004 (41.18%) aligned concordantly 0 times 2039858 (22.54%) aligned concordantly exactly 1 time 3282891 (36.28%) aligned concordantly >1 times 58.82% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9013907 (99.61%) aligned concordantly 0 times 13875 (0.15%) aligned concordantly exactly 1 time 20971 (0.23%) aligned concordantly >1 times 0.39% overall alignment rate 9048753 reads; of these: 9048753 (100.00%) were paired; of these: 9014790 (99.62%) aligned concordantly 0 times 13630 (0.15%) aligned concordantly exactly 1 time 20333 (0.22%) aligned concordantly >1 times 0.38% overall alignment rate Processed 9048753 sequences in total Successfully deleted the temporary files 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9048753 Final Cytosine Methylation Report ================================= Total number of C's analysed: 265060053 Total methylated C's in CpG context: 4996215 Total methylated C's in CHG context: 316416 Total methylated C's in CHH context: 1358310 Total methylated C's in Unknown context: 8856 Total unmethylated C's in CpG context: 37317569 Total unmethylated C's in CHG context: 45198677 Total unmethylated C's in CHH context: 175872866 Total unmethylated C's in Unknown context: 370290 C methylated in CpG context: 11.8% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.3% Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far 9048752 reads; of these: 9048752 (100.00%) were paired; of these: 3726336 (41.18%) aligned concordantly 0 times 2037354 (22.52%) aligned concordantly exactly 1 time 3285062 (36.30%) aligned concordantly >1 times 58.82% overall alignment rate 9048752 reads; of these: 9048752 (100.00%) were paired; of these: 3729296 (41.21%) aligned concordantly 0 times 2038296 (22.53%) aligned concordantly exactly 1 time 3281160 (36.26%) aligned concordantly >1 times 58.79% overall alignment rate 9048752 reads; of these: 9048752 (100.00%) were paired; of these: 9014361 (99.62%) aligned concordantly 0 times 13609 (0.15%) aligned concordantly exactly 1 time 20782 (0.23%) aligned concordantly >1 times 0.38% overall alignment rate 9048752 reads; of these: 9048752 (100.00%) were paired; of these: 9014955 (99.63%) aligned concordantly 0 times 13697 (0.15%) aligned concordantly exactly 1 time 20100 (0.22%) aligned concordantly >1 times 0.37% overall alignment rate Processed 9048752 sequences in total Successfully deleted the temporary files 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B4_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9048752 Final Cytosine Methylation Report ================================= Total number of C's analysed: 265002969 Total methylated C's in CpG context: 4994911 Total methylated C's in CHG context: 315065 Total methylated C's in CHH context: 1344075 Total methylated C's in Unknown context: 8495 Total unmethylated C's in CpG context: 37302231 Total unmethylated C's in CHG context: 45181205 Total unmethylated C's in CHH context: 175865482 Total unmethylated C's in Unknown context: 369968 C methylated in CpG context: 11.8% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.2% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1B4_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1B4_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1B4_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/1B4_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1B4_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/1B4_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B4_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B4_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: 45243764 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1325257400 Total methylated C's in CpG context: 24996452 Total methylated C's in CHG context: 1572344 Total methylated C's in CHH context: 6738482 Total methylated C's in Unknown context: 43019 Total unmethylated C's in CpG context: 186527483 Total unmethylated C's in CHG context: 225951166 Total unmethylated C's in CHH context: 879471473 Total unmethylated C's in Unknown context: 1849339 C methylated in CpG context: 11.8% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.3% Deleting temporary report files... Bismark completed in 0d 6h 25m 53s ==================== Bismark run complete ====================