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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_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/1A10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_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/1A10_R1_001.fastp-trim.fq.gz for PID: 97738 and offset 5 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_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/1A10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_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/1A10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_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/1A10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_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/1A10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A10_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/1A10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A10_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/1A10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A10_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/1A10_R2_001.fastp-trim.fq.gz for PID: 97738 and offset 5 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A10_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/1A10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8293735) Using the subset file >1A10_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/1A10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A10_R1_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 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz (8293735 sequences in total) Writing a C -> T converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz (8293735 sequences in total) Writing a C -> T converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz (8293735 sequences in total) Writing a C -> T converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz (8293735 sequences in total) Writing a C -> T converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz (8293735 sequences in total) Writing a C -> T converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A10_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 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz (8293735 sequences in total) Input files are 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:44585:1084_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 TTGGATAATTTTAGGTAAAAGTGGTTAAAAATTGGGTTTTTTGGTTTGAAAGTTGGAAAATTGGAATTTGTTTAGTATTTGAGGATGATATGTTTTAGGTTTATATAAGTATGGGGTTTTTTGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44585:1084_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 AAACACAACATCAAATAATAACCTTAAAATTCCAACTAAAAAACCAAAACCCTATCCTTCAAAAAATCCATAATCACACACAAATCTATTAATAACATTAAATAAAAAACATTACAAATATACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII99III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A10_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz (8293735 sequences in total) Input files are 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A10_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 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz (8293735 sequences in total) Input files are 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50298:1056_1:N:0:AGCCTATC+GTTACGCA/1 99 ptg000018l_CT_converted 14440089 40 125M = 14440386 422 GTGATGTTGAGTTGTTTGTGGTAAAATAGGGATTTTAGTAAGTATGGTTGAGGTTAGTGATAGATATGGATAGTAATGTGGATGAAATTAGTGGTATTATGGTTATGATTATATAAAGTAAAGTA IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII-9II9IIIIIIIIIIIII-IIIIIII9III-I-III9I9I--9-I9II9IIIIII9IIIII9III-I9IIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:110G14 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50298:1056_2:N:0:AGCCTATC+GTTACGCA/2 147 ptg000018l_CT_converted 14440386 40 125M = 14440089 -422 AATTGATTTTTGTGAATGTAGAGTGTAAGTTAAGGGATTAGTGAGATATTAAGGATATTTATATTAAATAGTATGATTATATATTTGAGAATGGATTAATTTTATGTTGTTATTTTTAAAAAAGA 99-99999-9-9--IIIII-II-9I-II-III9II-IIIII99IIIIIIIII-IIIII9I9IIIIIIIIIIIIIII-IIIIIIII9IIIIIII9II9I9II9IIIIIIIII9IIIIIIIII9III AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:10G11A5A6T16T72 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A10_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz (8293735 sequences in total) Input files are 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:44585:1084_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 TTAAATAATTTTAAATAAAAATAATTAAAAATTAAATTTTTTAATTTAAAAATTAAAAAATTAAAATTTATTTAATATTTAAAAATAATATATTTTAAATTTATATAAATATAAAATTTTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44585:1084_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 AAATATAATATTAAATAATAATTTTAAAATTTTAATTAAAAAATTAAAATTTTATTTTTTAAAAAATTTATAATTATATATAAATTTATTAATAATATTAAATAAAAAATATTATAAATATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII99III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50298:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 ATAATATTAAATTATTTATAATAAAATAAAAATTTTAATAAATATAATTAAAATTAATAATAAATATAAATAATAATATAAATAAAATTAATAATATTATAATTATAATTATATAAAATAAAATA IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII-9II9IIIIIIIIIIIII-IIIIIII9III-I-III9I9I--9-I9II9IIIIII9IIIII9III-I9IIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50298:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTTTTTTTAAAAATAATAATATAAAATTAATTTATTTTTAAATATATAATTATATTATTTAATATAAATATTTTTAATATTTTATTAATTTTTTAATTTATATTTTATATTTATAAAAATTAATT III9IIIIIIIII9IIIIIIIII9II9I9II9IIIIIII9IIIIIIII-IIIIIIIIIIIIIII9I9IIIII-IIIIIIIII99IIIII-II9III-II-I9-II-IIIII--9-9-99999-99 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50282:1056_1:N:0:AGCCTATC+GTTACGCA/1 99 ptg000018l_CT_converted 14440089 42 125M = 14440386 422 GTGATGTTGAGTTGTTTGTGGTAAAATAGGGATTTTAGTAAGTATGGTTGAGGTTAGTGATAGATATGGATAGTAATGTGGATGAAATTAGTGGTATTATGGTTATGATTGTATAAAGTAAAGTA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII9I-IIIIIIIIII9IIIIIIIIIIII9II9IIIIII9IIIIIIII9III AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50282:1056_2:N:0:AGCCTATC+GTTACGCA/2 147 ptg000018l_CT_converted 14440386 42 125M = 14440089 -422 AATTGATTTTGGTGAATGTAGAATGTAAATTAAGGTATTAGTGAGATATTAATGATATTTATATTAAATAGTATGATTATATATTTGAGAATGGATTAATTTTATGTTGTGATTTTTAAAAAAGA -III-9IIIIIII9I-----II-9III-I9IIIIII9II-III99IIII9I-II99IIII-IIIIIIIIIII9I9III-I9III-IIII-II999IIIII9-9IIII9II-IIIIII9I9IIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:110T14 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50298:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 ATAATATTAAATTATTTATAATAAAATAAAAATTTTAATAAATATAATTAAAATTAATAATAAATATAAATAATAATATAAATAAAATTAATAATATTATAATTATAATTATATAAAATAAAATA IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII-9II9IIIIIIIIIIIII-IIIIIII9III-I-III9I9I--9-I9II9IIIIII9IIIII9III-I9IIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50298:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTTTTTTTAAAAATAATAATATAAAATTAATTTATTTTTAAATATATAATTATATTATTTAATATAAATATTTTTAATATTTTATTAATTTTTTAATTTATATTTTATATTTATAAAAATTAATT III9IIIIIIIII9IIIIIIIII9II9I9II9IIIIIII9IIIIIIII-IIIIIIIIIIIIIII9I9IIIII-IIIIIIIII99IIIII-II9III-II-I9-II-IIIII--9-9-99999-99 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50282:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 ATAATATTAAATTATTTATAATAAAATAAAAATTTTAATAAATATAATTAAAATTAATAATAAATATAAATAATAATATAAATAAAATTAATAATATTATAATTATAATTATATAAAATAAAATA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII9I-IIIIIIIIII9IIIIIIIIIIII9II9IIIIII9IIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50282:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTTTTTTTAAAAATTATAATATAAAATTAATTTATTTTTAAATATATAATTATATTATTTAATATAAATATTATTAATATTTTATTAATATTTTAATTTATGTTTTATATTTATTAAAATTAATT IIIII9I9IIIIII-II9IIII9-9IIIII999II-IIII-III9I-III9I9IIIIIIIIIII-IIII99II-I9IIII99III-II9IIIIII9I-III9-II-----I9IIIIIII9-III- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:51091:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 TTATATAAGTTTGTGAGATTATAATGAATATTTTAATTATAAAAGTGATTTGTTTTAAGTTTATTGAATGTAATAAAGAATGATTATATAATTTATTTTGATTTTTGTTTTTGTGAAAAATGAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51091:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 CTACACAAATTCATAAAATCATAACAAACATCTTAACCACAAAAATAATTTATTTCAAATTCACTAAACATAACAAAAAATAATTACACAATTTACTTCAATTTTTATTTTCTACTACATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:44585:1084_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 TTAAATAATTTTAAATAAAAATAATTAAAAATTAAATTTTTTAATTTAAAAATTAAAAAATTAAAATTTATTTAATATTTAAAAATAATATATTTTAAATTTATATAAATATAAAATTTTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44585:1084_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 AAATATAATATTAAATAATAATTTTAAAATTTTAATTAAAAAATTAAAATTTTATTTTTTAAAAAATTTATAATTATATATAAATTTATTAATAATATTAAATAAAAAATATTATAAATATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII99III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:51091:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 TTATATAAATTTATAAAATTATAATAAATATTTTAATTATAAAAATAATTTATTTTAAATTTATTAAATATAATAAAAAATAATTATATAATTTATTTTAATTTTTATTTTTATAAAAAATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51091:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTATATAAATTTATAAAATTATAATAAATATTTTAATTATAAAAATAATTTATTTTAAATTTATTAAATATAATAAAAAATAATTATATAATTTATTTTAATTTTTATTTTTTATTATATTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50298:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 GTGATGTTGAGTTGTTTGTGGTAAAATAGGGATTTTAGTAAGTATGGTTGAGGTTAGTGATAGATATGGATAGTAATGTGGATGAAATTAGTGGTATTATGGTTATGATTATATAAAGTAAAGTA IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII-9II9IIIIIIIIIIIII-IIIIIII9III-I-III9I9I--9-I9II9IIIIII9IIIII9III-I9IIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50298:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TCTTTTTTAAAAATAACAACATAAAATTAATCCATTCTCAAATATATAATCATACTATTTAATATAAATATCCTTAATATCTCACTAATCCCTTAACTTACACTCTACATTCACAAAAATCAATT III9IIIIIIIII9IIIIIIIII9II9I9II9IIIIIII9IIIIIIII-IIIIIIIIIIIIIII9I9IIIII-IIIIIIIII99IIIII-II9III-II-I9-II-IIIII--9-9-99999-99 YT:Z:UP >>> Writing bisulfite mapping results to 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:44585:1084_1:N:0:AGCCTATC+GTTACGCA/1 83 ptg000011l_GA_converted 3285232 42 49M1D76M = 3284954 -404 TACAAAAAACCCCATACTTATATAAACCTAAAACATATCATCCTCAAATACTAAACAAATTCCAATTTTCCAACTTTCAAACCAAAAAACCCAATTTTTAACCACTTTTACCTAAAATTATCCAA IIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:9T39^A76 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44585:1084_2:N:0:AGCCTATC+GTTACGCA/2 163 ptg000011l_GA_converted 3284954 42 125M = 3285232 404 AAACACAACATCAAATAATAACCTTAAAATTCCAACTAAAAAACCAAAACCCTATCCTTCAAAAAATCCATAATCACACACAAATCTATTAATAACATTAAATAAAAAACATTACAAATATACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII99III AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:53C28T42 YS:i:-14 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:50282:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 ATAATATTAAATTATTTATAATAAAATAAAAATTTTAATAAATATAATTAAAATTAATAATAAATATAAATAATAATATAAATAAAATTAATAATATTATAATTATAATTATATAAAATAAAATA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII9I-IIIIIIIIII9IIIIIIIIIIII9II9IIIIII9IIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50282:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTTTTTTTAAAAATTATAATATAAAATTAATTTATTTTTAAATATATAATTATATTATTTAATATAAATATTATTAATATTTTATTAATATTTTAATTTATGTTTTATATTTATTAAAATTAATT IIIII9I9IIIIII-II9IIII9-9IIIII999II-IIII-III9I-III9I9IIIIIIIIIII-IIII99II-I9IIII99III-II9IIIIII9I-III9-II-----I9IIIIIII9-III- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A10_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)) >>> Writing bisulfite mapping results to 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:51091:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 TTATATAAATTTATAAAATTATAATAAATATTTTAATTATAAAAATAATTTATTTTAAATTTATTAAATATAATAAAAAATAATTATATAATTTATTTTAATTTTTATTTTTATAAAAAATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51091:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTATATAAATTTATAAAATTATAATAAATATTTTAATTATAAAAATAATTTATTTTAAATTTATTAAATATAATAAAAAATAATTATATAATTTATTTTAATTTTTATTTTTTATTATATTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50282:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 GTGATGTTGAGTTGTTTGTGGTAAAATAGGGATTTTAGTAAGTATGGTTGAGGTTAGTGATAGATATGGATAGTAATGTGGATGAAATTAGTGGTATTATGGTTATGATTGTATAAAGTAAAGTA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII9I-IIIIIIIIII9IIIIIIIIIIII9II9IIIIII9IIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50282:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TCTTTTTTAAAAATCACAACATAAAATTAATCCATTCTCAAATATATAATCATACTATTTAATATAAATATCATTAATATCTCACTAATACCTTAATTTACATTCTACATTCACCAAAATCAATT IIIII9I9IIIIII-II9IIII9-9IIIII999II-IIII-III9I-III9I9IIIIIIIIIII-IIII99II-I9IIII99III-II9IIIIII9I-III9-II-----I9IIIIIII9-III- YT:Z:UP >>> Writing bisulfite mapping results to 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz (8293735 sequences in total) Reading in the sequence files 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz Input files are 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A10_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 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:51091:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 TTATATAAGTTTGTGAGATTATAATGAATATTTTAATTATAAAAGTGATTTGTTTTAAGTTTATTGAATGTAATAAAGAATGATTATATAATTTATTTTGATTTTTGTTTTTGTGAAAAATGAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51091:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 CTACACAAATTCATAAAATCATAACAAACATCTTAACCACAAAAATAATTTATTTCAAATTCACTAAACATAACAAAAAATAATTACACAATTTACTTCAATTTTTATTTTCTACTACATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:41558:1084_1:N:0:AGCCTATC+GTTACGCA/1 99 ptg000047l_CT_converted 876214 1 125M = 876463 374 AAGGTTGTTTTTTATGGTAGAATTATTGTTTGTGAAATTGTTTTGAGGGTTTGTATGTTTTGGAAATTTAATATTTTTTAAAGTGATTTATATATGTTGATTTTTTATATATTATTGTAGTTGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41558:1084_2:N:0:AGCCTATC+GTTACGCA/2 147 ptg000047l_CT_converted 876463 1 125M = 876214 -374 GGGTTGTTTTATGTTAATGGTTTAAAAGTATTTTTATATAGGGGTATTTAATTGTTATTTAGAAATATTTAATGTATATGGTTTTAAAGTTGTTAGTAATATAATTAGATGTTAGAATTTGGGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A10_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)) Reading in the sequence files 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:41558:1084_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 AAAATTATTTTTTATAATAAAATTATTATTTATAAAATTATTTTAAAAATTTATATATTTTAAAAATTTAATATTTTTTAAAATAATTTATATATATTAATTTTTTATATATTATTATAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41558:1084_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTTTTAAATTTTAATATTTAATTATATTATTAATAATTTTAAAATTATATATATTAAATATTTTTAAATAATAATTAAATATTTTTATATAAAAATATTTTTAAATTATTAATATAAAATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:41558:1084_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 AAAATTATTTTTTATAATAAAATTATTATTTATAAAATTATTTTAAAAATTTATATATTTTAAAAATTTAATATTTTTTAAAATAATTTATATATATTAATTTTTTATATATTATTATAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41558:1084_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TTTTTAAATTTTAATATTTAATTATATTATTAATAATTTTAAAATTATATATATTAAATATTTTTAAATAATAATTAAATATTTTTATATAAAAATATTTTTAAATTATTAATATAAAATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A10_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: LH00526:197:22KFKVLT4:3:1101:41558:1084_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 AAGGTTGTTTTTTATGGTAGAATTATTGTTTGTGAAATTGTTTTGAGGGTTTGTATGTTTTGGAAATTTAATATTTTTTAAAGTGATTTATATATGTTGATTTTTTATATATTATTGTAGTTGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41558:1084_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 CTCCCAAATTCTAACATCTAATTATATTACTAACAACTTTAAAACCATATACATTAAATATTTCTAAATAACAATTAAATACCCCTATATAAAAATACTTTTAAACCATTAACATAAAACAACCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1125:25552:19602_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1125:25560:19588_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1125:25536:19602_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1181:2060:22782_1:N:0:AGCCTATC+GTTACGCA ptg000066l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1210:5078:24561_1:N:0:AGCCTATC+GTTACGCA ptg000046l 1 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far 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 LH00526:197:22KFKVLT4:3:1466:30391:21591_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1451:22752:14616_1:N:0:AGCCTATC+GTTACGCA ptg000092l 28976 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1457:7911:13467_1:N:0:AGCCTATC+GTTACGCA ptg000117l 29992 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2108:43379:28105_1:N:0:AGCCTATC+GTTACGCA ptg000011l 1 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2178:43250:7233_1:N:0:AGCCTATC+GTTACGCA ptg000092l 28980 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2351:32357:3031_1:N:0:AGCCTATC+GTTACGCA ptg000105l 83217 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2441:44034:14335_1:N:0:AGCCTATC+GTTACGCA ptg000083l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2282:33701:2415_1:N:0:AGCCTATC+GTTACGCA ptg000046l 2 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2422:20340:6043_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1102:29922:18818_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1232:38977:28497_1:N:0:AGCCTATC+GTTACGCA ptg000045l 57982 Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1274:20106:7149_1:N:0:AGCCTATC+GTTACGCA ptg000075l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1169:3144:21381_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1347:42052:3507_1:N:0:AGCCTATC+GTTACGCA ptg000046l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1376:2627:10259_1:N:0:AGCCTATC+GTTACGCA ntLink_0 96460 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1387:7425:20415_1:N:0:AGCCTATC+GTTACGCA ptg000063l 30346 Processed 6000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2268:9173:3746_1:N:0:AGCCTATC+GTTACGCA ptg000066l 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1171:47110:23300_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2340:38071:22082_1:N:0:AGCCTATC+GTTACGCA ptg000039l 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1414:2667:3045_1:N:0:AGCCTATC+GTTACGCA ptg000096l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2406:37723:16240_1:N:0:AGCCTATC+GTTACGCA ptg000075l 1 Processed 8000000 sequence pairs so far 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8276921 (99.80%) aligned concordantly 0 times 6403 (0.08%) aligned concordantly exactly 1 time 10411 (0.13%) aligned concordantly >1 times 0.20% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3763484 (45.38%) aligned concordantly 0 times 1696082 (20.45%) aligned concordantly exactly 1 time 2834169 (34.17%) aligned concordantly >1 times 54.62% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8275161 (99.78%) aligned concordantly 0 times 6488 (0.08%) aligned concordantly exactly 1 time 12086 (0.15%) aligned concordantly >1 times 0.22% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3759959 (45.33%) aligned concordantly 0 times 1696609 (20.46%) aligned concordantly exactly 1 time 2837167 (34.21%) aligned concordantly >1 times 54.67% overall alignment rate Processed 8293735 sequences in total Successfully deleted the temporary files 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8293735 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221164916 Total methylated C's in CpG context: 3676678 Total methylated C's in CHG context: 208613 Total methylated C's in CHH context: 908625 Total methylated C's in Unknown context: 6481 Total unmethylated C's in CpG context: 30441398 Total unmethylated C's in CHG context: 37109380 Total unmethylated C's in CHH context: 148820222 Total unmethylated C's in Unknown context: 325955 C methylated in CpG context: 10.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Now waiting for all child processes to complete Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2257:28748:26032_1:N:0:AGCCTATC+GTTACGCA ptg000011l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1278:20769:21185_1:N:0:AGCCTATC+GTTACGCA ptg000011l 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1382:20211:5006_1:N:0:AGCCTATC+GTTACGCA ptg000098l 55086 Processed 6000000 sequence pairs so far 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8275306 (99.78%) aligned concordantly 0 times 6349 (0.08%) aligned concordantly exactly 1 time 12080 (0.15%) aligned concordantly >1 times 0.22% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8277003 (99.80%) aligned concordantly 0 times 6356 (0.08%) aligned concordantly exactly 1 time 10376 (0.13%) aligned concordantly >1 times 0.20% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3766414 (45.41%) aligned concordantly 0 times 1696827 (20.46%) aligned concordantly exactly 1 time 2830494 (34.13%) aligned concordantly >1 times 54.59% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3762541 (45.37%) aligned concordantly 0 times 1696260 (20.45%) aligned concordantly exactly 1 time 2834934 (34.18%) aligned concordantly >1 times 54.63% overall alignment rate Processed 8293735 sequences in total Successfully deleted the temporary files 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8293735 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221123986 Total methylated C's in CpG context: 3676832 Total methylated C's in CHG context: 207740 Total methylated C's in CHH context: 898868 Total methylated C's in Unknown context: 6490 Total unmethylated C's in CpG context: 30430240 Total unmethylated C's in CHG context: 37110955 Total unmethylated C's in CHH context: 148799351 Total unmethylated C's in Unknown context: 325535 C methylated in CpG context: 10.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2348:26879:6099_1:N:0:AGCCTATC+GTTACGCA ptg000075l 1 Processed 8000000 sequence pairs so far Processed 6000000 sequence pairs so far 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8277108 (99.80%) aligned concordantly 0 times 6362 (0.08%) aligned concordantly exactly 1 time 10265 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3760889 (45.35%) aligned concordantly 0 times 1695732 (20.45%) aligned concordantly exactly 1 time 2837114 (34.21%) aligned concordantly >1 times 54.65% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8275369 (99.78%) aligned concordantly 0 times 6366 (0.08%) aligned concordantly exactly 1 time 12000 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3765261 (45.40%) aligned concordantly 0 times 1695715 (20.45%) aligned concordantly exactly 1 time 2832759 (34.16%) aligned concordantly >1 times 54.60% overall alignment rate Processed 8293735 sequences in total Successfully deleted the temporary files 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8293735 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221013244 Total methylated C's in CpG context: 3683378 Total methylated C's in CHG context: 207194 Total methylated C's in CHH context: 903019 Total methylated C's in Unknown context: 6344 Total unmethylated C's in CpG context: 30400465 Total unmethylated C's in CHG context: 37095264 Total unmethylated C's in CHH context: 148723924 Total unmethylated C's in Unknown context: 326915 C methylated in CpG context: 10.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2108:46843:23987_1:N:0:AGCCTATC+GTTACGCA ptg000015l 14997104 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2257:28740:26046_1:N:0:AGCCTATC+GTTACGCA ptg000011l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2177:50848:27167_1:N:0:AGCCTATC+GTTACGCA ptg000020l 17861297 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2413:50953:26928_1:N:0:AGCCTATC+GTTACGCA ptg000114l 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2323:50144:1322_1:N:0:AGCCTATC+GTTACGCA ntLink_0 96467 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8275304 (99.78%) aligned concordantly 0 times 6407 (0.08%) aligned concordantly exactly 1 time 12024 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8277199 (99.80%) aligned concordantly 0 times 6339 (0.08%) aligned concordantly exactly 1 time 10197 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3762634 (45.37%) aligned concordantly 0 times 1694566 (20.43%) aligned concordantly exactly 1 time 2836535 (34.20%) aligned concordantly >1 times 54.63% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3765261 (45.40%) aligned concordantly 0 times 1695510 (20.44%) aligned concordantly exactly 1 time 2832964 (34.16%) aligned concordantly >1 times 54.60% overall alignment rate Processed 8293735 sequences in total Successfully deleted the temporary files 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8293735 Final Cytosine Methylation Report ================================= Total number of C's analysed: 220990436 Total methylated C's in CpG context: 3679872 Total methylated C's in CHG context: 207153 Total methylated C's in CHH context: 898752 Total methylated C's in Unknown context: 6380 Total unmethylated C's in CpG context: 30419387 Total unmethylated C's in CHG context: 37081632 Total unmethylated C's in CHH context: 148703640 Total unmethylated C's in Unknown context: 326355 C methylated in CpG context: 10.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2340:38079:22096_1:N:0:AGCCTATC+GTTACGCA ptg000039l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2461:37310:24463_1:N:0:AGCCTATC+GTTACGCA ptg000133l 1 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8277130 (99.80%) aligned concordantly 0 times 6321 (0.08%) aligned concordantly exactly 1 time 10284 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 8275231 (99.78%) aligned concordantly 0 times 6345 (0.08%) aligned concordantly exactly 1 time 12159 (0.15%) aligned concordantly >1 times 0.22% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3766915 (45.42%) aligned concordantly 0 times 1694954 (20.44%) aligned concordantly exactly 1 time 2831866 (34.14%) aligned concordantly >1 times 54.58% overall alignment rate 8293735 reads; of these: 8293735 (100.00%) were paired; of these: 3761182 (45.35%) aligned concordantly 0 times 1696277 (20.45%) aligned concordantly exactly 1 time 2836276 (34.20%) aligned concordantly >1 times 54.65% overall alignment rate Processed 8293735 sequences in total Successfully deleted the temporary files 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A10_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8293735 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221078466 Total methylated C's in CpG context: 3668095 Total methylated C's in CHG context: 209223 Total methylated C's in CHH context: 907763 Total methylated C's in Unknown context: 6484 Total unmethylated C's in CpG context: 30429821 Total unmethylated C's in CHG context: 37087881 Total unmethylated C's in CHH context: 148775683 Total unmethylated C's in Unknown context: 326069 C methylated in CpG context: 10.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1A10_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1A10_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1A10_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/1A10_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1A10_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/1A10_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A10_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: 41468675 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1105371048 Total methylated C's in CpG context: 18384855 Total methylated C's in CHG context: 1039923 Total methylated C's in CHH context: 4517027 Total methylated C's in Unknown context: 32179 Total unmethylated C's in CpG context: 152121311 Total unmethylated C's in CHG context: 185485112 Total unmethylated C's in CHH context: 743822820 Total unmethylated C's in Unknown context: 1630829 C methylated in CpG context: 10.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Deleting temporary report files... Bismark completed in 0d 6h 18m 55s ==================== Bismark run complete ====================