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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_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/1D8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_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/1D8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8018705) Using the subset file >1D8_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/1D8_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/1D8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_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/1D8_R1_001.fastp-trim.fq.gz for PID: 70165 and offset 5 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_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/1D8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_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/1D8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D8_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/1D8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8018705) Using the subset file >1D8_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/1D8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D8_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/1D8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D8_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/1D8_R2_001.fastp-trim.fq.gz for PID: 70165 and offset 5 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D8_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/1D8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8018704) Using the subset file >1D8_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/1D8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz (8018705 sequences in total) Writing a C -> T converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz (8018704 sequences in total) Writing a C -> T converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz (8018704 sequences in total) Writing a C -> T converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz (8018704 sequences in total) Writing a C -> T converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz (8018704 sequences in total) Writing a C -> T converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D8_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 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz (8018704 sequences in total) Created C -> T as well as G -> A converted versions of the FastQ file 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz (8018704 sequences in total) Created C -> T as well as G -> A converted versions of the FastQ file 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz (8018704 sequences in total) Input files are 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D8_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)) Input files are 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Input files are 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D8_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz (8018705 sequences in total) Input files are 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32576:1084_1:N:0:CTTACAGC+CTTCACCA/1 99 ptg000008l_CT_converted 8222536 40 125M = 8222626 215 TATGTATGTAGATTTTTTGAAGTAATAATTATTTTTTTAAAGAGAAGGATGAATTTAAGTTTGTTTAAAATTTTTTTAGAAATATTAAGTTATTTTGTTTTTATTATTTTTTTAGTTTATATATT 9-I9II-I9I9-I9IIII-IIIIIIIIIII-II9III9-IIIII-I9I9-IIIII99I--99-III-IIIIIIIII9999I-II-II-I99-II-I--999-999-999--I9--9---9999-9 AS:i:-36 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:23T60A24A0A5A6A1 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:32576:1084_2:N:0:CTTACAGC+CTTCACCA/2 147 ptg000008l_CT_converted 8222626 40 125M = 8222536 -215 TATTTTGTTTTTATTATTTAATTAGTATATATAATATGATAATGTTTATATATGGGTATGTGGGTTAGTTAAGTTATTGTGTTGTTTATTTAATATATATAGAGGATATTATATGTTTGTGTGTG I9IIIIII-IIIIIIIIIIIII9IIIIIIIIIIIIII9I9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:122A2 YS:i:-36 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:44997:1070_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TGTTTTTAATTGTGTATTTATGAATTTTTAAGTATATTTATATGTTGTTTTGTATTATTGTAATAGTATATTTTTTGTGGATTTTGTGTGAATATGGTAAAATTTGATAGTTGTTGAATGTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44997:1070_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 TTCTAAAAATAACCAAAAATAACAATAAACATACAAATTACAATACTACTAACAAACATATCAAAAAATAAATATATATAATCCACCCCACCCCAAAAAATATAAAAACACATTATCATAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9III9I-I-I9I-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32527:1084_1:N:0:CTTACAGC+CTTCACCA/1 99 ntLink_6_CT_converted 9984197 31 125M = 9984173 -149 AATAGGTAATAGGTATTAAGGTAATAAGATAATAGGGTAATAAGGTAATTGGTAATATGGTGATAAGGTAATAGGGTAATGGGGTAATAGGATAATAGGATAATAAGGTAATAGGTAATAAGGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII AS:i:0 XS:i:-28 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:32527:1084_2:N:0:CTTACAGC+CTTCACCA/2 147 ntLink_6_CT_converted 9984173 31 125M = 9984197 149 AATGGGGTAATAGAGTAATATGAAAATAGGTAATAGGTATTAAGGTAATAAGATAATAGGGTAATAAGGTAATTGGTAATATGGTGATAAGGTAATAGGGTAATGGGGTAATAGGATAATAGGAT IIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-12 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 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:27996:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 AATTAAGATAGTATTAGATAAAGTTTTTAGGTTTAAGGGGGTATTATATGATATGGATAATTAGATAAAGTTTGATGTTATTTTGATTATAAATGAATGTAGTTTAAAAGGTTATGATAGATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:27996:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 ATTAAAATATAACATTCACATTTAAATAATATAAAAATTCCTAAAACAAAACATTTTATTCCCAAAAAATTTAAATTAAATACAACATTAAATTAACCAATTAAATCTATCATAACCTTTTAAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D8_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz (8018704 sequences in total) Input files are 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D8_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 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32576:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TATATATATAAATTTTTTAAAATAATAATTATTTTTTTAAAAAAAAAAACAAATTTAAATTTATTTAAAATTTTTTTAAAAATACTAAATTATTTTATTTTTATTATTTCCTTAATCTATATACT 9-I9II-I9I9-I9IIII-IIIIIIIIIII-II9III9-IIIII-I9I9-IIIII99I--99-III-IIIIIIIII9999I-II-II-I99-II-I--999-999-999--I9--9---9999-9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:32576:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 TATATATGAATATATAATATTTTTTATATATATTAAATAAATAATATGATAATTTAATTAATTTATATATTTATATATAAATATTATTGTATTATATATATTAATTAAATAATAAAAATAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9I9IIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:27996:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 AATTAAAATAATATTAAATAAAATTTTTAAATTTAAAAAAATATTATATAATATAAATAATTAAATAAAATTTAATATTATTTTAATTATAAATAAATATAATTTAAAAAATTATAATAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:27996:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 ATTAAAATATAATATTTATATTTAAATAATATAAAAATTTTTAAAATAAAATATTTTATTTTTAAAAAATTTAAATTAAATATAATATTAAATTAATTAATTAAATTTATTATAATTTTTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:44997:1070_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TATTTTTAATTATATATTTATAAATTTTTAAATATATTTATATATTATTTTATATTATTATAATAATATATTTTTTATAAATTTTATATAAATATAATAAAATTTAATAATTATTAAATATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44997:1070_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 TTTTAAAAATAATTAAAAATAATAATAAATATATAAATTATAATATTATTAATAAATATATTAAAAAATAAATATATATAATTTATTTTATTTTAAAAAATATAAAAATATATTATTATAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9III9I-I-I9I-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32527:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 AATAAATAATAAATATTAAAATAATAAAATAATAAAATAATAAAATAATTAATAATATAATAATAAAATAATAAAATAATAAAATAATAAAATAATAAAATAATAAAATAATAAATAATAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:32527:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 ATTTTATTATTTTATTATTTTATTATTTTATTATTTTATTATTATATTATTAATTATTTTATTATTTTATTATTTTATTATTTTAATATTTATTATTTATTTTTATATTATTTTATTATTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:27996:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 AATTAAAATAATATTAAATAAAATTTTTAAATTTAAAAAAATATTATATAATATAAATAATTAAATAAAATTTAATATTATTTTAATTATAAATAAATATAATTTAAAAAATTATAATAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:27996:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 ATTAAAATATAATATTTATATTTAAATAATATAAAAATTTTTAAAATAAAATATTTTATTTTTAAAAAATTTAAATTAAATATAATATTAAATTAATTAATTAAATTTATTATAATTTTTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:49108:1070_1:N:0:CTTACAGC+CTTCACCA/1 99 ptg000007l_CT_converted 10103757 1 125M = 10103876 244 TGTTTGAATTTGTTGTGGTTTTTTAGAAAGGGTATTGATTTTTTTATATTTATTTGGTTTATTATTTTTTTGATATATAAGTGGGATTTTTTGTTGAGTATATTGATATGTGGTTTAAATTTAAG 9IIIIIII999III9IIIIII9II9IIIIIII9IIIIII9IIIIII--9II99I-I9-9--9I--99IIII-I-I99II9--9999--999-99I99-9-9I99---9-99-999--9-999-9- AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:54A70 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49108:1070_2:N:0:CTTACAGC+CTTCACCA/2 147 ptg000007l_CT_converted 10103876 1 125M = 10103757 -244 TTTAAGGAAGAAGTTAGTGGGTATTTTGAATATTGTATTATAGGATATTTTTAATGTGAATATGTTTGATGATGGAATGAATGTGAAAATATTGTTTTTTATTATGTTAATATTTGTAAGAATTT IIII-II9III-IIIII9II9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:44997:1070_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TATTTTTAATTATATATTTATAAATTTTTAAATATATTTATATATTATTTTATATTATTATAATAATATATTTTTTATAAATTTTATATAAATATAATAAAATTTAATAATTATTAAATATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44997:1070_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 TTTTAAAAATAATTAAAAATAATAATAAATATATAAATTATAATATTATTAATAAATATATTAAAAAATAAATATATATAATTTATTTTATTTTAAAAAATATAAAAATATATTATTATAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9III9I-I-I9I-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32576:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TATATATATAAATTTTTTAAAATAATAATTATTTTTTTAAAAAAAAAAACAAATTTAAATTTATTTAAAATTTTTTTAAAAATACTAAATTATTTTATTTTTATTATTTCCTTAATCTATATACT 9-I9II-I9I9-I9IIII-IIIIIIIIIII-II9III9-IIIII-I9I9-IIIII99I--99-III-IIIIIIIII9999I-II-II-I99-II-I--999-999-999--I9--9---9999-9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:32576:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 TATATATGAATATATAATATTTTTTATATATATTAAATAAATAATATGATAATTTAATTAATTTATATATTTATATATAAATATTATTGTATTATATATATTAATTAAATAATAAAAATAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9I9IIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32527:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 AATAAATAATAAATATTAAAATAATAAAATAATAAAATAATAAAATAATTAATAATATAATAATAAAATAATAAAATAATAAAATAATAAAATAATAAAATAATAAAATAATAAATAATAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:32527:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 ATTTTATTATTTTATTATTTTATTATTTTATTATTTTATTATTATATTATTAATTATTTTATTATTTTATTATTTTATTATTTTAATATTTATTATTTATTTTTATATTATTTTATTATTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32527:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 AATAGGTAATAGGTATTAAGGTAATAAGATAATAGGGTAATAAGGTAATTGGTAATATGGTGATAAGGTAATAGGGTAATGGGGTAATAGGATAATAGGATAATAAGGTAATAGGTAATAAGGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:32527:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 ATCCTATTATCCTATTACCCCATTACCCTATTACCTTATCACCATATTACCAATTACCTTATTACCCTATTATCTTATTACCTTAATACCTATTACCTATTTTCATATTACTCTATTACCCCATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:49108:1070_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TATTTAAATTCATCATAATTTTTTAAAAAAAATATCAATTTTTTTATATTTATTCAATTTATTATTTTTTTAATATACAAATAAAATTTTTTATTAAATATATTAATACATAATTTAAATTTAAA 9IIIIIII999III9IIIIII9II9IIIIIII9IIIIII9IIIIII--9II99I-I9-9--9I--99IIII-I-I99II9--9999--999-99I99-9-9I99---9-99-999--9-999-9- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49108:1070_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 AAATTTTTATGAATATTAATATAATAAAAAATAATATTTTTGTGTTTATTTTATTGTTAAATATATTTGTGTTAAAAATATTTTATAATATAATATTTGAAATATTTGTTAATTTTTTTTTTAAA IIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9II9IIIII-III9II-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D8_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: LH00526:197:22KFKVLT4:3:1101:32576:1084_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TATGTATGTAGATTTTTTGAAGTAATAATTATTTTTTTAAAGAGAAGGATGAATTTAAGTTTGTTTAAAATTTTTTTAGAAATATTAAGTTATTTTGTTTTTATTATTTTTTTAGTTTATATATT 9-I9II-I9I9-I9IIII-IIIIIIIIIII-II9III9-IIIII-I9I9-IIIII99I--99-III-IIIIIIIII9999I-II-II-I99-II-I--999-999-999--I9--9---9999-9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:32576:1084_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 CACACACAAACATATAATATCCTCTATATATATTAAATAAACAACACAATAACTTAACTAACCCACATACCCATATATAAACATTATCATATTATATATACTAATTAAATAATAAAAACAAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9I9IIIIIIIIIIIIII9IIIIIIIIIIIII-IIIIII9I YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:27996:1084_1:N:0:CTTACAGC+CTTCACCA/1 83 ptg000004l_GA_converted 12292493 42 125M = 12292392 -226 TAAATCTATCATAACCTTTTAAACTACATTCATTTATAATCAAAATAACATCAAACTTTATCTAATTATCCATATCATATAATACCCCCTTAAACCTAAAAACTTTATCTAATACTATCTTAATT 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 LH00526:197:22KFKVLT4:3:1101:27996:1084_2:N:0:CTTACAGC+CTTCACCA/2 163 ptg000004l_GA_converted 12292392 42 125M = 12292493 226 ATTAAAATATAACATTCACATTTAAATAATATAAAAATTCCTAAAACAAAACATTTTATTCCCAAAAAATTTAAATTAAATACAACATTAAATTAACCAATTAAATCTATCATAACCTTTTAAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:44997:1070_1:N:0:CTTACAGC+CTTCACCA/1 83 ptg000019l_GA_converted 2931611 40 125M = 2931316 -420 AAATACATTCAACAACTATCAAATTTTACCATATTCACACAAAATCCACAAAAAATATACTATTACAATAATACAAAACAACATATAAATATACTTAAAAATTCATAAATACACAATTAAAAACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:33C69T21 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44997:1070_2:N:0:CTTACAGC+CTTCACCA/2 163 ptg000019l_GA_converted 2931316 40 125M = 2931611 420 TTCTAAAAATAACCAAAAATAACAATAAACATACAAATTACAATACTACTAACAAACATATCAAAAAATAAATATATATAATCCACCCCACCCCAAAAAATATAAAAACACATTATCATAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9III9I-I-I9I-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:43A4A25C6C30A12 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:49108:1070_1:N:0:CTTACAGC+CTTCACCA/1 77 * 0 0 * * 0 0 TATTTAAATTCATCATAATTTTTTAAAAAAAATATCAATTTTTTTATATTTATTCAATTTATTATTTTTTTAATATACAAATAAAATTTTTTATTAAATATATTAATACATAATTTAAATTTAAA 9IIIIIII999III9IIIIII9II9IIIIIII9IIIIII9IIIIII--9II99I-I9-9--9I--99IIII-I-I99II9--9999--999-99I99-9-9I99---9-99-999--9-999-9- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49108:1070_2:N:0:CTTACAGC+CTTCACCA/2 141 * 0 0 * * 0 0 AAATTTTTATGAATATTAATATAATAAAAAATAATATTTTTGTGTTTATTTTATTGTTAAATATATTTGTGTTAAAAATATTTTATAATATAATATTTGAAATATTTGTTAATTTTTTTTTTAAA IIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9II9IIIII-III9II-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D8_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)) Reading in the sequence files 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:49108:1070_1:N:0:CTTACAGC+CTTCACCA/1 83 ptg000008l_GA_converted 15401753 1 125M = 15401634 -244 CTTAAATTTAAACCACATATCAATATACTCAACAAAAAATCCCACTTATATATCAAAAAAATAATAAACCAAATAAATATAAAAAAATCAATACCCTTTCTAAAAAACCACAACAAATTCAAACA -9-999-9--999-99-9---99I9-9-99I99-999--9999--9II99I-I-IIII99--I9--9-9I-I99II9--IIIIII9IIIIII9IIIIIII9II9IIIIII9III999IIIIIII9 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:70T54 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49108:1070_2:N:0:CTTACAGC+CTTCACCA/2 163 ptg000008l_GA_converted 15401634 1 125M = 15401753 244 AAATTCTTACAAATATTAACATAATAAAAAACAATATTTTCACATTCATTCCATCATCAAACATATTCACATTAAAAATATCCTATAATACAATATTCAAAATACCCACTAACTTCTTCCTTAAA IIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9II9IIIII-III9II-IIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1208:24241:25962_1:N:0:CTTACAGC+CTTCACCA ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1262:11811:23328_1:N:0:CTTACAGC+CTTCACCA ptg000006l 3 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1306:41502:12220_1:N:0:CTTACAGC+CTTCACCA ptg000025l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1387:13826:16619_1:N:0:CTTACAGC+CTTCACCA ptg000057l 39949 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1409:11690:12584_1:N:0:CTTACAGC+CTTCACCA ptg000066l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1434:44480:22614_1:N:0:CTTACAGC+CTTCACCA ptg000080l 40111 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2215:22800:25962_1:N:0:CTTACAGC+CTTCACCA ptg000174l 27225 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2480:27575:15820_1:N:0:CTTACAGC+CTTCACCA ptg000065l 49673 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 LH00526:197:22KFKVLT4:4:1183:25965:28441_1:N:0:CTTACAGC+CTTCACCA ptg000160l 32573 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1364:44844:6799_1:N:0:CTTACAGC+CTTCACCA ntLink_0 96467 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1414:3363:28960_1:N:0:CTTACAGC+CTTCACCA ptg000077l 42471 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 LH00526:197:22KFKVLT4:4:2221:22485:19616_1:N:0:CTTACAGC+CTTCACCA ptg000015l 14997092 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 7000000 sequence pairs so far 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8000605 (99.77%) aligned concordantly 0 times 6550 (0.08%) aligned concordantly exactly 1 time 11549 (0.14%) aligned concordantly >1 times 0.23% overall alignment rate Processed 8000000 sequence pairs so far 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8001913 (99.79%) aligned concordantly 0 times 6470 (0.08%) aligned concordantly exactly 1 time 10321 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3647296 (45.48%) aligned concordantly 0 times 1660695 (20.71%) aligned concordantly exactly 1 time 2710713 (33.80%) aligned concordantly >1 times 54.52% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3641377 (45.41%) aligned concordantly 0 times 1663545 (20.75%) aligned concordantly exactly 1 time 2713782 (33.84%) aligned concordantly >1 times 54.59% overall alignment rate Processed 8018704 sequences in total Successfully deleted the temporary files 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8018704 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215558824 Total methylated C's in CpG context: 3663199 Total methylated C's in CHG context: 196755 Total methylated C's in CHH context: 853863 Total methylated C's in Unknown context: 6348 Total unmethylated C's in CpG context: 29577742 Total unmethylated C's in CHG context: 36290342 Total unmethylated C's in CHH context: 144976923 Total unmethylated C's in Unknown context: 316327 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2370:41243:12472_1:N:0:CTTACAGC+CTTCACCA ptg000039l 2 8018705 reads; of these: 8018705 (100.00%) were paired; of these: 8002092 (99.79%) aligned concordantly 0 times 6399 (0.08%) aligned concordantly exactly 1 time 10214 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 8018705 reads; of these: 8018705 (100.00%) were paired; of these: 3646932 (45.48%) aligned concordantly 0 times 1663466 (20.74%) aligned concordantly exactly 1 time 2708307 (33.77%) aligned concordantly >1 times 54.52% overall alignment rate 8018705 reads; of these: 8018705 (100.00%) were paired; of these: 3644859 (45.45%) aligned concordantly 0 times 1660880 (20.71%) aligned concordantly exactly 1 time 2712966 (33.83%) aligned concordantly >1 times 54.55% overall alignment rate 8018705 reads; of these: 8018705 (100.00%) were paired; of these: 8000826 (99.78%) aligned concordantly 0 times 6514 (0.08%) aligned concordantly exactly 1 time 11365 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate Processed 8018705 sequences in total Successfully deleted the temporary files 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8018705 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215516007 Total methylated C's in CpG context: 3645752 Total methylated C's in CHG context: 194534 Total methylated C's in CHH context: 844731 Total methylated C's in Unknown context: 6349 Total unmethylated C's in CpG context: 29612842 Total unmethylated C's in CHG context: 36307256 Total unmethylated C's in CHH context: 144910892 Total unmethylated C's in Unknown context: 315269 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2380:24079:3185_1:N:0:CTTACAGC+CTTCACCA ptg000046l 39578 Processed 8000000 sequence pairs so far 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3648950 (45.51%) aligned concordantly 0 times 1662944 (20.74%) aligned concordantly exactly 1 time 2706810 (33.76%) aligned concordantly >1 times 54.49% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8002047 (99.79%) aligned concordantly 0 times 6552 (0.08%) aligned concordantly exactly 1 time 10105 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3645189 (45.46%) aligned concordantly 0 times 1662224 (20.73%) aligned concordantly exactly 1 time 2711291 (33.81%) aligned concordantly >1 times 54.54% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8000945 (99.78%) aligned concordantly 0 times 6490 (0.08%) aligned concordantly exactly 1 time 11269 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate Processed 8018704 sequences in total Successfully deleted the temporary files 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8018704 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215404709 Total methylated C's in CpG context: 3647474 Total methylated C's in CHG context: 195655 Total methylated C's in CHH context: 841146 Total methylated C's in Unknown context: 6086 Total unmethylated C's in CpG context: 29582556 Total unmethylated C's in CHG context: 36269888 Total unmethylated C's in CHH context: 144867990 Total unmethylated C's in Unknown context: 315807 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8000855 (99.78%) aligned concordantly 0 times 6507 (0.08%) aligned concordantly exactly 1 time 11342 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate Processed 8000000 sequence pairs so far 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8001987 (99.79%) aligned concordantly 0 times 6574 (0.08%) aligned concordantly exactly 1 time 10143 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3649149 (45.51%) aligned concordantly 0 times 1661720 (20.72%) aligned concordantly exactly 1 time 2707835 (33.77%) aligned concordantly >1 times 54.49% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3641400 (45.41%) aligned concordantly 0 times 1664711 (20.76%) aligned concordantly exactly 1 time 2712593 (33.83%) aligned concordantly >1 times 54.59% overall alignment rate Processed 8018704 sequences in total Successfully deleted the temporary files 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8018704 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215603344 Total methylated C's in CpG context: 3651896 Total methylated C's in CHG context: 196383 Total methylated C's in CHH context: 850429 Total methylated C's in Unknown context: 6218 Total unmethylated C's in CpG context: 29621436 Total unmethylated C's in CHG context: 36304350 Total unmethylated C's in CHH context: 144978850 Total unmethylated C's in Unknown context: 316333 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% 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 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8000677 (99.78%) aligned concordantly 0 times 6559 (0.08%) aligned concordantly exactly 1 time 11468 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate Processed 8000000 sequence pairs so far 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3644000 (45.44%) aligned concordantly 0 times 1661971 (20.73%) aligned concordantly exactly 1 time 2712733 (33.83%) aligned concordantly >1 times 54.56% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 3645975 (45.47%) aligned concordantly 0 times 1664788 (20.76%) aligned concordantly exactly 1 time 2707941 (33.77%) aligned concordantly >1 times 54.53% overall alignment rate 8018704 reads; of these: 8018704 (100.00%) were paired; of these: 8002120 (99.79%) aligned concordantly 0 times 6502 (0.08%) aligned concordantly exactly 1 time 10082 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate Processed 8018704 sequences in total Successfully deleted the temporary files 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D8_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8018704 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215546258 Total methylated C's in CpG context: 3653380 Total methylated C's in CHG context: 195453 Total methylated C's in CHH context: 848000 Total methylated C's in Unknown context: 6211 Total unmethylated C's in CpG context: 29584694 Total unmethylated C's in CHG context: 36314414 Total unmethylated C's in CHH context: 144950317 Total unmethylated C's in Unknown context: 317164 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% 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 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1D8_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1D8_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1D8_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/1D8_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1D8_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/1D8_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D8_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: 40093521 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1077629142 Total methylated C's in CpG context: 18261701 Total methylated C's in CHG context: 978780 Total methylated C's in CHH context: 4238169 Total methylated C's in Unknown context: 31212 Total unmethylated C's in CpG context: 147979270 Total unmethylated C's in CHG context: 181486250 Total unmethylated C's in CHH context: 724684972 Total unmethylated C's in Unknown context: 1580900 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% 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 4h 53m 55s ==================== Bismark run complete ====================