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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_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/10--1E7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_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/10--1E7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_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/10--1E7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_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/10--1E7_R1_001.fastp-trim.fq.gz for PID: 7795 and offset 5 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_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/10--1E7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz to 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz to 10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz to 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz to 10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz to 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz to 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/10--1E7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz to 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz to 10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz for PID: 7795 and offset 5 (sequences written out: 7850998) Using the subset file >10--1E7_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/10--1E7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz to 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz to 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz (7850998 sequences in total) Writing a C -> T converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz to 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz to 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz (7850998 sequences in total) Writing a C -> T converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz to 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz to 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz (7850998 sequences in total) Writing a C -> T converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz to 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz to 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz (7850998 sequences in total) Writing a C -> T converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz to 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz to 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz (7850998 sequences in total) Writing a C -> T converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz to 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz to 10--1E7_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 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz (7850998 sequences in total) Input files are 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz (7850998 sequences in total) Input files are 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:29970:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 99 ptg000001l_CT_converted 9316242 11 125M = 9316404 287 AAATAAAATATTGTGATTATTTTTTATTGTTATAATAATATATGTTAAATAATTAAATTTTTTATTTTGTTTGTTTTTGAATGATTTTAAGTTGATTTTATAATTTTTTATTAATTTTTTGTTTA III-9III-III-9I----9IIIII-IIIII9I-II9I----II9III9III99II9-III9I-99I99III9IIIII9II-I9-I9III9-I9I9III99-I9I9-II99III-I9I9I99II- AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:62G43A15A2 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:29970:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 147 ptg000001l_CT_converted 9316404 11 125M = 9316242 -287 TTAGTTGTTTAGAGTGAGAATATGTAAATTATGATTGGTTGATTTAAATTGTATTTTTTATAATATATTGATTATTAGGTTGTGATTTATTTTTTTTTATTTAATTTTTAAATTTTATATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-58 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:48A17G14T43 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:28465:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 ATATTAAGTGGTGTTATTTATGATGTTATGTAGAAATGATGTTATGAAAATTGTTTTAAATGTTGAATTTGAATAATGTTATTAGATAATGTAAATAATAAAAAATATATATATAAAAAGTATTA IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28465:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 ATCAATTATAAAACATATAATAATACTCAATATATTATAAAAATTTTATACACCTACCATACATATTTAACAAACCATTTCTTCTAATTAAAAATCAAATAACACTAAACCTACTACATTTCACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9II-IIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:28465:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 ATATTAAATAATATTATTTATAATATTATATAAAAATAATATTATAAAAATTATTTTAAATATTAAATTTAAATAATATTATTAAATAATATAAATAATAAAAAATATATATATAAAAAATATTA IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28465:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 ATTAATTATAAAATATATAATAATATTTAATATATTATAAAAATTTTATATATTTATTATATATATTTAATAAATTATTTTTTTTAATTAAAAATTAAATAATATTAAATTTATTATATTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9II-IIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:29970:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AAACAAAATATTATAATCATTTTTTATTATTATAATAATATATATTAAATAATTAAATTTTTTATTTTATTTATTTTTAAATAATTTTAAATTAATTTTATAATTTCTTATTAATTTTTTATTTA III-9III-III-9I----9IIIII-IIIII9I-II9I----II9III9III99II9-III9I-99I99III9IIIII9II-I9-I9III9-I9I9III99-I9I9-II99III-I9I9I99II- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29970:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 AAAAAATATAAAATTTAAAAATTAAATAAAAAAAAATAAATTATAATTTAATAATTAATATATTATAAAAAATATAATTTAAATTAATTAATTATAATTTATATATTTTTATTTTAAATAATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIII-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:28465:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 ATATTAAATAATATTATTTATAATATTATATAAAAATAATATTATAAAAATTATTTTAAATATTAAATTTAAATAATATTATTAAATAATATAAATAATAAAAAATATATATATAAAAAATATTA IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28465:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 ATTAATTATAAAATATATAATAATATTTAATATATTATAAAAATTTTATATATTTATTATATATATTTAATAAATTATTTTTTTTAATTAAAAATTAAATAATATTAAATTTATTATATTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9II-IIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:29970:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AAACAAAATATTATAATCATTTTTTATTATTATAATAATATATATTAAATAATTAAATTTTTTATTTTATTTATTTTTAAATAATTTTAAATTAATTTTATAATTTCTTATTAATTTTTTATTTA III-9III-III-9I----9IIIII-IIIII9I-II9I----II9III9III99II9-III9I-99I99III9IIIII9II-I9-I9III9-I9I9III99-I9I9-II99III-I9I9I99II- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29970:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 AAAAAATATAAAATTTAAAAATTAAATAAAAAAAAATAAATTATAATTTAATAATTAATATATTATAAAAAATATAATTTAAATTAATTAATTATAATTTATATATTTTTATTTTAAATAATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIII-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:28465:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 ATATTAAGTGGTGTTATTTATGATGTTATGTAGAAATGATGTTATGAAAATTGTTTTAAATGTTGAATTTGAATAATGTTATTAGATAATGTAAATAATAAAAAATATATATATAAAAAGTATTA IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28465:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 ATCAATTATAAAACATATAATAATACTCAATATATTATAAAAATTTTATACACCTACCATACATATTTAACAAACCATTTCTTCTAATTAAAAATCAAATAACACTAAACCTACTACATTTCACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9II-IIIIII9IIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:29970:1084_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AAATAAAATATTGTGATTATTTTTTATTGTTATAATAATATATGTTAAATAATTAAATTTTTTATTTTGTTTGTTTTTGAATGATTTTAAGTTGATTTTATAATTTTTTATTAATTTTTTGTTTA III-9III-III-9I----9IIIII-IIIII9I-II9I----II9III9III99II9-III9I-99I99III9IIIII9II-I9-I9III9-I9I9III99-I9I9-II99III-I9I9I99II- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29970:1084_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 AAAAAATATAAAATTTAAAAATTAAATAAAAAAAAATAAATCACAACCTAATAATCAATATATTATAAAAAATACAATTTAAATCAACCAATCATAATTTACATATTCTCACTCTAAACAACTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIII-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz Created C -> T as well as G -> A converted versions of the FastQ file 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz (7850998 sequences in total) Input files are 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 10--1E7_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)) Created C -> T as well as G -> A converted versions of the FastQ file 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz (7850998 sequences in total) Input files are 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:50371:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 99 ptg000008l_CT_converted 30607700 1 61M5I26M = 30607873 265 GGTAAAGTATAAAGTAATGAGGGGGTTTATAAAAGTTGGTGATATTGGTGAATTTAGTAAATAAATTATGGTGAAAATGATAATATTGTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-20 XS:i:-32 XN:i:0 XM:i:0 XO:i:1 XG:i:5 NM:i:5 MD:Z:87 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50371:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 147 ptg000008l_CT_converted 30607873 1 92M = 30607700 -265 ATAATATTGTTAGAATTGTTAATAAGGTAAAGTATAAAGTAATGAGGGGGTTTATAAAAGTTGGTGATATTGGTGAATTTGGTAAATATGGT IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:12T67A11 YS:i:-20 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:48364:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 99 ptg000047l_CT_converted 5258090 1 112M = 5258425 447 AAAATTAAAAATGTTAAAAATATGTAAAAAATTATTTTATAGGATTATTAGAGTTATTTTGTGTAAAAAATTGTGTGAGAAAATATTAAATATTTGAGAAATGAGATGATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:25G29G56 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:48364:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 147 ptg000047l_CT_converted 5258425 1 112M = 5258090 -447 TATGTAAAATGGTTAGTTTTGGTTTAAAATTAAAAATGTTAAAAATATGTGAAAAATTATTTTTAAGGATTATTAGAGTAGTTTTGTGTAAAAAATTGTGTGAGAAAATATT IIIIIIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:24G38A0T14T32 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:50371:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AATAAAATATAAAATAATAAAAAAATTTATAAAAATTAATAATATTAATAAATTTAATAAATAAATTATAATAAAAATAATAATATTATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50371:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 ATTATATTTATTAAATTTATTAATATTATTAATTTTTATAAATTTTTTTATTATTTTATATTTTATTTTATTAATAATTTTAATAATATTAT IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:48364:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AAAATTAAAAATATTAAAAATATATAAAAAATTATTTTATAAAATTATTAAAATTATTTTATATAAAAAATTATATAAAAAAATATTAAATATTTAAAAAATAAAATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48364:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 AATATTTTTTTATATAATTTTTTATATAAAATTATTTTAATAATTTTTAAAAATAATTTTTTATATATTTTTAATATTTTTAATTTTAAATTAAAATTAATTATTTTATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:48364:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AAAATTAAAAATATTAAAAATATATAAAAAATTATTTTATAAAATTATTAAAATTATTTTATATAAAAAATTATATAAAAAAATATTAAATATTTAAAAAATAAAATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48364:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 AATATTTTTTTATATAATTTTTTATATAAAATTATTTTAATAATTTTTAAAAATAATTTTTTATATATTTTTAATATTTTTAATTTTAAATTAAAATTAATTATTTTATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:50371:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AATAAAATATAAAATAATAAAAAAATTTATAAAAATTAATAATATTAATAAATTTAATAAATAAATTATAATAAAAATAATAATATTATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50371:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 ATTATATTTATTAAATTTATTAATATTATTAATTTTTATAAATTTTTTTATTATTTTATATTTTATTTTATTAATAATTTTAATAATATTAT IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:48364:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 83 ptg000047l_GA_converted 4542088 1 112M = 4541942 -258 AAATCATCTCATTTCTCAAATATTTAATATTTTCTCACACAATTTTTTACACAAAATAACTCTAATAATCCTATAAAATAATTTTTTACATATTTTTAACATTTTTAATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:56C29C25 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:48364:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 163 ptg000047l_GA_converted 4541942 1 112M = 4542088 258 AATATTTTCTCACACAATTTTTTACACAAAACTACTCTAATAATCCTTAAAAATAATTTTTCACATATTTTTAACATTTTTAATTTTAAACCAAAACTAACCATTTTACATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:32A14A0T38T24 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:50371:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 83 ptg000008l_GA_converted 13512198 6 24M5I63M = 13512218 112 CTAACAATATTATCATTTTCACCATAATTTATTTACTAAATTCACCAATATCACCAACTTTTATAAACCCCCTCATTACTTTATACTTTACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-26 XS:i:-32 XN:i:0 XM:i:1 XO:i:1 XG:i:5 NM:i:6 MD:Z:31C55 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50371:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 163 ptg000008l_GA_converted 13512218 6 92M = 13512198 -112 ACCATATTTACCAAATTCACCAATATCACCAACTTTTATAAACCCCCTCATTACTTTATACTTTACCTTATTAACAATTCTAACAATATTAT IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:92 YS:i:-26 YT:Z:CP >>> Writing bisulfite mapping results to 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz (7850998 sequences in total) Input files are 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 10--1E7_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 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:39624:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 99 ptg000008l_CT_converted 21054450 42 125M = 21054648 323 GATAATAGGTTATATTTGATATATATTGGTAATAATAGAGTAAAAGATATATTTTTTATTTTTTGGGTTTTGTATATTTTAGGTTTAGTTTAGTTTTTATTTAAGTAAGTATGTAATGAAGGAAT IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII99IIII9III9IIIII-II-IIII-II AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:108T4G7A3 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39624:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 147 ptg000008l_CT_converted 21054648 42 125M = 21054450 -323 TGGAATAGAGGATATTGATTTTTTAGTGGTTAAGTTTATAGAAGTTGAGGATAAGAATTTTGTATTTTTGAATTATGTTAATGAATTTAATAATGAAATTGAGTTGTTGTAAGAATAAATAAATG IIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIII9IIIII9II-IIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:69T55 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:39624:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AATAATAAATTATATTTAATATATATTAATAATAATAAAATAAAAAATATATTTTTTATTTTTTAAATTTTATATATTTTAAATTTAATTTAATTTTTATTTAAATAAATATATAATAAAAAAAT IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII99IIII9III9IIIII-II-IIII-II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39624:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 TATTTATTTATTTTTATAATAATTTAATTTTATTATTAAATTTATTAATATAATTTAAAAATATAAAATTTTTATTTTTAATTTTTATAAATTTAATTATTAAAAAATTAATATTTTTTATTTTA IIIIIIIIIIIIIIIII-II9IIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:39624:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 AATAATAAATTATATTTAATATATATTAATAATAATAAAATAAAAAATATATTTTTTATTTTTTAAATTTTATATATTTTAAATTTAATTTAATTTTTATTTAAATAAATATATAATAAAAAAAT IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII99IIII9III9IIIII-II-IIII-II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39624:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 TATTTATTTATTTTTATAATAATTTAATTTTATTATTAAATTTATTAATATAATTTAAAAATATAAAATTTTTATTTTTAATTTTTATAAATTTAATTATTAAAAAATTAATATTTTTTATTTTA IIIIIIIIIIIIIIIII-II9IIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 10--1E7_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: LH00526:197:22KFKVLT4:3:1101:39624:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 GATAATAGGTTATATTTGATATATATTGGTAATAATAGAGTAAAAGATATATTTTTTATTTTTTGGGTTTTGTATATTTTAGGTTTAGTTTAGTTTTTATTTAAGTAAGTATGTAATGAAGGAAT IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII99IIII9III9IIIII-II-IIII-II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39624:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 CATTTATTTATTCTTACAACAACTCAATTTCATTATTAAATTCATTAACATAATTCAAAAATACAAAATTCTTATCCTCAACTTCTATAAACTTAACCACTAAAAAATCAATATCCTCTATTCCA IIIIIIIIIIIIIIIII-II9IIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1154:22388:10875_1:N:0:GCCTTAAC+AGCTCCTA ntLink_0 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1201:42432:5679_1:N:0:GCCTTAAC+AGCTCCTA ptg000082l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1206:32940:27461_1:N:0:GCCTTAAC+AGCTCCTA ptg000130l 35798 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 LH00526:197:22KFKVLT4:3:1368:45046:14461_1:N:0:GCCTTAAC+AGCTCCTA ntLink_7 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1376:35141:7037_1:N:0:GCCTTAAC+AGCTCCTA ptg000159l 21831 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2147:42756:12262_1:N:0:GCCTTAAC+AGCTCCTA ptg000096l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2251:4925:11520_1:N:0:GCCTTAAC+AGCTCCTA ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2160:25956:27307_1:N:0:GCCTTAAC+AGCTCCTA ptg000113l 59560 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2160:25965:27321_1:N:0:GCCTTAAC+AGCTCCTA ptg000113l 59560 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2251:4917:11534_1:N:0:GCCTTAAC+AGCTCCTA ptg000066l 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2304:47433:27223_1:N:0:GCCTTAAC+AGCTCCTA ntLink_4 1 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2378:20300:3844_1:N:0:GCCTTAAC+AGCTCCTA ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2283:41785:29100_1:N:0:GCCTTAAC+AGCTCCTA ptg000132l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2304:47449:27223_1:N:0:GCCTTAAC+AGCTCCTA ntLink_4 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2364:2416:24883_1:N:0:GCCTTAAC+AGCTCCTA ptg000029c 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2483:19944:3479_1:N:0:GCCTTAAC+AGCTCCTA ptg000021l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2483:3363:9433_1:N:0:GCCTTAAC+AGCTCCTA ptg000031l 15849141 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2493:34267:27517_1:N:0:GCCTTAAC+AGCTCCTA ptg000025l 1 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 LH00526:197:22KFKVLT4:4:1111:25082:25990_1:N:0:GCCTTAAC+AGCTCCTA ptg000155l 36785 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1165:40191:12921_1:N:0:GCCTTAAC+AGCTCCTA ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1165:40183:12935_1:N:0:GCCTTAAC+AGCTCCTA ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1155:13138:16100_1:N:0:GCCTTAAC+AGCTCCTA ptg000106l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1340:32123:16353_1:N:0:GCCTTAAC+AGCTCCTA ptg000025l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1448:32009:7360_1:N:0:GCCTTAAC+AGCTCCTA ptg000057l 39948 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1450:9918:24141_1:N:0:GCCTTAAC+AGCTCCTA ptg000115l 42041 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2176:45677:4600_1:N:0:GCCTTAAC+AGCTCCTA ptg000060c 88492 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1420:50524:27111_1:N:0:GCCTTAAC+AGCTCCTA ptg000126l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2280:9901:19434_1:N:0:GCCTTAAC+AGCTCCTA ptg000002l 2 Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2297:21320:27685_1:N:0:GCCTTAAC+AGCTCCTA ptg000083l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2107:38184:27181_1:N:0:GCCTTAAC+AGCTCCTA ptg000082l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2118:27413:15932_1:N:0:GCCTTAAC+AGCTCCTA ptg000093l 36765 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2258:50897:13159_1:N:0:GCCTTAAC+AGCTCCTA ptg000009l 19095996 Processed 7000000 sequence pairs so far 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7830439 (99.74%) aligned concordantly 0 times 6385 (0.08%) aligned concordantly exactly 1 time 14174 (0.18%) aligned concordantly >1 times 0.26% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3547290 (45.18%) aligned concordantly 0 times 1639656 (20.88%) aligned concordantly exactly 1 time 2664052 (33.93%) aligned concordantly >1 times 54.82% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7833781 (99.78%) aligned concordantly 0 times 6483 (0.08%) aligned concordantly exactly 1 time 10734 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3550451 (45.22%) aligned concordantly 0 times 1638564 (20.87%) aligned concordantly exactly 1 time 2661983 (33.91%) aligned concordantly >1 times 54.78% overall alignment rate Processed 7850998 sequences in total Successfully deleted the temporary files 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7850998 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213920744 Total methylated C's in CpG context: 4114000 Total methylated C's in CHG context: 205968 Total methylated C's in CHH context: 929841 Total methylated C's in Unknown context: 6911 Total unmethylated C's in CpG context: 28741039 Total unmethylated C's in CHG context: 35842971 Total unmethylated C's in CHH context: 144086925 Total unmethylated C's in Unknown context: 300974 C methylated in CpG context: 12.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.2% Now waiting for all child processes to complete 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7830399 (99.74%) aligned concordantly 0 times 6467 (0.08%) aligned concordantly exactly 1 time 14132 (0.18%) aligned concordantly >1 times 0.26% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3546433 (45.17%) aligned concordantly 0 times 1638577 (20.87%) aligned concordantly exactly 1 time 2665988 (33.96%) aligned concordantly >1 times 54.83% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7833948 (99.78%) aligned concordantly 0 times 6321 (0.08%) aligned concordantly exactly 1 time 10729 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3553184 (45.26%) aligned concordantly 0 times 1637405 (20.86%) aligned concordantly exactly 1 time 2660409 (33.89%) aligned concordantly >1 times 54.74% overall alignment rate Processed 7850998 sequences in total Successfully deleted the temporary files 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7850998 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213859422 Total methylated C's in CpG context: 4111930 Total methylated C's in CHG context: 204444 Total methylated C's in CHH context: 926607 Total methylated C's in Unknown context: 7088 Total unmethylated C's in CpG context: 28732102 Total unmethylated C's in CHG context: 35826213 Total unmethylated C's in CHH context: 144058126 Total unmethylated C's in Unknown context: 301580 C methylated in CpG context: 12.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% Processed 7000000 sequence pairs so far 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7830523 (99.74%) aligned concordantly 0 times 6432 (0.08%) aligned concordantly exactly 1 time 14043 (0.18%) aligned concordantly >1 times 0.26% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7833851 (99.78%) aligned concordantly 0 times 6521 (0.08%) aligned concordantly exactly 1 time 10626 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3547146 (45.18%) aligned concordantly 0 times 1637906 (20.86%) aligned concordantly exactly 1 time 2665946 (33.96%) aligned concordantly >1 times 54.82% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3551348 (45.23%) aligned concordantly 0 times 1638651 (20.87%) aligned concordantly exactly 1 time 2660999 (33.89%) aligned concordantly >1 times 54.77% overall alignment rate Processed 7850998 sequences in total Successfully deleted the temporary files 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7850998 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213840318 Total methylated C's in CpG context: 4105511 Total methylated C's in CHG context: 205669 Total methylated C's in CHH context: 928802 Total methylated C's in Unknown context: 6980 Total unmethylated C's in CpG context: 28742923 Total unmethylated C's in CHG context: 35828219 Total unmethylated C's in CHH context: 144029194 Total unmethylated C's in Unknown context: 301930 C methylated in CpG context: 12.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7833957 (99.78%) aligned concordantly 0 times 6386 (0.08%) aligned concordantly exactly 1 time 10655 (0.14%) aligned concordantly >1 times 0.22% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7830374 (99.74%) aligned concordantly 0 times 6545 (0.08%) aligned concordantly exactly 1 time 14079 (0.18%) aligned concordantly >1 times 0.26% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3546223 (45.17%) aligned concordantly 0 times 1638278 (20.87%) aligned concordantly exactly 1 time 2666497 (33.96%) aligned concordantly >1 times 54.83% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3552887 (45.25%) aligned concordantly 0 times 1635777 (20.84%) aligned concordantly exactly 1 time 2662334 (33.91%) aligned concordantly >1 times 54.75% overall alignment rate Processed 7850998 sequences in total Successfully deleted the temporary files 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7850998 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213759757 Total methylated C's in CpG context: 4112317 Total methylated C's in CHG context: 205560 Total methylated C's in CHH context: 927740 Total methylated C's in Unknown context: 7084 Total unmethylated C's in CpG context: 28724919 Total unmethylated C's in CHG context: 35804687 Total unmethylated C's in CHH context: 143984534 Total unmethylated C's in Unknown context: 300495 C methylated in CpG context: 12.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7830582 (99.74%) aligned concordantly 0 times 6458 (0.08%) aligned concordantly exactly 1 time 13958 (0.18%) aligned concordantly >1 times 0.26% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 7833946 (99.78%) aligned concordantly 0 times 6467 (0.08%) aligned concordantly exactly 1 time 10585 (0.13%) aligned concordantly >1 times 0.22% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3552367 (45.25%) aligned concordantly 0 times 1636808 (20.85%) aligned concordantly exactly 1 time 2661823 (33.90%) aligned concordantly >1 times 54.75% overall alignment rate 7850998 reads; of these: 7850998 (100.00%) were paired; of these: 3547222 (45.18%) aligned concordantly 0 times 1638196 (20.87%) aligned concordantly exactly 1 time 2665580 (33.95%) aligned concordantly >1 times 54.82% overall alignment rate Processed 7850998 sequences in total Successfully deleted the temporary files 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 10--1E7_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7850998 Final Cytosine Methylation Report ================================= Total number of C's analysed: 213813759 Total methylated C's in CpG context: 4115889 Total methylated C's in CHG context: 205863 Total methylated C's in CHH context: 926889 Total methylated C's in Unknown context: 7002 Total unmethylated C's in CpG context: 28721606 Total unmethylated C's in CHG context: 35817142 Total unmethylated C's in CHH context: 144026370 Total unmethylated C's in Unknown context: 302680 C methylated in CpG context: 12.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 10--1E7_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 10--1E7_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 10--1E7_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/10--1E7_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 10--1E7_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/10--1E7_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 10--1E7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 10--1E7_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: 39254990 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1069194000 Total methylated C's in CpG context: 20559647 Total methylated C's in CHG context: 1027504 Total methylated C's in CHH context: 4639879 Total methylated C's in Unknown context: 35065 Total unmethylated C's in CpG context: 143662589 Total unmethylated C's in CHG context: 179119232 Total unmethylated C's in CHH context: 720185149 Total unmethylated C's in Unknown context: 1507659 C methylated in CpG context: 12.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.3% Deleting temporary report files... Bismark completed in 0d 6h 37m 37s ==================== Bismark run complete ====================