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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_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/1G5_R1_001.fastp-trim.fq.gz for PID: 90890 and offset 5 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_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/1G5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_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/1G5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_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/1G5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_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/1G5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8535056) Using the subset file >1G5_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/1G5_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/1G5_R2_001.fastp-trim.fq.gz for PID: 90890 and offset 5 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1G5_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/1G5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1G5_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/1G5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1G5_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/1G5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8535056) Using the subset file >1G5_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/1G5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1G5_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/1G5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8535055) Using the subset file >1G5_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/1G5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1G5_R1_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 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz (8535055 sequences in total) Writing a C -> T converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz (8535055 sequences in total) Writing a C -> T converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz (8535055 sequences in total) Writing a C -> T converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz (8535056 sequences in total) Writing a C -> T converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz (8535055 sequences in total) Writing a C -> T converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1G5_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 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz (8535055 sequences in total) Input files are 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:29841:1084_1:N:0:CAACTCCA+ACGGATTC/1 99 ntLink_6_CT_converted 16946135 3 54M1D28M5D43M = 16946126 -140 GTAAAGAAATATTTAAAAATTATTTTTAATTTATATATGATTGTGATATGTGGGTTTTTATTAATTAGAGTGAATTTTTTTATTTAAATTTTGTTTAGTTATTTTGTGTTGTAAGTTTATTTATG IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-52 XN:i:0 XM:i:4 XO:i:2 XG:i:6 NM:i:10 MD:Z:5A27A10A9^T28^TTAAT42T0 YS:i:-46 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:29841:1084_2:N:0:CAACTCCA+ACGGATTC/2 147 ntLink_6_CT_converted 16946126 3 63M1D28M5D34M = 16946135 140 AAAGTTTGAGTAAAGAAATATTTAAAAATTATTTTTAATTTATATATGATTGTGATATGTGGGTTTTTATTAATTAGAGTGAATTTTTTTATTTAAATTTTGTTTAGTTATTTTGTGTTGTAAGT I9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-46 XN:i:0 XM:i:3 XO:i:2 XG:i:6 NM:i:9 MD:Z:14A27A10A9^T28^TTAAT34 YS:i:-52 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:29841:1084_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 ATAAAAAAATATTTAAAAATTATTTTTAATTTATATACAATCACAATATATAAATTTTTATTAATTAAAATAAATTTTTTTATTTAAATTTTATTTAATTATTTTATATTATAAATTTATTTATA IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29841:1084_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 ATTTATAATATAAAATAATTAAATAAAATTTAAATAAAAAAATTTATTTTAATTAATAAAAATTTATATATTGTGATTGTATATAAATTAAAAATAATTTTTAAATATTTTTTTATTTAAATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1G5_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz (8535055 sequences in total) Input files are 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45904:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 ATAATATAAATTTGTAAAATGAAATTATGTGGTGTAAGAGAAATAGAGTTTTTTAATTTTTGTTATAGATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45904:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 AACTCTATTTCTCTTACACCACATAATTTCATTTTACAAATTTATATTATTTTTACATAAAACAATTCTTCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:29841:1084_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 ATAAAAAAATATTTAAAAATTATTTTTAATTTATATACAATCACAATATATAAATTTTTATTAATTAAAATAAATTTTTTTATTTAAATTTTATTTAATTATTTTATATTATAAATTTATTTATA IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29841:1084_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 ATTTATAATATAAAATAATTAAATAAAATTTAAATAAAAAAATTTATTTTAATTAATAAAAATTTATATATTGTGATTGTATATAAATTAAAAATAATTTTTAAATATTTTTTTATTTAAATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:45904:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 ATAATATAAATTTATAAAATAAAATTATATAATATAAAAAAAATAAAATTTTTTAATTTTTATTATAAATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45904:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 AATTTTATTTTTTTTATATTATATAATTTTATTTTATAAATTTATATTATTTTTATATAAAATAATTTTTTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:29841:1084_1:N:0:CAACTCCA+ACGGATTC/1 83 ptg000020l_GA_converted 16218756 42 66M1D59M = 16218765 135 CATAAATAAACTTACAACACAAAATAACTAAACAAAATTTAAATAAAAAAATTCACTCTAATTAATAAAAACCCACATATCACAATCATATATAAATTAAAAATAATTTTTAAATATTTCTTTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:66^A53T5 YS:i:-14 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:29841:1084_2:N:0:CAACTCCA+ACGGATTC/2 163 ptg000020l_GA_converted 16218765 42 57M1D68M = 16218756 -135 ACTTACAACACAAAATAACTAAACAAAATTTAAATAAAAAAATTCACTCTAATTAATAAAAACCCACATATCACAATCATATATAAATTAAAAATAATTTTTAAATATTTCTTTACTCAAACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9I AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:57^A53T14 YS:i:-14 YT:Z:CP >>> Writing bisulfite mapping results to 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Created C -> T as well as G -> A converted versions of the FastQ file 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz (8535056 sequences in total) Input files are 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:45904:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 ATAATATAAATTTATAAAATAAAATTATATAATATAAAAAAAATAAAATTTTTTAATTTTTATTATAAATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45904:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 AATTTTATTTTTTTTATATTATATAATTTTATTTTATAAATTTATATTATTTTTATATAAAATAATTTTTTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz (8535055 sequences in total) Input files are 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:44124:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTGAGGTTGGATTTGTTATGTTGTTGTTATTTGGTTTTTTTTTTTTTTTTTTTGAAAAGGAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99-III-9III-9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44124:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 AAAAAACCAAACAACAACAACATAACAAATCCAACCTCAAATCCAAATTCTCTCTCTTTTCCTTC 9IIIII9IIII-IIIIIII99I-I99III9IIIIIIIIIII-IIIII9I-I-9II-IIII9-I9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:45904:1070_1:N:0:CAACTCCA+ACGGATTC/1 83 ptg000027l_GA_converted 14455206 42 75M = 14455231 100 AAAAAATCTATAACAAAAATTAAAAAACTCTATTTCTCTTACACCACATAATTTCATTTTACAAATTTATATTAT IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45904:1070_2:N:0:CAACTCCA+ACGGATTC/2 163 ptg000027l_GA_converted 14455231 42 75M = 14455206 -100 AACTCTATTTCTCTTACACCACATAATTTCATTTTACAAATTTATATTATTTTTACATAAAACAATTCTTCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:39414:1070_1:N:0:CAACTCCA+ACGGATTC/1 99 ptg000017l_CT_converted 1723 6 125M = 1729 131 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAATTTTAAATTTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIII99IIIII9II9IIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:104A20 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39414:1070_2:N:0:CAACTCCA+ACGGATTC/2 147 ptg000017l_CT_converted 1729 6 125M = 1723 -131 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAATTTTAAATTTTAATTTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-16 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:98A26 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:44124:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTAAAATTAAATTTATTATATTATTATTATTTAATTTTTTTTTTTTTTTTTTTAAAAAAAAAACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99-III-9III-9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44124:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 AAAAAATTAAATAATAATAATATAATAAATTTAATTTTAAATTTAAATTTTTTTTTTTTTTTTTT 9IIIII9IIII-IIIIIII99I-I99III9IIIIIIIIIII-IIIII9I-I-9II-IIII9-I9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1G5_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)) Reading in the sequence files 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:39414:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAATTTTAAATTTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIII99IIIII9II9IIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39414:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 ATTAAAATTAAAATTTAAAATTAAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:44124:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTAAAATTAAATTTATTATATTATTATTATTTAATTTTTTTTTTTTTTTTTTTAAAAAAAAAACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99-III-9III-9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44124:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 AAAAAATTAAATAATAATAATATAATAAATTTAATTTTAAATTTAAATTTTTTTTTTTTTTTTTT 9IIIII9IIII-IIIIIII99I-I99III9IIIIIIIIIII-IIIII9I-I-9II-IIII9-I9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:39414:1070_1:N:0:CAACTCCA+ACGGATTC/1 83 ptg000008l_CT_converted 18178247 1 7M1I8M1I58M1I49M = 18178241 -128 ATTAAAATTTAAAATTAAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAAT IIIIIIIIIIII9II9IIIII99IIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-38 XN:i:0 XM:i:0 XO:i:3 XG:i:3 NM:i:3 MD:Z:122 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39414:1070_2:N:0:CAACTCCA+ACGGATTC/2 163 ptg000008l_CT_converted 18178241 1 13M1I8M1I58M1I43M = 18178247 128 ATTAAAATTAAAATTTAAAATTAAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-24 XN:i:0 XM:i:0 XO:i:3 XG:i:3 NM:i:3 MD:Z:122 YS:i:-24 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:44124:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTGAGGTTGGATTTGTTATGTTGTTGTTATTTGGTTTTTTTTTTTTTTTTTTTGAAAAGGAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99-III-9III-9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44124:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 AAAAAACCAAACAACAACAACATAACAAATCCAACCTCAAATCCAAATTCTCTCTCTTTTCCTTC 9IIIII9IIII-IIIIIII99I-I99III9IIIIIIIIIII-IIIII9I-I-9II-IIII9-I9I YT:Z:UP >>> Writing bisulfite mapping results to 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:39414:1070_1:N:0:CAACTCCA+ACGGATTC/1 83 ptg000010l_GA_converted 2424136 6 125M = 2424130 -131 ATTAAAATTTAAAATTAAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAAT IIIIIIIIIIII9II9IIIII99IIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:9A115 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39414:1070_2:N:0:CAACTCCA+ACGGATTC/2 163 ptg000010l_GA_converted 2424130 6 125M = 2424136 131 ATTAAAATTAAAATTTAAAATTAAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-14 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2C12A109 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz (8535055 sequences in total) Input files are 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G5_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 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:50759:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTGTTTGTTGTAGAGGGTTGAAATTGTAGGGTTTTGTTTTTTTTTATATTTGGTTTTGTTATTTTGGGTTTGTTTTTATGTTTGGGTATTTTTTTATTATATTTTTGTTTGAAGTATTTTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III-IIII-9-9---I-999999--999999-99-9---9----9-9999------99-9-----9-99-999-99--9--99----9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50759:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 ATATCTTCAATTCTAATACACACACCAATCTACTCCATAACAAAATACCAAAACAACACTACATATCTAAACCCAATTACTCTAAATTCTTTCTCTTATCCAACAACCTACACACATAATCAACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIII-I9IIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:50759:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTATTTATCATAAAAAATTAAAATTATAAAATTTTATTTTTTTTCATATTCAATTTTATTATTTTAAATTTATTTTTACATTTAAATACCTTTTCATTACATTTTTATTTAAAATACTTTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III-IIII-9-9---I-999999--999999-99-9---9----9-9999------99-9-----9-99-999-99--9--99----9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50759:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 ATATTTTTAATTTTAATATATATATTAATTTATTTTATAATAAAATATTAAAATAATATTATATATTTAAATTTAATTATTTTAAATTTTTTTTTTTATTTAATAATTTATATATATAATTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIII-I9IIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:50759:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTATTTATCATAAAAAATTAAAATTATAAAATTTTATTTTTTTTCATATTCAATTTTATTATTTTAAATTTATTTTTACATTTAAATACCTTTTCATTACATTTTTATTTAAAATACTTTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III-IIII-9-9---I-999999--999999-99-9---9----9-9999------99-9-----9-99-999-99--9--99----9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50759:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 ATATTTTTAATTTTAATATATATATTAATTTATTTTATAATAAAATATTAAAATAATATTATATATTTAAATTTAATTATTTTAAATTTTTTTTTTTATTTAATAATTTATATATATAATTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIII-I9IIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G5_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: LH00526:197:22KFKVLT4:3:1101:50759:1070_1:N:0:CAACTCCA+ACGGATTC/1 77 * 0 0 * * 0 0 TTGTTTGTTGTAGAGGGTTGAAATTGTAGGGTTTTGTTTTTTTTTATATTTGGTTTTGTTATTTTGGGTTTGTTTTTATGTTTGGGTATTTTTTTATTATATTTTTGTTTGAAGTATTTTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III-IIII-9-9---I-999999--999999-99-9---9----9-9999------99-9-----9-99-999-99--9--99----9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50759:1070_2:N:0:CAACTCCA+ACGGATTC/2 141 * 0 0 * * 0 0 ATATCTTCAATTCTAATACACACACCAATCTACTCCATAACAAAATACCAAAACAACACTACATATCTAAACCCAATTACTCTAAATTCTTTCTCTTATCCAACAACCTACACACATAATCAACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII-IIIII-I9IIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1132:4544:6407_1:N:0:CAACTCCA+ACGGATTC ptg000009l 19096022 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1132:4552:6393_1:N:0:CAACTCCA+ACGGATTC ptg000009l 19096022 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1135:42983:10189_1:N:0:CAACTCCA+ACGGATTC ptg000006l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1162:47870:15904_1:N:0:CAACTCCA+ACGGATTC ptg000066l 66346 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 LH00526:197:22KFKVLT4:3:1365:22873:27096_1:N:0:CAACTCCA+ACGGATTC ptg000009l 19095996 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 Processed 3000000 sequence pairs so far Processed 3000000 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 LH00526:197:22KFKVLT4:3:2471:17087:17585_1:N:0:CAACTCCA+ACGGATTC ptg000006l 3 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2434:23343:28273_1:N:0:CAACTCCA+ACGGATTC ptg000015l 14997092 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1158:38815:21633_1:N:0:CAACTCCA+ACGGATTC ptg000153l 25749 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 LH00526:197:22KFKVLT4:4:1347:15987:29016_1:N:0:CAACTCCA+ACGGATTC ptg000015l 14997092 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1497:36039:29660_1:N:0:CAACTCCA+ACGGATTC ptg000027l 1 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2230:48097:11394_1:N:0:CAACTCCA+ACGGATTC ptg000025l 1 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2337:33620:15050_1:N:0:CAACTCCA+ACGGATTC ptg000092l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2370:49950:13285_1:N:0:CAACTCCA+ACGGATTC ptg000095l 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3921820 (45.95%) aligned concordantly 0 times 1534996 (17.98%) aligned concordantly exactly 1 time 3078239 (36.07%) aligned concordantly >1 times 54.05% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8504138 (99.64%) aligned concordantly 0 times 10848 (0.13%) aligned concordantly exactly 1 time 20069 (0.24%) aligned concordantly >1 times 0.36% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3920120 (45.93%) aligned concordantly 0 times 1534175 (17.97%) aligned concordantly exactly 1 time 3080760 (36.10%) aligned concordantly >1 times 54.07% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8503045 (99.62%) aligned concordantly 0 times 10932 (0.13%) aligned concordantly exactly 1 time 21078 (0.25%) aligned concordantly >1 times 0.38% overall alignment rate Processed 8535055 sequences in total Successfully deleted the temporary files 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8535055 Final Cytosine Methylation Report ================================= Total number of C's analysed: 199722651 Total methylated C's in CpG context: 2686409 Total methylated C's in CHG context: 209239 Total methylated C's in CHH context: 932577 Total methylated C's in Unknown context: 6543 Total unmethylated C's in CpG context: 31666622 Total unmethylated C's in CHG context: 35134461 Total unmethylated C's in CHH context: 129093343 Total unmethylated C's in Unknown context: 262834 C methylated in CpG context: 7.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.4% 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8503017 (99.62%) aligned concordantly 0 times 10929 (0.13%) aligned concordantly exactly 1 time 21109 (0.25%) aligned concordantly >1 times 0.38% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3919997 (45.93%) aligned concordantly 0 times 1535393 (17.99%) aligned concordantly exactly 1 time 3079665 (36.08%) aligned concordantly >1 times 54.07% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8503898 (99.63%) aligned concordantly 0 times 10768 (0.13%) aligned concordantly exactly 1 time 20389 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3923319 (45.97%) aligned concordantly 0 times 1534043 (17.97%) aligned concordantly exactly 1 time 3077693 (36.06%) aligned concordantly >1 times 54.03% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8503166 (99.63%) aligned concordantly 0 times 10891 (0.13%) aligned concordantly exactly 1 time 20998 (0.25%) aligned concordantly >1 times 0.37% overall alignment rate Processed 8535055 sequences in total Successfully deleted the temporary files 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8535055 Final Cytosine Methylation Report ================================= Total number of C's analysed: 199576599 Total methylated C's in CpG context: 2681053 Total methylated C's in CHG context: 209947 Total methylated C's in CHH context: 935958 Total methylated C's in Unknown context: 6684 Total unmethylated C's in CpG context: 31657111 Total unmethylated C's in CHG context: 35095463 Total unmethylated C's in CHH context: 128997067 Total unmethylated C's in Unknown context: 262913 C methylated in CpG context: 7.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.5% Now waiting for all child processes to complete 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8504183 (99.64%) aligned concordantly 0 times 10591 (0.12%) aligned concordantly exactly 1 time 20281 (0.24%) aligned concordantly >1 times 0.36% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3923316 (45.97%) aligned concordantly 0 times 1533009 (17.96%) aligned concordantly exactly 1 time 3078730 (36.07%) aligned concordantly >1 times 54.03% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3918302 (45.91%) aligned concordantly 0 times 1536260 (18.00%) aligned concordantly exactly 1 time 3080493 (36.09%) aligned concordantly >1 times 54.09% overall alignment rate Processed 8535055 sequences in total Successfully deleted the temporary files 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8535055 Final Cytosine Methylation Report ================================= Total number of C's analysed: 199655912 Total methylated C's in CpG context: 2683122 Total methylated C's in CHG context: 206441 Total methylated C's in CHH context: 927764 Total methylated C's in Unknown context: 6548 Total unmethylated C's in CpG context: 31659460 Total unmethylated C's in CHG context: 35113616 Total unmethylated C's in CHH context: 129065509 Total unmethylated C's in Unknown context: 263087 C methylated in CpG context: 7.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.4% Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2386:32754:17165_1:N:0:CAACTCCA+ACGGATTC ptg000127l 27791 Processed 8000000 sequence pairs so far 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8503943 (99.64%) aligned concordantly 0 times 10645 (0.12%) aligned concordantly exactly 1 time 20467 (0.24%) aligned concordantly >1 times 0.36% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3920882 (45.94%) aligned concordantly 0 times 1535459 (17.99%) aligned concordantly exactly 1 time 3078714 (36.07%) aligned concordantly >1 times 54.06% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 8503053 (99.63%) aligned concordantly 0 times 10856 (0.13%) aligned concordantly exactly 1 time 21146 (0.25%) aligned concordantly >1 times 0.37% overall alignment rate 8535055 reads; of these: 8535055 (100.00%) were paired; of these: 3919203 (45.92%) aligned concordantly 0 times 1535274 (17.99%) aligned concordantly exactly 1 time 3080578 (36.09%) aligned concordantly >1 times 54.08% overall alignment rate Processed 8535055 sequences in total Successfully deleted the temporary files 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8535055 Final Cytosine Methylation Report ================================= Total number of C's analysed: 199775759 Total methylated C's in CpG context: 2689813 Total methylated C's in CHG context: 208719 Total methylated C's in CHH context: 930826 Total methylated C's in Unknown context: 6559 Total unmethylated C's in CpG context: 31681965 Total unmethylated C's in CHG context: 35144231 Total unmethylated C's in CHH context: 129120205 Total unmethylated C's in Unknown context: 263371 C methylated in CpG context: 7.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.4% 8535056 reads; of these: 8535056 (100.00%) were paired; of these: 3922381 (45.96%) aligned concordantly 0 times 1533779 (17.97%) aligned concordantly exactly 1 time 3078896 (36.07%) aligned concordantly >1 times 54.04% overall alignment rate 8535056 reads; of these: 8535056 (100.00%) were paired; of these: 8502834 (99.62%) aligned concordantly 0 times 10855 (0.13%) aligned concordantly exactly 1 time 21367 (0.25%) aligned concordantly >1 times 0.38% overall alignment rate 8535056 reads; of these: 8535056 (100.00%) were paired; of these: 8503755 (99.63%) aligned concordantly 0 times 10753 (0.13%) aligned concordantly exactly 1 time 20548 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate 8535056 reads; of these: 8535056 (100.00%) were paired; of these: 3919564 (45.92%) aligned concordantly 0 times 1534926 (17.98%) aligned concordantly exactly 1 time 3080566 (36.09%) aligned concordantly >1 times 54.08% overall alignment rate Processed 8535056 sequences in total Successfully deleted the temporary files 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1G5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8535056 Final Cytosine Methylation Report ================================= Total number of C's analysed: 199667289 Total methylated C's in CpG context: 2673726 Total methylated C's in CHG context: 207042 Total methylated C's in CHH context: 930198 Total methylated C's in Unknown context: 6400 Total unmethylated C's in CpG context: 31662099 Total unmethylated C's in CHG context: 35129533 Total unmethylated C's in CHH context: 129064691 Total unmethylated C's in Unknown context: 263018 C methylated in CpG context: 7.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.4% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1G5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1G5_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1G5_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/1G5_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1G5_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/1G5_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1G5_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: 42675276 Final Cytosine Methylation Report ================================= Total number of C's analysed: 998398210 Total methylated C's in CpG context: 13414123 Total methylated C's in CHG context: 1041388 Total methylated C's in CHH context: 4657323 Total methylated C's in Unknown context: 32734 Total unmethylated C's in CpG context: 158327257 Total unmethylated C's in CHG context: 175617304 Total unmethylated C's in CHH context: 645340815 Total unmethylated C's in Unknown context: 1315223 C methylated in CpG context: 7.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.4% Deleting temporary report files... Bismark completed in 0d 7h 1m 12s ==================== Bismark run complete ====================