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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_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/1F5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_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/1F5_R1_001.fastp-trim.fq.gz for PID: 70183 and offset 5 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_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/1F5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_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/1F5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_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/1F5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9167719) Using the subset file >1F5_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/1F5_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/1F5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1F5_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/1F5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1F5_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/1F5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9167719) Using the subset file >1F5_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/1F5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1F5_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/1F5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1F5_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/1F5_R2_001.fastp-trim.fq.gz for PID: 70183 and offset 5 (sequences written out: 9167718) Using the subset file >1F5_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/1F5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz (9167718 sequences in total) Writing a C -> T converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz (9167718 sequences in total) Writing a C -> T converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz (9167719 sequences in total) Writing a C -> T converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz (9167718 sequences in total) Writing a C -> T converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz (9167718 sequences in total) Writing a C -> T converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1F5_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 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz (9167718 sequences in total) Input files are 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:50751:1056_1:N:0:CGCAACTA+GAATCCGA/1 99 ptg000001l_CT_converted 11325627 0 8M1I43M1I72M = 11325684 182 AGTTTTTTATGTTTGTGTATTTTATAATTATGTTTATTGTTAGATTGTTATTGTTTTTTTTTTAATTATATATTTATTATTATTTTTTTTTTGATAAATTTGAGTAATTTGTTGTGAAGATGAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-52 XS:i:-68 XN:i:0 XM:i:6 XO:i:2 XG:i:2 NM:i:8 MD:Z:2A1A0A41A21G20T32 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50751:1056_2:N:0:CGCAACTA+GAATCCGA/2 147 ptg000001l_CT_converted 11325684 0 125M = 11325627 -182 TTTTAATTATATATTTATTATTATTTTTTTTTTGATAAATTTGAGTAATTTGTTGTGAAGATGAAGAAATTTTGGGTGAAATATAGGATTTTTTTGTTAGTAAGTGTTTAATAAATGATATTTAG IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-30 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:12G20T43A32T14 YS:i:-52 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:50751:1056_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 AATCTTTTATATCTACACATCTCATAATTATATTCATTATCAAATTACTATTATTTTTTTTCCAATTACATACTTATCATCACCTCCTTTTCAATAAATTCAAACAATTTATTACAAAAATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50751:1056_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 TTAGATATTATTTATTGAATATTTGTTGGTAAGAAGATTTTATGTTTTGTTTAGAGTTTTTTTATTTTTGTAATAAATTGTTTGAATTTATTGAAAAGGAGGTGATGATAAGTATGTAATTGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F5_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz (9167719 sequences in total) Input files are 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Created C -> T as well as G -> A converted versions of the FastQ file 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz (9167718 sequences in total) 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 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F5_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)) Input files are 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F5_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 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz (9167718 sequences in total) Input files are 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:51641:1056_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TTATTTGTTTGGGTAGGAATTATGTTAGTAAGTATAATATTTTTAAATAGATTTTGAATATTTTTGGGTAAATTTAATATATAAAGTATTATTGGTTATATGGAATAAGTTATTTTGTTGTTGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51641:1056_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 CAATAATTTTTACTAATCTATTAAAATAAATTTACACCTAAAAATCCAAAAAATATACTCTTACAACTATCAACTAACAATATAAACCCATTCAACAACAACAAAATAACTTATTCCATATAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9III9IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:41048:1070_1:N:0:CGCAACTA+GAATCCGA/1 99 ptg000005l_CT_converted 463765 11 125M = 463897 257 TTATTTATTGTTTGGGATTTGTTTTTTGTATGAGTGAAGGTTAATTATATAAGAGTTTATTTATGTATTTTGGTTAAGGTGTGGTGTTGTTGTTATGGTAATGGGGTTGGTTAAAAATAAGGTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-30 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2G122 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41048:1070_2:N:0:CGCAACTA+GAATCCGA/2 147 ptg000005l_CT_converted 463897 11 125M = 463765 -257 GGTTTTTATTTATTTAAGGAAAATTTAGTTATTAGATTTTTTTTATTGTTTGTTAATTATGAATTGATATGAAATTTGTTTTTTAAATATTGTTTTAATAAAATTTTAATAGAGGTGATTTTTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII AS:i:-24 XS:i:-42 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:27A26T22T13A33 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:50735:1056_1:N:0:CGCAACTA+GAATCCGA/1 99 ptg000001l_CT_converted 11325627 0 8M1I43M1I72M = 11325684 182 AGTTTTTTATGTTTGTGTATTTTATAATTATGTTTATTGTTAGATTGTTATTGTTTTTTTTTTAATTATATATTTATTATTATTTTTTTTTTGATAAATTTGAGTAATTTGTTGTGAAGATGAAG IIIIIIIIIIII9II-IIII-IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII99IIIIII9IIIIIIIIII AS:i:-52 XS:i:-68 XN:i:0 XM:i:6 XO:i:2 XG:i:2 NM:i:8 MD:Z:2A1A0A41A21G20T32 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50735:1056_2:N:0:CGCAACTA+GAATCCGA/2 147 ptg000001l_CT_converted 11325684 0 125M = 11325627 -182 TTTTAATTATATATTTATTATTATTTTTTTTTTGATAAATTTGAGTAATTTGTTGTGAAGATGAAGAAATTTTGGGTGAAATATAGGATTTTTTTGTTAGTAAGTGTTTAATAAATGATATTTAG IIIIII9IIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II AS:i:-24 XS:i:-30 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:12G20T43A32T14 YS:i:-52 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:50751:1056_1:N:0:CGCAACTA+GAATCCGA/1 83 ptg000001l_CT_converted 10870542 2 62M1I62M = 10870483 -183 TTTTATTTTTGTAATAAATTGTTTGAATTTATTGAAAAGGAGGTGATGATAAGTATGTAATTGGAAAAAAAATAATAGTAATTTGATAATGAATATAATTATGAGATGTGTAGATATAAAAGATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-38 XS:i:-47 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:52A9T8A27G16T7 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50751:1056_2:N:0:CGCAACTA+GAATCCGA/2 163 ptg000001l_CT_converted 10870483 2 125M = 10870542 183 TTAGATATTATTTATTGAATATTTGTTGGTAAGAAGATTTTATGTTTTGTTTAGAGTTTTTTTATTTTTGTAATAAATTGTTTGAATTTATTGAAAAGGAGGTGATGATAAGTATGTAATTGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:13G0A96A9T0A2 YS:i:-38 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F5_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz (9167718 sequences in total) Input files are 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F5_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 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:50735:1056_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 AATCTTTTATATCTACACATCTCATAATTATATTCATTATCAAATTACTATTATTTTTTTTCCAATTACATACTTATCATCACCTCCTTTTCAATAAATTCAAACAATTTATTACAAAAATAAAA IIIIIIIIIIII9II-IIII-IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII99IIIIII9IIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50735:1056_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 TTAGATATTATTTATTGAATATTTGTTGGTAAGAAGATTTTATGTTTTGTTTAGAGTTTTTTTATTTTTGTAATAAATTGTTTGAATTTATTGAAAAGGAGGTGATGATAAGTATGTAATTGGAA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIII9IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:51641:1056_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TTATTTATTTAAATAAAAATTATATTAATAAATATAATATTTTTAAATAAATTTTAAATATTTTTAAATAAATTTAATATATAAAATATTATTAATTATATAAAATAAATTATTTTATTATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51641:1056_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 TAATAATTTTTATTAATTTATTAAAATAAATTTATATTTAAAAATTTAAAAAATATATTTTTATAATTATTAATTAATAATATAAATTTATTTAATAATAATAAAATAATTTATTTTATATAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9III9IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:41048:1070_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TTATTTATCATTTAAAATTCATTTTTTATATAAATAAAAATTAATTATATAAAAATTTATTTACATATTTTAATTAAAATATAATATTATTATTATAATAATAAAATTAATTAAAAATAAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41048:1070_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 ATGAAAATTGTTTTTATTAAAATTTTATTAAAATAATATTTAAAAAATGAATTTTATATTAATTTGTAATTAATAAATGATAAAAAAAATTTAATAATTAAATTTTTTTTAAATAAATAAAAATT IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:50751:1056_1:N:0:CGCAACTA+GAATCCGA/1 83 ptg000001l_GA_converted 7044444 1 71M2I52M = 7044385 -182 CTTCATCTTCACAACAAATTACTCAAATTTATCAAAAAAAAAATAATAATAAATATATAATTAAAAAAAAAACAATAACAATCTAACAATAAACATAATTATAAAATACACAAACATAAAAAACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-35 XS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:2 NM:i:6 MD:Z:53C20T40T6C0 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50751:1056_2:N:0:CGCAACTA+GAATCCGA/2 163 ptg000001l_GA_converted 7044385 1 125M = 7044444 182 CTAAATATCATTTATTAAACACTTACTAACAAAAAAATCCTATATTTCACCCAAAATTTCTTCATCTTCACAACAAATTACTCAAATTTATCAAAAAAAAAATAATAATAAATATATAATTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14A97C12 YS:i:-35 YT:Z:CP >>> Writing bisulfite mapping results to 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:41647:1070_1:N:0:CGCAACTA+GAATCCGA/1 99 ptg000008l_CT_converted 14829898 6 125M = 14830011 238 TGTGGTGTTTTTAGTAAGTTAATGATATAAATATTGTTTTTGTTTAATAGATTTATATGTTGGGGATTAAATAAGTTTTATTTTTTTTTTTGTAGTATGTTTGTAGATAGGAGATGTTTGGAAAT II9IIII9IIIII9IIIIII9IIII9-IIIIIIIIIIIIII9IIIIIII9IIII9II9IIIIIII9IIIIIIIII9IIIIIIIIIIIIIII9I9I-9IIIII9I-II9I9999I9IIIIIIIII- AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:72G6G45 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41647:1070_2:N:0:CGCAACTA+GAATCCGA/2 147 ptg000008l_CT_converted 14830011 6 125M = 14829898 -238 ATGTTTGGAAATTTTTGTTATATTAATATTTTTTGAGGAGAAATGGTTATTTTTTAAAAATTATAAATTATGATTAGTTTTTAATAAAATATTTTAATAGATTAATAGATTAATTTTTTAGTATA IIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:123A1 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:41048:1070_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TTATTTATCATTTAAAATTCATTTTTTATATAAATAAAAATTAATTATATAAAAATTTATTTACATATTTTAATTAAAATATAATATTATTATTATAATAATAAAATTAATTAAAAATAAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41048:1070_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 ATGAAAATTGTTTTTATTAAAATTTTATTAAAATAATATTTAAAAAATGAATTTTATATTAATTTGTAATTAATAAATGATAAAAAAAATTTAATAATTAAATTTTTTTTAAATAAATAAAAATT IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:51641:1056_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TTATTTATTTAAATAAAAATTATATTAATAAATATAATATTTTTAAATAAATTTTAAATATTTTTAAATAAATTTAATATATAAAATATTATTAATTATATAAAATAAATTATTTTATTATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51641:1056_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 TAATAATTTTTATTAATTTATTAAAATAAATTTATATTTAAAAATTTAAAAAATATATTTTTATAATTATTAATTAATAATATAAATTTATTTAATAATAATAAAATAATTTATTTTATATAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9III9IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:50735:1056_1:N:0:CGCAACTA+GAATCCGA/1 83 ptg000001l_CT_converted 10870542 0 62M1I62M = 10870483 -183 TTTTATTTTTGTAATAAATTGTTTGAATTTATTGAAAAGGAGGTGATGATAAGTATGTAATTGGAAAAAAAATAATAGTAATTTGATAATGAATATAATTATGAGATGTGTAGATATAAAAGATT IIIIIIIIII9IIIIII99IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII-IIII-II9IIIIIIIIIIII AS:i:-38 XS:i:-53 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:52A9T8A27G16T7 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50735:1056_2:N:0:CGCAACTA+GAATCCGA/2 163 ptg000001l_CT_converted 10870483 0 125M = 10870542 183 TTAGATATTATTTATTGAATATTTGTTGGTAAGAAGATTTTATGTTTTGTTTAGAGTTTTTTTATTTTTGTAATAAATTGTTTGAATTTATTGAAAAGGAGGTGATGATAAGTATGTAATTGGAA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIII9IIIIII AS:i:-30 XS:i:-36 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:13G0A96A9T0A2 YS:i:-38 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F5_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: LH00526:197:22KFKVLT4:3:1101:41048:1070_1:N:0:CGCAACTA+GAATCCGA/1 83 ptg000007l_GA_converted 9159837 32 125M = 9159706 -256 AAACCTTATTTTTAACCAACCCCATTACCATAACAACAACACCACACCTTAACCAAAATACATAAATAAACTCTTATATAATTAACCTTCACTCATACAAAAAACAAATCCCAAACAATAAATAA IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-30 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41048:1070_2:N:0:CGCAACTA+GAATCCGA/2 163 ptg000007l_GA_converted 9159706 32 125M = 9159837 256 ACAAAAATCACCTCTATTAAAATTTTATTAAAACAATATTTAAAAAACAAATTTCATATCAATTCATAATTAACAAACAATAAAAAAAATCTAATAACTAAATTTTCCTTAAATAAATAAAAACC IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-24 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:41647:1070_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TATAATATTTTTAATAAATTAATAATATAAATATTATTTTTATTTAATAAATTTATATATTAAAAATTAAATAAATTTTATTTTTTTTTTTATAATATATTTATAAATAAAAAATATTTAAAAAT II9IIII9IIIII9IIIIII9IIII9-IIIIIIIIIIIIII9IIIIIII9IIII9II9IIIIIII9IIIIIIIII9IIIIIIIIIIIIIII9I9I-9IIIII9I-II9I9999I9IIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41647:1070_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 TATATTAAAAAATTAATTTATTAATTTATTAAAATATTTTATTAAAAATTAATTATAATTTATAATTTTTAAAAAATAATTATTTTTTTTTAAAAAATATTAATATAATAAAAATTTTTAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F5_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)) Reading in the sequence files 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:51641:1056_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TTATTTGTTTGGGTAGGAATTATGTTAGTAAGTATAATATTTTTAAATAGATTTTGAATATTTTTGGGTAAATTTAATATATAAAGTATTATTGGTTATATGGAATAAGTTATTTTGTTGTTGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51641:1056_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 CAATAATTTTTACTAATCTATTAAAATAAATTTACACCTAAAAATCCAAAAAATATACTCTTACAACTATCAACTAACAATATAAACCCATTCAACAACAACAAAATAACTTATTCCATATAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9III9IIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:50735:1056_1:N:0:CGCAACTA+GAATCCGA/1 83 ptg000001l_GA_converted 7130193 1 71M2I52M = 7130134 -182 CTTCATCTTCACAACAAATTACTCAAATTTATCAAAAAAAAAATAATAATAAATATATAATTAAAAAAAAAACAATAACAATCTAACAATAAACATAATTATAAAATACACAAACATAAAAAACT IIIIIIIIII9IIIIII99IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII-IIII-II9IIIIIIIIIIII AS:i:-35 XS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:2 NM:i:6 MD:Z:53C20T40T6C0 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50735:1056_2:N:0:CGCAACTA+GAATCCGA/2 163 ptg000001l_GA_converted 7130134 1 125M = 7130193 182 CTAAATATCATTTATTAAACACTTACTAACAAAAAAATCCTATATTTCACCCAAAATTTCTTCATCTTCACAACAAATTACTCAAATTTATCAAAAAAAAAATAATAATAAATATATAATTAAAA II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIII9IIIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14A97C12 YS:i:-35 YT:Z:CP >>> Writing bisulfite mapping results to 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:41647:1070_1:N:0:CGCAACTA+GAATCCGA/1 77 * 0 0 * * 0 0 TATAATATTTTTAATAAATTAATAATATAAATATTATTTTTATTTAATAAATTTATATATTAAAAATTAAATAAATTTTATTTTTTTTTTTATAATATATTTATAAATAAAAAATATTTAAAAAT II9IIII9IIIII9IIIIII9IIII9-IIIIIIIIIIIIII9IIIIIII9IIII9II9IIIIIII9IIIIIIIII9IIIIIIIIIIIIIII9I9I-9IIIII9I-II9I9999I9IIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41647:1070_2:N:0:CGCAACTA+GAATCCGA/2 141 * 0 0 * * 0 0 TATATTAAAAAATTAATTTATTAATTTATTAAAATATTTTATTAAAAATTAATTATAATTTATAATTTTTAAAAAATAATTATTTTTTTTTAAAAAATATTAATATAATAAAAATTTTTAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F5_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)) Reading in the sequence files 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:41647:1070_1:N:0:CGCAACTA+GAATCCGA/1 83 ptg000016l_GA_converted 57250 1 125M = 57137 -238 ATTTCCAAACATCTCCTATCTACAAACATACTACAAAAAAAAAAATAAAACTTATTTAATCCCCAACATATAAATCTATTAAACAAAAACAATATTTATATCATTAACTTACTAAAAACACCACA -IIIIIIIII9I9999I9II-I9IIIII9-I9I9IIIIIIIIIIIIIII9IIIIIIIII9IIIIIII9II9IIII9IIIIIII9IIIIIIIIIIIIII-9IIII9IIIIII9IIIII9IIII9II AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:33T11C6C72 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41647:1070_2:N:0:CGCAACTA+GAATCCGA/2 163 ptg000016l_GA_converted 57137 1 125M = 57250 238 TATACTAAAAAATTAATCTATTAATCTATTAAAATATTTTATTAAAAACTAATCATAATTTATAATTTTTAAAAAATAACCATTTCTCCTCAAAAAATATTAATATAACAAAAATTTCCAAACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIIIIIII AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1T73T21C27 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1148:19717:3171_1:N:0:CGCAACTA+GAATCCGA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1181:44124:28413_1:N:0:CGCAACTA+GAATCCGA ptg000057l 39941 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1435:6357:17613_1:N:0:CGCAACTA+GAATCCGA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1493:4423:14518_1:N:0:CGCAACTA+GAATCCGA ptg000015l 14997092 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 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1184:2295:3689_1:N:0:CGCAACTA+GAATCCGA ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1208:34162:17781_1:N:0:CGCAACTA+GAATCCGA ptg000046l 39580 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 LH00526:197:22KFKVLT4:4:1191:43962:27825_1:N:0:CGCAACTA+GAATCCGA ptg000133l 37099 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1383:41372:1434_1:N:0:CGCAACTA+GAATCCGA ptg000039l 1 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2192:42950:16128_1:N:0:CGCAACTA+GAATCCGA ptg000083l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2258:3581:5160_1:N:0:CGCAACTA+GAATCCGA ptg000020l 17861297 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4035589 (44.02%) aligned concordantly 0 times 1941916 (21.18%) aligned concordantly exactly 1 time 3190213 (34.80%) aligned concordantly >1 times 55.98% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9143233 (99.73%) aligned concordantly 0 times 9511 (0.10%) aligned concordantly exactly 1 time 14974 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9144386 (99.75%) aligned concordantly 0 times 9402 (0.10%) aligned concordantly exactly 1 time 13930 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4041964 (44.09%) aligned concordantly 0 times 1940752 (21.17%) aligned concordantly exactly 1 time 3185002 (34.74%) aligned concordantly >1 times 55.91% overall alignment rate Processed 9167718 sequences in total Successfully deleted the temporary files 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9167718 Final Cytosine Methylation Report ================================= Total number of C's analysed: 253083856 Total methylated C's in CpG context: 3870381 Total methylated C's in CHG context: 241232 Total methylated C's in CHH context: 1032965 Total methylated C's in Unknown context: 7042 Total unmethylated C's in CpG context: 36026230 Total unmethylated C's in CHG context: 42837048 Total unmethylated C's in CHH context: 169076000 Total unmethylated C's in Unknown context: 356777 C methylated in CpG context: 9.7% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4039143 (44.06%) aligned concordantly 0 times 1938670 (21.15%) aligned concordantly exactly 1 time 3189905 (34.79%) aligned concordantly >1 times 55.94% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9143429 (99.74%) aligned concordantly 0 times 9324 (0.10%) aligned concordantly exactly 1 time 14965 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9144538 (99.75%) aligned concordantly 0 times 9322 (0.10%) aligned concordantly exactly 1 time 13858 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4042521 (44.10%) aligned concordantly 0 times 1940559 (21.17%) aligned concordantly exactly 1 time 3184638 (34.74%) aligned concordantly >1 times 55.90% overall alignment rate Processed 9167718 sequences in total Successfully deleted the temporary files 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9167718 Final Cytosine Methylation Report ================================= Total number of C's analysed: 252931761 Total methylated C's in CpG context: 3862605 Total methylated C's in CHG context: 239766 Total methylated C's in CHH context: 1023322 Total methylated C's in Unknown context: 6881 Total unmethylated C's in CpG context: 36018183 Total unmethylated C's in CHG context: 42807049 Total unmethylated C's in CHH context: 168980836 Total unmethylated C's in Unknown context: 355103 C methylated in CpG context: 9.7% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Processed 9000000 sequence pairs so far 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9143273 (99.73%) aligned concordantly 0 times 9494 (0.10%) aligned concordantly exactly 1 time 14951 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4035373 (44.02%) aligned concordantly 0 times 1939624 (21.16%) aligned concordantly exactly 1 time 3192721 (34.83%) aligned concordantly >1 times 55.98% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9144501 (99.75%) aligned concordantly 0 times 9361 (0.10%) aligned concordantly exactly 1 time 13856 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4040914 (44.08%) aligned concordantly 0 times 1938632 (21.15%) aligned concordantly exactly 1 time 3188172 (34.78%) aligned concordantly >1 times 55.92% overall alignment rate Processed 9167718 sequences in total Successfully deleted the temporary files 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9167718 Final Cytosine Methylation Report ================================= Total number of C's analysed: 252979065 Total methylated C's in CpG context: 3867159 Total methylated C's in CHG context: 240892 Total methylated C's in CHH context: 1029193 Total methylated C's in Unknown context: 7000 Total unmethylated C's in CpG context: 36014872 Total unmethylated C's in CHG context: 42812983 Total unmethylated C's in CHH context: 169013966 Total unmethylated C's in Unknown context: 356570 C methylated in CpG context: 9.7% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Now waiting for all child processes to complete Processed 9000000 sequence pairs so far 9167719 reads; of these: 9167719 (100.00%) were paired; of these: 9143195 (99.73%) aligned concordantly 0 times 9565 (0.10%) aligned concordantly exactly 1 time 14959 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate 9167719 reads; of these: 9167719 (100.00%) were paired; of these: 4034591 (44.01%) aligned concordantly 0 times 1939665 (21.16%) aligned concordantly exactly 1 time 3193463 (34.83%) aligned concordantly >1 times 55.99% overall alignment rate 9167719 reads; of these: 9167719 (100.00%) were paired; of these: 9144517 (99.75%) aligned concordantly 0 times 9255 (0.10%) aligned concordantly exactly 1 time 13947 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 9167719 reads; of these: 9167719 (100.00%) were paired; of these: 4038617 (44.05%) aligned concordantly 0 times 1941011 (21.17%) aligned concordantly exactly 1 time 3188091 (34.78%) aligned concordantly >1 times 55.95% overall alignment rate Processed 9167719 sequences in total Successfully deleted the temporary files 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9167719 Final Cytosine Methylation Report ================================= Total number of C's analysed: 253040587 Total methylated C's in CpG context: 3868467 Total methylated C's in CHG context: 241713 Total methylated C's in CHH context: 1029772 Total methylated C's in Unknown context: 6940 Total unmethylated C's in CpG context: 36018739 Total unmethylated C's in CHG context: 42820883 Total unmethylated C's in CHH context: 169061013 Total unmethylated C's in Unknown context: 356422 C methylated in CpG context: 9.7% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Processed 9000000 sequence pairs so far 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9144307 (99.74%) aligned concordantly 0 times 9460 (0.10%) aligned concordantly exactly 1 time 13951 (0.15%) aligned concordantly >1 times 0.26% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4042642 (44.10%) aligned concordantly 0 times 1938313 (21.14%) aligned concordantly exactly 1 time 3186763 (34.76%) aligned concordantly >1 times 55.90% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 9143356 (99.73%) aligned concordantly 0 times 9335 (0.10%) aligned concordantly exactly 1 time 15027 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate 9167718 reads; of these: 9167718 (100.00%) were paired; of these: 4034043 (44.00%) aligned concordantly 0 times 1939685 (21.16%) aligned concordantly exactly 1 time 3193990 (34.84%) aligned concordantly >1 times 56.00% overall alignment rate Processed 9167718 sequences in total Successfully deleted the temporary files 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F5_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9167718 Final Cytosine Methylation Report ================================= Total number of C's analysed: 252863909 Total methylated C's in CpG context: 3857374 Total methylated C's in CHG context: 241207 Total methylated C's in CHH context: 1028958 Total methylated C's in Unknown context: 7014 Total unmethylated C's in CpG context: 36003281 Total unmethylated C's in CHG context: 42799550 Total unmethylated C's in CHH context: 168933539 Total unmethylated C's in Unknown context: 355766 C methylated in CpG context: 9.7% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1F5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1F5_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1F5_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/1F5_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1F5_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/1F5_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F5_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: 45838591 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1264899178 Total methylated C's in CpG context: 19325986 Total methylated C's in CHG context: 1204810 Total methylated C's in CHH context: 5144210 Total methylated C's in Unknown context: 34877 Total unmethylated C's in CpG context: 180081305 Total unmethylated C's in CHG context: 214077513 Total unmethylated C's in CHH context: 845065354 Total unmethylated C's in Unknown context: 1780638 C methylated in CpG context: 9.7% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Deleting temporary report files... Bismark completed in 0d 5h 34m 58s ==================== Bismark run complete ====================