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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_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/1F1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9355851) Using the subset file >1F1_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/1F1_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/1F1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_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/1F1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_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/1F1_R1_001.fastp-trim.fq.gz for PID: 70116 and offset 5 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_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/1F1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_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/1F1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9355851) Using the subset file >1F1_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/1F1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz to 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz to 1F1_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/1F1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz to 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz to 1F1_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/1F1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz to 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz to 1F1_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/1F1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz to 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz to 1F1_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/1F1_R2_001.fastp-trim.fq.gz for PID: 70116 and offset 5 (sequences written out: 9355850) Using the subset file >1F1_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/1F1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz to 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz to 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz (9355851 sequences in total) Writing a C -> T converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz to 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz to 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz (9355850 sequences in total) Writing a C -> T converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz to 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz to 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz (9355850 sequences in total) Writing a C -> T converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz to 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz to 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz (9355850 sequences in total) Writing a C -> T converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz to 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz to 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz (9355850 sequences in total) Writing a C -> T converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz to 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz to 1F1_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 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz (9355851 sequences in total) Input files are 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F1_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz (9355850 sequences in total) Input files are 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz (9355850 sequences in total) Input files are 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz (9355850 sequences in total) Input files are 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:45192:1070_1:N:0:TATGGCAC+TCTCGCAA/1 99 ptg000020l_CT_converted 15097613 18 125M = 15097647 159 AGTAAATTTTATTAAGTGATTTTGTTATATAATATATTAAATATGATATTTTGTTTTTGTTTTTATGAAAATTTGTGAATTTTGTTTAAAGGAGGGTTTTTGTTTAGATATTTTTAGAAGGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-36 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:18T106 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45192:1070_2:N:0:TATGGCAC+TCTCGCAA/2 147 ptg000020l_CT_converted 15097647 18 125M = 15097613 -159 TATTAAATATGATATTTTGTTTTTGTTTTTATGAAAATTTGTGAATTTTGTTTAAAGGAGGGTTTTTGTTTAGATATTTTTAGAAGGGGAATGAAGGTTTTAGTTTGTTGTGATTTATTAAGATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-18 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:52022:1070_1:N:0:TATGGCAC+TCTCGCAA/1 99 ptg000004l_CT_converted 3016925 6 125M = 3016919 -131 TTTATTAAATAATAGTTATTTTTGGAGGATGTGTTGGATATGAGTTGATATATATAATTAATGAGGTTGTAGGTATATATTTGGTAAGTTTGAGAAGAATAATTGTTTTAGTAAATTTTTAAGTA II9I9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9I AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:52022:1070_2:N:0:TATGGCAC+TCTCGCAA/2 147 ptg000004l_CT_converted 3016919 6 125M = 3016925 131 TAAAAATTTATTAAATAATAGTTATTTTTGGAGGATGTGTTGGATATGAGTTGATATATATAATTAATGAGGTTATAGGTATATATTTGGTAAGTTTGAGAAGAATAATTGTTTTAGTAAATTTT 9IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII99I-II9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:74G50 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:31508:1084_1:N:0:TATGGCAC+TCTCGCAA/1 99 ptg000006l_CT_converted 143614 6 125M = 143679 190 AAAGGATTGATATTTGTTTGGTTGTTTTTTTTGTAATTTGTGGATATTTTGTTTTTTTGAGGTTATTTAGAATTAGTTTTATTTTTTAGTGTTTGTTATGAGATTGAGTTGTTAGTTTGTTGGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-III AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:85A39 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:31508:1084_2:N:0:TATGGCAC+TCTCGCAA/2 147 ptg000006l_CT_converted 143679 6 125M = 143614 -190 TTTAGAATTAGTTTTATTTTTTAGTGTTTGTTATGAGATTGATTTATTAGTTTGTTGGAGTATTTTGTTAAAAATTGATTGTGATTTATAGTTTTTAAAGGATGATTGTTTTTTTTTAGGGAATG IIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIII9-9I-9I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:20A21G2G79 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:46114:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 ATTTAGAAATTTAAGTTGATGTTTTGAGTGTTAGTTTTTTGTTAGAGTGTTGTTTTGATGAAGGGTTAATGATGTAGTATTATAGTTTTTTTTGAAATTAGAAATTTATTTATAATGAGAGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIII9I9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46114:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 ACAATATCTCTCATTATAAATAAATTTCTAATTTCTAAAAAAACTATAATACTACATCATTAACCCTTCATCAAAACAACACTCTAACAAAAAACTAACACTCAAAACATCAACTTAAATTTCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:31508:1084_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 AAAAAATTAATATTTATTTAATTATTTTTTTTATAATTTATAAATATTTTATTTTTTTAAAATTATTTAAAATTAATTTTATTTTTTAATATTTATTATAAAATTAAATTATTAATTTATTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31508:1084_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 TATTTTTTAAAAAAAAATAATTATTTTTTAAAAATTATAAATTATAATTAATTTTTAATAAAATATTTTAATAAATTAATAAGTTAATTTTATAATAAATATTAAAAAATAAAATTAATTTTAAA IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-I9-I9-9IIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:46114:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 ATTTAAAAATTTAAATTAATATTTTAAATATTAATTTTTTATTAAAATATTATTTTAATAAAAAATTAATAATATAATATTATAATTTTTTTCAAAATTAAAAATTTATTTATAATAAAAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIII9I9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46114:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 ATAATATTTTTTATTATAAATAAATTTTTAATTTTTAAAAAAATTATAATATTATATTATTAATTTTTTATTAAAATAATATTTTAATAAAAAATTAATATTTAAAATATTAATTTAAATTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45192:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 AATAAATTTTATTAAATAATTTTATTATATAATATATTAAATATAATATTTTATTTTTATTTTTATAAAAATTTATAAATTTTATTTAAAAAAAAATTTTTATTTAAATATTTTTAAAAAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45192:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 AATTTTAATAAATTATAATAAATTAAAATTTTTATTTTTTTTTTAAAAATATTTAAATAAAAATTTTTTTTTAAATAAAATTTATAAATTTTTATAAAAATAAAAATAAAATATTATATTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1F1_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz (9355850 sequences in total) Found first alignment: LH00526:197:22KFKVLT4:3:1101:52022:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 TTTATTAAATAATAATTATTTTTAAAAAATATATTAAATATAAATTAATATATATAATTAATAAAATTATAAATATATATTTAATAAATTTAAAAAAAATAATTATTTTAATAAATTTTTAAATA II9I9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52022:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 AAAATTTATTAAAATAATTATTTTTTTTAAATTTATTAAATATATATTTATAATTTTATTAATTATATATATTAATTTATATTTAATATATTTTTTAAAAATAATTATTATTTAATAAATTTTTA IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9II-I99IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1F1_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)) Input files are 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F1_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 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:46114:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 ATTTAAAAATTTAAATTAATATTTTAAATATTAATTTTTTATTAAAATATTATTTTAATAAAAAATTAATAATATAATATTATAATTTTTTTCAAAATTAAAAATTTATTTATAATAAAAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIII9I9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46114:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 ATAATATTTTTTATTATAAATAAATTTTTAATTTTTAAAAAAATTATAATATTATATTATTAATTTTTTATTAAAATAATATTTTAATAAAAAATTAATATTTAAAATATTAATTTAAATTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:45192:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 AATAAATTTTATTAAATAATTTTATTATATAATATATTAAATATAATATTTTATTTTTATTTTTATAAAAATTTATAAATTTTATTTAAAAAAAAATTTTTATTTAAATATTTTTAAAAAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45192:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 AATTTTAATAAATTATAATAAATTAAAATTTTTATTTTTTTTTTAAAAATATTTAAATAAAAATTTTTTTTTAAATAAAATTTATAAATTTTTATAAAAATAAAAATAAAATATTATATTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:31508:1084_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 AAAAAATTAATATTTATTTAATTATTTTTTTTATAATTTATAAATATTTTATTTTTTTAAAATTATTTAAAATTAATTTTATTTTTTAATATTTATTATAAAATTAAATTATTAATTTATTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:31508:1084_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 TATTTTTTAAAAAAAAATAATTATTTTTTAAAAATTATAAATTATAATTAATTTTTAATAAAATATTTTAATAAATTAATAAGTTAATTTTATAATAAATATTAAAAAATAAAATTAATTTTAAA IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-I9-I9-9IIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:52022:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 TTTATTAAATAATAATTATTTTTAAAAAATATATTAAATATAAATTAATATATATAATTAATAAAATTATAAATATATATTTAATAAATTTAAAAAAAATAATTATTTTAATAAATTTTTAAATA II9I9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52022:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 AAAATTTATTAAAATAATTATTTTTTTTAAATTTATTAAATATATATTTATAATTTTATTAATTATATATATTAATTTATATTTAATATATTTTTTAAAAATAATTATTATTTAATAAATTTTTA IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9II-I99IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:30860:1084_1:N:0:TATGGCAC+TCTCGCAA/1 99 ptg000024l_CT_converted 4546677 0 19M2I76M2I7M1I1M1I16M = 4546682 124 TATGTAAAGGTATTGTATATGGAAAGGTATTGTATAGAAAGGTATTGTATGGAAAGGTATTGTATATAAAGGTATTGTATGGAAAGGTAGTGTGTATGGAAAGGTAGTGTGTATGGAAAGGTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII AS:i:-62 XS:i:-61 XN:i:0 XM:i:4 XO:i:4 XG:i:6 NM:i:10 MD:Z:4G72G9T3A27 YS:i:-56 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:30860:1084_2:N:0:TATGGCAC+TCTCGCAA/2 147 ptg000024l_CT_converted 4546682 0 14M2I76M2I7M1I1M1I21M = 4546677 -124 AAAGGTATTGTATATGGAAAGGTATTGTATAGAAAGGTATTGTATGGAAAGGTATTGTATATAAAGGTATTGTATGGAAAGGTAGTGTGTATGGAAAGGTAGTGTGTATGGAAAGGTATTGTATG IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-57 XN:i:0 XM:i:3 XO:i:4 XG:i:6 NM:i:9 MD:Z:72G9T3A32 YS:i:-62 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F1_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: LH00526:197:22KFKVLT4:3:1101:45192:1070_1:N:0:TATGGCAC+TCTCGCAA/1 83 ptg000020l_GA_converted 15340804 17 125M = 15340770 -159 TTCCCCTTCTAAAAATATCTAAACAAAAACCCTCCTTTAAACAAAATTCACAAATTTTCATAAAAACAAAAACAAAATATCATATTTAATATATTATATAACAAAATCACTTAATAAAATTTACT IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-26 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:72A33A18 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45192:1070_2:N:0:TATGGCAC+TCTCGCAA/2 163 ptg000020l_GA_converted 15340770 17 125M = 15340804 159 AATCTTAATAAATCACAACAAACTAAAACCTTCATTCCCCTTCTAAAAATATCTAAACAAAAACCCTCCTTTAAACAAAATTCACAAATTTTCATAAAAACAAAAACAAAATATCATATTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-26 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:106A18 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:31508:1084_1:N:0:TATGGCAC+TCTCGCAA/1 83 ptg000008l_GA_converted 15644079 1 125M = 15644014 -190 CTCCAACAAACTAACAACTCAATCTCATAACAAACACTAAAAAATAAAACTAATTCTAAATAACCTCAAAAAAACAAAATATCCACAAATTACAAAAAAAACAACCAAACAAATATCAATCCTTT III-IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:39T45T30T8 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:31508:1084_2:N:0:TATGGCAC+TCTCGCAA/2 163 ptg000008l_GA_converted 15644014 1 125M = 15644079 190 CATTCCCTAAAAAAAAACAATCATCCTTTAAAAACTATAAATCACAATCAATTTTTAACAAAATACTCCAACAAACTAATAAATCAATCTCATAACAAACACTAAAAAATAAAACTAATTCTAAA IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-I9-I9-9IIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:79C2C21T20 YS:i:-18 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:52022:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 TTTATTAAATAATAGTTATTTTTGGAGGATGTGTTGGATATGAGTTGATATATATAATTAATGAGGTTGTAGGTATATATTTGGTAAGTTTGAGAAGAATAATTGTTTTAGTAAATTTTTAAGTA II9I9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52022:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 AAAATTTACTAAAACAATTATTCTTCTCAAACTTACCAAATATATACCTATAACCTCATTAATTATATATATCAACTCATATCCAACACATCCTCCAAAAATAACTATTATTTAATAAATTTTTA IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9II-I99IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9 YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:46114:1070_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 ATTTAGAAATTTAAGTTGATGTTTTGAGTGTTAGTTTTTTGTTAGAGTGTTGTTTTGATGAAGGGTTAATGATGTAGTATTATAGTTTTTTTTGAAATTAGAAATTTATTTATAATGAGAGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIII9I9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46114:1070_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 ACAATATCTCTCATTATAAATAAATTTCTAATTTCTAAAAAAACTATAATACTACATCATTAACCCTTCATCAAAACAACACTCTAACAAAAAACTAACACTCAAAACATCAACTTAAATTTCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:30860:1084_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 TATATAAAAATATTATATATAAAAAAATATTATATAAAAAAATATTATATAAAAAAATATTATATATAAAAATATTATATAAAAAAATAATATATATAAAAAAATAATATATATAAAAAAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30860:1084_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 TATATAATATTTTTTTATATATATTATTTTTTTATATATATTATTTTTTTATATAATATTTTTATATATAATATTTTTTTATATAATATTTTTTTATATAATATTTTTTTATATATAATATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1F1_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)) Reading in the sequence files 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:30860:1084_1:N:0:TATGGCAC+TCTCGCAA/1 77 * 0 0 * * 0 0 TATATAAAAATATTATATATAAAAAAATATTATATAAAAAAATATTATATAAAAAAATATTATATATAAAAATATTATATAAAAAAATAATATATATAAAAAAATAATATATATAAAAAAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30860:1084_2:N:0:TATGGCAC+TCTCGCAA/2 141 * 0 0 * * 0 0 TATATAATATTTTTTTATATATATTATTTTTTTATATATATTATTTTTTTATATAATATTTTTATATATAATATTTTTTTATATAATATTTTTTTATATAATATTTTTTTATATATAATATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F1_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)) Reading in the sequence files 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:30860:1084_1:N:0:TATGGCAC+TCTCGCAA/1 83 ptg000031l_GA_converted 3482228 0 16M1I1M1I14M1I1M1I89M = 3482223 -126 AATACCTTTCCATACACACTACCTTTCCATACACACTACCTTTCCATACAATACCTTTATATACAATACCTTTCCATACAATACCTTTCTATACAATACCTTTCCATATACAATACCTTTACATA IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-44 XS:i:-57 XN:i:0 XM:i:2 XO:i:4 XG:i:4 NM:i:6 MD:Z:70T1A48 YS:i:-50 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:30860:1084_2:N:0:TATGGCAC+TCTCGCAA/2 163 ptg000031l_GA_converted 3482223 0 21M1I1M1I14M1I1M1I84M = 3482228 126 CATACAATACCTTTCCATACACACTACCTTTCCATACACACTACCTTTCCATACAATACCTTTATATACAATACCTTTCCATACAATACCTTTCTATACAATACCTTTCCATATACAATACCTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII AS:i:-50 XS:i:-57 XN:i:0 XM:i:3 XO:i:4 XG:i:4 NM:i:7 MD:Z:0T74T1A43 YS:i:-44 YT:Z:CP >>> Writing bisulfite mapping results to 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1105:17087:11198_1:N:0:TATGGCAC+TCTCGCAA ptg000066l 66350 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 LH00526:197:22KFKVLT4:3:1325:20947:4656_1:N:0:TATGGCAC+TCTCGCAA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1369:49974:15764_1:N:0:TATGGCAC+TCTCGCAA ptg000029c 1802584 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1374:12054:2233_1:N:0:TATGGCAC+TCTCGCAA ptg000023l 45111784 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 LH00526:197:22KFKVLT4:3:1469:19717:24827_1:N:0:TATGGCAC+TCTCGCAA ptg000185l 34487 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2437:41574:6351_1:N:0:TATGGCAC+TCTCGCAA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2488:30642:6449_1:N:0:TATGGCAC+TCTCGCAA ptg000033l 2625597 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2412:41494:13495_1:N:0:TATGGCAC+TCTCGCAA ptg000026l 2 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 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 LH00526:197:22KFKVLT4:4:1365:7522:8760_1:N:0:TATGGCAC+TCTCGCAA ptg000006l 2 Processed 6000000 sequence pairs so far 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 LH00526:197:22KFKVLT4:4:1470:5766:16703_1:N:0:TATGGCAC+TCTCGCAA ptg000149l 81044 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1491:25447:13341_1:N:0:TATGGCAC+TCTCGCAA ptg000066l 66347 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far 9355851 reads; of these: 9355851 (100.00%) were paired; of these: 9309932 (99.51%) aligned concordantly 0 times 18399 (0.20%) aligned concordantly exactly 1 time 27520 (0.29%) aligned concordantly >1 times 0.49% overall alignment rate 9355851 reads; of these: 9355851 (100.00%) were paired; of these: 9310843 (99.52%) aligned concordantly 0 times 18197 (0.19%) aligned concordantly exactly 1 time 26811 (0.29%) aligned concordantly >1 times 0.48% overall alignment rate 9355851 reads; of these: 9355851 (100.00%) were paired; of these: 3876010 (41.43%) aligned concordantly 0 times 2077768 (22.21%) aligned concordantly exactly 1 time 3402073 (36.36%) aligned concordantly >1 times 58.57% overall alignment rate 9355851 reads; of these: 9355851 (100.00%) were paired; of these: 3874261 (41.41%) aligned concordantly 0 times 2075947 (22.19%) aligned concordantly exactly 1 time 3405643 (36.40%) aligned concordantly >1 times 58.59% overall alignment rate Processed 9355851 sequences in total Successfully deleted the temporary files 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9355851 Final Cytosine Methylation Report ================================= Total number of C's analysed: 262755616 Total methylated C's in CpG context: 5241444 Total methylated C's in CHG context: 320231 Total methylated C's in CHH context: 1416239 Total methylated C's in Unknown context: 9754 Total unmethylated C's in CpG context: 36904227 Total unmethylated C's in CHG context: 45303788 Total unmethylated C's in CHH context: 173569687 Total unmethylated C's in Unknown context: 365980 C methylated in CpG context: 12.4% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.6% Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3873803 (41.41%) aligned concordantly 0 times 2076613 (22.20%) aligned concordantly exactly 1 time 3405434 (36.40%) aligned concordantly >1 times 58.59% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9310313 (99.51%) aligned concordantly 0 times 18102 (0.19%) aligned concordantly exactly 1 time 27435 (0.29%) aligned concordantly >1 times 0.49% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9310818 (99.52%) aligned concordantly 0 times 18259 (0.20%) aligned concordantly exactly 1 time 26773 (0.29%) aligned concordantly >1 times 0.48% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3876287 (41.43%) aligned concordantly 0 times 2076895 (22.20%) aligned concordantly exactly 1 time 3402668 (36.37%) aligned concordantly >1 times 58.57% overall alignment rate Processed 9355850 sequences in total Successfully deleted the temporary files 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9355850 Final Cytosine Methylation Report ================================= Total number of C's analysed: 262714454 Total methylated C's in CpG context: 5238658 Total methylated C's in CHG context: 318593 Total methylated C's in CHH context: 1409811 Total methylated C's in Unknown context: 9511 Total unmethylated C's in CpG context: 36896621 Total unmethylated C's in CHG context: 45319550 Total unmethylated C's in CHH context: 173531221 Total unmethylated C's in Unknown context: 365333 C methylated in CpG context: 12.4% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.5% 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9310330 (99.51%) aligned concordantly 0 times 18045 (0.19%) aligned concordantly exactly 1 time 27475 (0.29%) aligned concordantly >1 times 0.49% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9310778 (99.52%) aligned concordantly 0 times 18336 (0.20%) aligned concordantly exactly 1 time 26736 (0.29%) aligned concordantly >1 times 0.48% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3874357 (41.41%) aligned concordantly 0 times 2077403 (22.20%) aligned concordantly exactly 1 time 3404090 (36.38%) aligned concordantly >1 times 58.59% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3877967 (41.45%) aligned concordantly 0 times 2078948 (22.22%) aligned concordantly exactly 1 time 3398935 (36.33%) aligned concordantly >1 times 58.55% overall alignment rate Processed 9355850 sequences in total Successfully deleted the temporary files 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9355850 Final Cytosine Methylation Report ================================= Total number of C's analysed: 262766383 Total methylated C's in CpG context: 5242514 Total methylated C's in CHG context: 318988 Total methylated C's in CHH context: 1414070 Total methylated C's in Unknown context: 9599 Total unmethylated C's in CpG context: 36873784 Total unmethylated C's in CHG context: 45311489 Total unmethylated C's in CHH context: 173605538 Total unmethylated C's in Unknown context: 365676 C methylated in CpG context: 12.4% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.6% Processed 9000000 sequence pairs so far 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9310571 (99.52%) aligned concordantly 0 times 18328 (0.20%) aligned concordantly exactly 1 time 26951 (0.29%) aligned concordantly >1 times 0.48% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3873411 (41.40%) aligned concordantly 0 times 2075814 (22.19%) aligned concordantly exactly 1 time 3406625 (36.41%) aligned concordantly >1 times 58.60% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3877428 (41.44%) aligned concordantly 0 times 2076049 (22.19%) aligned concordantly exactly 1 time 3402373 (36.37%) aligned concordantly >1 times 58.56% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9309974 (99.51%) aligned concordantly 0 times 18209 (0.19%) aligned concordantly exactly 1 time 27667 (0.30%) aligned concordantly >1 times 0.49% overall alignment rate Processed 9355850 sequences in total Successfully deleted the temporary files 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9355850 Final Cytosine Methylation Report ================================= Total number of C's analysed: 262678964 Total methylated C's in CpG context: 5235621 Total methylated C's in CHG context: 318772 Total methylated C's in CHH context: 1412553 Total methylated C's in Unknown context: 9519 Total unmethylated C's in CpG context: 36880296 Total unmethylated C's in CHG context: 45311755 Total unmethylated C's in CHH context: 173519967 Total unmethylated C's in Unknown context: 365862 C methylated in CpG context: 12.4% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.5% 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3873182 (41.40%) aligned concordantly 0 times 2075943 (22.19%) aligned concordantly exactly 1 time 3406725 (36.41%) aligned concordantly >1 times 58.60% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9310208 (99.51%) aligned concordantly 0 times 18421 (0.20%) aligned concordantly exactly 1 time 27221 (0.29%) aligned concordantly >1 times 0.49% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 9309580 (99.51%) aligned concordantly 0 times 18313 (0.20%) aligned concordantly exactly 1 time 27957 (0.30%) aligned concordantly >1 times 0.49% overall alignment rate 9355850 reads; of these: 9355850 (100.00%) were paired; of these: 3873734 (41.40%) aligned concordantly 0 times 2077009 (22.20%) aligned concordantly exactly 1 time 3405107 (36.40%) aligned concordantly >1 times 58.60% overall alignment rate Processed 9355850 sequences in total Successfully deleted the temporary files 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1F1_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9355850 Final Cytosine Methylation Report ================================= Total number of C's analysed: 262707308 Total methylated C's in CpG context: 5244462 Total methylated C's in CHG context: 320468 Total methylated C's in CHH context: 1419970 Total methylated C's in Unknown context: 9606 Total unmethylated C's in CpG context: 36896684 Total unmethylated C's in CHG context: 45304060 Total unmethylated C's in CHH context: 173521664 Total unmethylated C's in Unknown context: 366318 C methylated in CpG context: 12.4% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.6% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1F1_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1F1_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1F1_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/1F1_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1F1_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/1F1_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1F1_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: 46779251 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1313622725 Total methylated C's in CpG context: 26202699 Total methylated C's in CHG context: 1597052 Total methylated C's in CHH context: 7072643 Total methylated C's in Unknown context: 47989 Total unmethylated C's in CpG context: 184451612 Total unmethylated C's in CHG context: 226550642 Total unmethylated C's in CHH context: 867748077 Total unmethylated C's in Unknown context: 1829169 C methylated in CpG context: 12.4% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.6% Deleting temporary report files... Bismark completed in 0d 5h 23m 6s ==================== Bismark run complete ====================