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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_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/1A6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_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/1A6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_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/1A6_R1_001.fastp-trim.fq.gz for PID: 80753 and offset 5 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_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/1A6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7333648) Using the subset file >1A6_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/1A6_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/1A6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_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/1A6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7333648) Using the subset file >1A6_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/1A6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A6_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/1A6_R2_001.fastp-trim.fq.gz for PID: 80753 and offset 5 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A6_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/1A6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A6_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/1A6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7333647) Using the subset file >1A6_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/1A6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz (7333647 sequences in total) Writing a C -> T converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz (7333647 sequences in total) Writing a C -> T converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz (7333648 sequences in total) Writing a C -> T converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz (7333647 sequences in total) Writing a C -> T converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz (7333647 sequences in total) Writing a C -> T converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A6_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 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz (7333647 sequences in total) Input files are 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A6_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 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz (7333647 sequences in total) Input files are 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A6_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 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz (7333647 sequences in total) Input files are 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:18762:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 99 ptg000024l_CT_converted 2675680 42 125M = 2675935 380 TAGAATGATGAAAAATGTTATATAATAGTATTTTTAATTTTGTGTAATATTTTTTTAGTATTTTGTTAATTTGAGATTTTTAGTTTTTTTGTTGTATAAGGTTTTTAATGTAAAAAAGTATATTA IIIIIII9IIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIII9I9IIIIII99IIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:18762:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 147 ptg000024l_CT_converted 2675935 42 125M = 2675680 -380 GAGTGTAATATGGTGGTATTTTTGGAAGTGAAAGGATTAATTAAATAGAGTGTTTTATAATTATAATGAGATATTTTATTTTTTTAAGTAAAAAAGATTTGTATAAATAATAATGTATGTTATTT IIIIIIIIIIIII9III99IIIIIIIIIIIIIIIIIIIIIIII9I9IIIII-III9IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:18779:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 99 ptg000024l_CT_converted 2675680 42 125M = 2675935 380 TAGAATGATGAAAAATGTTATATAATAGTATTTTTAATTTTGTGTAATATTTTTTTAGTATTTTGTTAATTTGAGATTTTTAGTTTTTTTGTTGTATAAGGTTTTTAATGTAAAAAAGTATATTA I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:18779:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 147 ptg000024l_CT_converted 2675935 42 125M = 2675680 -380 GAGTGTAATATGGTGGTATTTTTGGAAGTGAAAGGATTAATTAAATAGAGTGTTTTATAATTATAATGAGATATTTTATTTTTTTAAGTAAAAAAGATTTGTATAAATAATAATGTATGTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-II9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:46373:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 GAATGAATGGATGAATGAATGAATGAAGAGATTAATGAATTAATTAGGGAGGGAGATGGTTGGTTGATTAGTTAGGGAGATAGTAAGTGTTATTTAGATAGTTGGTTAATTATTTTTTTTTTTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46373:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAAATAAATAAATAAATAAATAAAAAAATCAATAAATCAATCAAAAAAAAAAATAATTAACCAACTATCTAAATAACACTTACTATCTCCCTAACTAATCAACCAACCATCTCCCTCCCTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I99I-IIII9IIIIIIIIII9IIIIIIIII9I9IIIIIIII9I9I9IIIIII9IIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A6_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz (7333648 sequences in total) Input files are 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A6_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 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz (7333647 sequences in total) Input files are 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A6_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 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:51763:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 99 ptg000021l_CT_converted 20751748 42 125M = 20751835 212 TTTATGTGGGTGAAGGATGGTAAGTTTGTAGATTATGGATTTAGATAGATATATATGATGAAAATTGTGTGGAATATATATATTTGTTTTAATTTATAGTTTTTATATATGAAATTTAAGTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:59A65 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51763:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 147 ptg000021l_CT_converted 20751835 42 125M = 20751748 -212 TTTAATTTATAGTTTTTATATATGAAATTTAAGTATTTTATTTTATAAATATATTTATTATTTAATGTTATTTTTTAGAGTATAATAATGTTTAAAATGATAATAAATATTATGTTGTATTTGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:18762:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TAAAATAACAAAAAATATTATATAATAATATTTTTAATTTTACATAATATTTTTTTAATATTTTATTAATTTAAAATTTTTAATTTTTTTATTATATAAAATTTTTAATATAAAAAAATATATTA IIIIIII9IIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIII9I9IIIIII99IIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:18762:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAATATATATTATTATTTATATAAATTTTTTTTATTTAAAAAAATAAAATATTTTATTATAATTATAAAATATTTTATTTAATTAATTTTTTTATTTTTAAAAATATTATTATATTATATTT I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9III-IIIII9I9IIIIIIIIIIIIIIIIIIIIIIII99III9IIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:18779:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TAAAATAACAAAAAATATTATATAATAATATTTTTAATTTTACATAATATTTTTTTAATATTTTATTAATTTAAAATTTTTAATTTTTTTATTATATAAAATTTTTAATATAAAAAAATATATTA I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:18779:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAATATATATTATTATTTATATAAATTTTTTTTATTTAAAAAAATAAAATATTTTATTATAATTATAAAATATTTTATTTAATTAGTTTTTTTATTTTTAAAAATATTATTATATTATATTT IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9II-IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:46373:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 AAATAAATAAATAAATAAATAAATAAAAAAATTAATAAATTAATTAAAAAAAAAAATAATTAATTAATTAATTAAAAAAATAATAAATATTATTTAAATAATCAATTAATTATTTTTTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46373:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAAATAAATAAATAAATAAATAAAAAAATTAATAAATTAATTAAAAAAAAAAATAATTAATTGATTATTTAAATAATATTTATTATTTTTTTAATTAATTAATTAATTATTTTTTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I99I-IIII9IIIIIIIIII9IIIIIIIII9I9IIIIIIII9I9I9IIIIII9IIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:40061:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 99 ptg000025l_CT_converted 18456402 2 125M = 18456449 170 GAGGTTATTGATTTTTGATGAATGAATTTTGAGTATTGTTATGGGTTGTTAATTAGAGTTTGGTGAATTATATTGTTAAATTAAAGTATTTGGAGTTATTAATTTTTTAGTTAAAGAAGTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-48 XS:i:-48 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:19A24T16T0A8T2T16A26A6 YS:i:-65 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40061:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 147 ptg000025l_CT_converted 18456449 2 119M2I4M = 18456402 -170 GTTAATTAGAGTTTGGTGAATTATATTGTTAAATTAAAGTATTTGGAGTTATTAATTTTTTAGTTAAAGAAGTATAAATTGTTAGTGTTGAAGTTTAGAAATTTTTAGATAAGAGAGTAATATTA 9IIIIIIIIIIIIIIII9IIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-65 XS:i:-74 XN:i:0 XM:i:9 XO:i:1 XG:i:2 NM:i:11 MD:Z:14T0A8T2T16A26A11G29G0A8 YS:i:-48 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:18762:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TAAAATAACAAAAAATATTATATAATAATATTTTTAATTTTACATAATATTTTTTTAATATTTTATTAATTTAAAATTTTTAATTTTTTTATTATATAAAATTTTTAATATAAAAAAATATATTA IIIIIII9IIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIII9I9IIIIII99IIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:18762:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAATATATATTATTATTTATATAAATTTTTTTTATTTAAAAAAATAAAATATTTTATTATAATTATAAAATATTTTATTTAATTAATTTTTTTATTTTTAAAAATATTATTATATTATATTT I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9III-IIIII9I9IIIIIIIIIIIIIIIIIIIIIIII99III9IIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:46373:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 AAATAAATAAATAAATAAATAAATAAAAAAATTAATAAATTAATTAAAAAAAAAAATAATTAATTAATTAATTAAAAAAATAATAAATATTATTTAAATAATCAATTAATTATTTTTTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46373:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAAATAAATAAATAAATAAATAAAAAAATTAATAAATTAATTAAAAAAAAAAATAATTAATTGATTATTTAAATAATATTTATTATTTTTTTAATTAATTAATTAATTATTTTTTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I99I-IIII9IIIIIIIIII9IIIIIIIII9I9IIIIIIII9I9I9IIIIII9IIII9IIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:18779:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TAAAATAACAAAAAATATTATATAATAATATTTTTAATTTTACATAATATTTTTTTAATATTTTATTAATTTAAAATTTTTAATTTTTTTATTATATAAAATTTTTAATATAAAAAAATATATTA I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:18779:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAATATATATTATTATTTATATAAATTTTTTTTATTTAAAAAAATAAAATATTTTATTATAATTATAAAATATTTTATTTAATTAGTTTTTTTATTTTTAAAAATATTATTATATTATATTT IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9II-IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:40061:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 AAAATTATTAATTTTTAATAAATAAATTTTAAATATTATTATAAATTATTAATTAAAATTTAATAAATTATATTATTAAATTAAAATATTTAAAATTATTAATTTTTTAATTAAAAAAATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40061:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 TAATATTATTTTTTTATTTAAAAATTTTTAAATTTTAATATTAATAATTTATATTTTTTTAATTAAAAAATTAATAATTTTAAATATTTTAATTTAATAATATAATTTATTAAATTTTAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIII9IIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:51763:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TTTATATAAATAAAAAATAATAAATTTATAAATTATAAATTTAAATAAATATATATAATAAAAATTATATAAAATATATATATTTATTTTAATTTATAATTTTTATATATAAAATTTAAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51763:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 TATAAATATAATATAATATTTATTATTATTTTAAATATTATTATATTTTAAAAAATAATATTAAATAATAAATATATTTATAAAATAAAATATTTAAATTTTATATATAAAAATTATAAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:46373:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 GAATGAATGGATGAATGAATGAATGAAGAGATTAATGAATTAATTAGGGAGGGAGATGGTTGGTTGATTAGTTAGGGAGATAGTAAGTGTTATTTAGATAGTTGGTTAATTATTTTTTTTTTTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:46373:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAAATAAATAAATAAATAAATAAAAAAATCAATAAATCAATCAAAAAAAAAAATAATTAACCAACTATCTAAATAACACTTACTATCTCCCTAACTAATCAACCAACCATCTCCCTCCCTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I99I-IIII9IIIIIIIIII9IIIIIIIII9I9IIIIIIII9I9I9IIIIII9IIII9IIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:18779:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TAGAATGATGAAAAATGTTATATAATAGTATTTTTAATTTTGTGTAATATTTTTTTAGTATTTTGTTAATTTGAGATTTTTAGTTTTTTTGTTGTATAAGGTTTTTAATGTAAAAAAGTATATTA I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:18779:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAACATACATTATTATTTATACAAATCTTTTTTACTTAAAAAAATAAAATATCTCATTATAATTATAAAACACTCTATTTAATTAATCCTTTCACTTCCAAAAATACCACCATATTACACTC IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9II-IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:18762:1098_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TAGAATGATGAAAAATGTTATATAATAGTATTTTTAATTTTGTGTAATATTTTTTTAGTATTTTGTTAATTTGAGATTTTTAGTTTTTTTGTTGTATAAGGTTTTTAATGTAAAAAAGTATATTA IIIIIII9IIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIII9I9IIIIII99IIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:18762:1098_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 AAATAACATACATTATTATTTATACAAATCTTTTTTACTTAAAAAAATAAAATATCTCATTATAATTATAAAACACTCTATTTAATTAATCCTTTCACTTCCAAAAATACCACCATATTACACTC I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9III-IIIII9I9IIIIIIIIIIIIIIIIIIIIIIII99III9IIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:40061:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 AAAATTATTAATTTTTAATAAATAAATTTTAAATATTATTATAAATTATTAATTAAAATTTAATAAATTATATTATTAAATTAAAATATTTAAAATTATTAATTTTTTAATTAAAAAAATATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40061:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 TAATATTATTTTTTTATTTAAAAATTTTTAAATTTTAATATTAATAATTTATATTTTTTTAATTAAAAAATTAATAATTTTAAATATTTTAATTTAATAATATAATTTATTAAATTTTAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIII9IIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A6_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: LH00526:197:22KFKVLT4:3:1101:51763:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TTTATATAAATAAAAAATAATAAATTTATAAATTATAAATTTAAATAAATATATATAATAAAAATTATATAAAATATATATATTTATTTTAATTTATAATTTTTATATATAAAATTTAAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51763:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 TATAAATATAATATAATATTTATTATTATTTTAAATATTATTATATTTTAAAAAATAATATTAAATAATAAATATATTTATAAAATAAAATATTTAAATTTTATATATAAAAATTATAAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:51763:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 77 * 0 0 * * 0 0 TTTATGTGGGTGAAGGATGGTAAGTTTGTAGATTATGGATTTAGATAGATATATATGATGAAAATTGTGTGGAATATATATATTTGTTTTAATTTATAGTTTTTATATATGAAATTTAAGTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51763:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 141 * 0 0 * * 0 0 TACAAATACAACATAATATTTATTATCATTTTAAACATTATTATACTCTAAAAAATAACATTAAATAATAAATATATTTATAAAATAAAATACTTAAATTTCATATATAAAAACTATAAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:40061:1070_1:N:0:CAGGTTCA+GGCGTTAT/1 83 ptg000008l_GA_converted 18479915 38 125M = 18479868 -172 TTTATACTTCTTTAACTAAAAAATTAATAACTCCAAATACTTTAATTTAACAATATAATTCACCAAACTCTAATTAACAACCCATAACAATACTCAAAATTCATTCATCAAAAATCAATAACCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-54 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40061:1070_2:N:0:CAGGTTCA+GGCGTTAT/2 163 ptg000008l_GA_converted 18479868 38 125M = 18479915 172 TAATATTACTCTCTTATCTAAAAATTTCTAAACTTCAACACTAACAATTTATACTTCTTTAACTAAAAAATTAATAACTCCAAATACTTTAATTTAACAATATAATTCACCAAACTCTAATTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIII9IIIIIIIIIIIIIIII9 AS:i:0 XS:i:-71 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 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1117:26879:26858_1:N:0:CAGGTTCA+GGCGTTAT ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1117:26871:26844_1:N:0:CAGGTTCA+GGCGTTAT ptg000039l 1 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 LH00526:197:22KFKVLT4:3:1290:22784:2821_1:N:0:CAGGTTCA+GGCGTTAT ptg000039l 1 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1331:32074:21900_1:N:0:CAGGTTCA+GGCGTTAT ntLink_4 304022 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1345:35214:27755_1:N:0:CAGGTTCA+GGCGTTAT ptg000012l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1438:23958:5721_1:N:0:CAGGTTCA+GGCGTTAT ptg000048l 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1467:11641:19868_1:N:0:CAGGTTCA+GGCGTTAT ptg000048l 1 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 LH00526:197:22KFKVLT4:3:2148:30804:6673_1:N:0:CAGGTTCA+GGCGTTAT ptg000121l 50724 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2133:8251:1168_1:N:0:CAGGTTCA+GGCGTTAT ptg000012l 2 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2481:25892:23553_1:N:0:CAGGTTCA+GGCGTTAT ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1115:30488:6099_1:N:0:CAGGTTCA+GGCGTTAT ptg000066l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1150:36565:10539_1:N:0:CAGGTTCA+GGCGTTAT ptg000082l 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1347:39268:13397_1:N:0:CAGGTTCA+GGCGTTAT ptg000065l 49673 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2120:42060:23973_1:N:0:CAGGTTCA+GGCGTTAT ptg000083l 1 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 LH00526:197:22KFKVLT4:4:2240:30237:21633_1:N:0:CAGGTTCA+GGCGTTAT ptg000065l 49673 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2303:22954:23398_1:N:0:CAGGTTCA+GGCGTTAT ptg000066l 66368 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2395:35699:23833_1:N:0:CAGGTTCA+GGCGTTAT ptg000083l 1 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far 7333648 reads; of these: 7333648 (100.00%) were paired; of these: 7315364 (99.75%) aligned concordantly 0 times 7036 (0.10%) aligned concordantly exactly 1 time 11248 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 7333648 reads; of these: 7333648 (100.00%) were paired; of these: 7316211 (99.76%) aligned concordantly 0 times 7018 (0.10%) aligned concordantly exactly 1 time 10419 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 7333648 reads; of these: 7333648 (100.00%) were paired; of these: 3142384 (42.85%) aligned concordantly 0 times 1574440 (21.47%) aligned concordantly exactly 1 time 2616824 (35.68%) aligned concordantly >1 times 57.15% overall alignment rate 7333648 reads; of these: 7333648 (100.00%) were paired; of these: 3147804 (42.92%) aligned concordantly 0 times 1574956 (21.48%) aligned concordantly exactly 1 time 2610888 (35.60%) aligned concordantly >1 times 57.08% overall alignment rate Processed 7333648 sequences in total Successfully deleted the temporary files 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7333648 Final Cytosine Methylation Report ================================= Total number of C's analysed: 206397165 Total methylated C's in CpG context: 3126461 Total methylated C's in CHG context: 183075 Total methylated C's in CHH context: 778738 Total methylated C's in Unknown context: 5421 Total unmethylated C's in CpG context: 29528524 Total unmethylated C's in CHG context: 34935976 Total unmethylated C's in CHH context: 137844391 Total unmethylated C's in Unknown context: 291825 C methylated in CpG context: 9.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7316220 (99.76%) aligned concordantly 0 times 7097 (0.10%) aligned concordantly exactly 1 time 10330 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7315290 (99.75%) aligned concordantly 0 times 7130 (0.10%) aligned concordantly exactly 1 time 11227 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3147732 (42.92%) aligned concordantly 0 times 1571265 (21.43%) aligned concordantly exactly 1 time 2614650 (35.65%) aligned concordantly >1 times 57.08% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3141859 (42.84%) aligned concordantly 0 times 1573985 (21.46%) aligned concordantly exactly 1 time 2617803 (35.70%) aligned concordantly >1 times 57.16% overall alignment rate Processed 7333647 sequences in total Successfully deleted the temporary files 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7333647 Final Cytosine Methylation Report ================================= Total number of C's analysed: 206269306 Total methylated C's in CpG context: 3117945 Total methylated C's in CHG context: 183835 Total methylated C's in CHH context: 781326 Total methylated C's in Unknown context: 5273 Total unmethylated C's in CpG context: 29502147 Total unmethylated C's in CHG context: 34918034 Total unmethylated C's in CHH context: 137766019 Total unmethylated C's in Unknown context: 291651 C methylated in CpG context: 9.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3143471 (42.86%) aligned concordantly 0 times 1574353 (21.47%) aligned concordantly exactly 1 time 2615823 (35.67%) aligned concordantly >1 times 57.14% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3146563 (42.91%) aligned concordantly 0 times 1573795 (21.46%) aligned concordantly exactly 1 time 2613289 (35.63%) aligned concordantly >1 times 57.09% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7315150 (99.75%) aligned concordantly 0 times 7117 (0.10%) aligned concordantly exactly 1 time 11380 (0.16%) aligned concordantly >1 times 0.25% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7316229 (99.76%) aligned concordantly 0 times 7102 (0.10%) aligned concordantly exactly 1 time 10316 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate Processed 7333647 sequences in total Successfully deleted the temporary files 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7333647 Final Cytosine Methylation Report ================================= Total number of C's analysed: 206368276 Total methylated C's in CpG context: 3115960 Total methylated C's in CHG context: 182614 Total methylated C's in CHH context: 785528 Total methylated C's in Unknown context: 5347 Total unmethylated C's in CpG context: 29516587 Total unmethylated C's in CHG context: 34939446 Total unmethylated C's in CHH context: 137828141 Total unmethylated C's in Unknown context: 292430 C methylated in CpG context: 9.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7316233 (99.76%) aligned concordantly 0 times 7072 (0.10%) aligned concordantly exactly 1 time 10342 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3142170 (42.85%) aligned concordantly 0 times 1573545 (21.46%) aligned concordantly exactly 1 time 2617932 (35.70%) aligned concordantly >1 times 57.15% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3144929 (42.88%) aligned concordantly 0 times 1574381 (21.47%) aligned concordantly exactly 1 time 2614337 (35.65%) aligned concordantly >1 times 57.12% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7315377 (99.75%) aligned concordantly 0 times 7054 (0.10%) aligned concordantly exactly 1 time 11216 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate Processed 7333647 sequences in total Successfully deleted the temporary files 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7333647 Final Cytosine Methylation Report ================================= Total number of C's analysed: 206445298 Total methylated C's in CpG context: 3118250 Total methylated C's in CHG context: 182227 Total methylated C's in CHH context: 783731 Total methylated C's in Unknown context: 5483 Total unmethylated C's in CpG context: 29531221 Total unmethylated C's in CHG context: 34961454 Total unmethylated C's in CHH context: 137868415 Total unmethylated C's in Unknown context: 290869 C methylated in CpG context: 9.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7315244 (99.75%) aligned concordantly 0 times 6984 (0.10%) aligned concordantly exactly 1 time 11419 (0.16%) aligned concordantly >1 times 0.25% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3140736 (42.83%) aligned concordantly 0 times 1575633 (21.48%) aligned concordantly exactly 1 time 2617278 (35.69%) aligned concordantly >1 times 57.17% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 3146916 (42.91%) aligned concordantly 0 times 1572593 (21.44%) aligned concordantly exactly 1 time 2614138 (35.65%) aligned concordantly >1 times 57.09% overall alignment rate 7333647 reads; of these: 7333647 (100.00%) were paired; of these: 7316231 (99.76%) aligned concordantly 0 times 6946 (0.09%) aligned concordantly exactly 1 time 10470 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate Processed 7333647 sequences in total Successfully deleted the temporary files 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A6_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7333647 Final Cytosine Methylation Report ================================= Total number of C's analysed: 206444655 Total methylated C's in CpG context: 3117603 Total methylated C's in CHG context: 182560 Total methylated C's in CHH context: 775487 Total methylated C's in Unknown context: 5498 Total unmethylated C's in CpG context: 29529628 Total unmethylated C's in CHG context: 34952987 Total unmethylated C's in CHH context: 137886390 Total unmethylated C's in Unknown context: 292862 C methylated in CpG context: 9.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1A6_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1A6_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1A6_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/1A6_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1A6_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/1A6_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A6_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: 36668236 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1031924700 Total methylated C's in CpG context: 15596219 Total methylated C's in CHG context: 914311 Total methylated C's in CHH context: 3904810 Total methylated C's in Unknown context: 27022 Total unmethylated C's in CpG context: 147608107 Total unmethylated C's in CHG context: 174707897 Total unmethylated C's in CHH context: 689193356 Total unmethylated C's in Unknown context: 1459637 C methylated in CpG context: 9.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Deleting temporary report files... Bismark completed in 0d 4h 48m 16s ==================== Bismark run complete ====================