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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_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/2G2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8726002) Using the subset file >2G2_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/2G2_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/2G2_R1_001.fastp-trim.fq.gz for PID: 79763 and offset 5 (sequences written out: 8726002) Using the subset file >2G2_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/2G2_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/2G2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8726003) Using the subset file >2G2_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/2G2_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/2G2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8726003) Using the subset file >2G2_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/2G2_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/2G2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8726002) Using the subset file >2G2_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/2G2_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/2G2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8726003) Using the subset file >2G2_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/2G2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/2G2_R2_001.fastp-trim.fq.gz for PID: 79763 and offset 5 (sequences written out: 8726002) Using the subset file >2G2_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/2G2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz to 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz to 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz to 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz to 2G2_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/2G2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8726003) Using the subset file >2G2_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/2G2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz to 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz to 2G2_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/2G2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8726002) Using the subset file >2G2_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/2G2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz to 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz to 2G2_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/2G2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8726002) Using the subset file >2G2_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/2G2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz to 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz to 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz (8726002 sequences in total) Writing a C -> T converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz to 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz to 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz (8726002 sequences in total) Writing a C -> T converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz to 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz to 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz (8726003 sequences in total) Writing a C -> T converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz to 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz to 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz (8726003 sequences in total) Writing a C -> T converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz to 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz to 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz (8726002 sequences in total) Writing a C -> T converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz to 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz to 2G2_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 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz (8726002 sequences in total) Input files are 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2G2_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 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz (8726003 sequences in total) Input files are 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:7545:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 ATTTGTTAAAAATAAAATTGAGGTAATAAATTGTGGTTTTTTTTAGATATAATTGAAAGGTATTTTAATTTTTATTGGTTGGTTAAAATAGTTATTATAATTAAATTATTTAGTTTTGTATGTTA I-IIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9I-III9IIIIII-IIIIIIIII9IIIIII--9IIIIIIIIIII9I--I9-IIIIII99II-I--9IIIIIIIIIIII9I- YT:Z:UP LH00652:104:22KG7JLT4:7:1101:7545:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 ATTTACCAAAAACAAAACCAAAACAATAAATTATAATTCCTTCTAAATACAACTAAAAAATATTTTAACTTCCTCTAAAAAAAACTTCCAAAAAAATAATTAAAACTAAAAAAATCTCAACAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII-III9II9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:23531:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 AAATAAATAAATATATTAAAGAGTTTTAATTGATAAGGGATGATTAATTATATATTGTGATAAGGTATTAATAAGGTGTGGTGGAGTTTTAAGAATTTGGAGTAATTGATGATAAATATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:23531:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 AAATAAATAAATATATTAAAAAACCCCAATTAACAAAAAATAACTAATTATATACTATAATAAAATATTAATAAAACATAATAAAATTTCAAAAATTCAAAACAACCAATAACAAACATCCATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2G2_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)) Created C -> T as well as G -> A converted versions of the FastQ file 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz (8726003 sequences in total) Input files are 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:21128:1084_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 TATATTTATGGTGTTATTATATATGATTTTGTATGAAGTGGAAAGAGTTTGTTAATATGTATGATTGGTTTTTTATATTTATGAATAATTAAATATGTAGGGGAGGATTTAGGGGATAGGTGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:21128:1084_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 TTATTTATTTTATTATTATTTATTTATTTATTTCTTTATTTTTACAAAATACTACTTATTTTAAATTTAAAAAACTACAAATCACCTCAAAAAAATACCCACCCCCTACACCTATCCCCTAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2G2_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)) Created C -> T as well as G -> A converted versions of the FastQ file 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz (8726002 sequences in total) Input files are 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:23531:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 AAATAAATAAATATATTAAAAAATTTTAATTAATAAAAAATAATTAATTATATATTATAATAAAATATTAATAAAATATAATAAAATTTTAAAAATTTAAAATAATTAATAATAAATATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:23531:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 AAATAAATAAATATATTAAAAAATTTTAATTAATAAAAAATAATTAATTATATATTATAATAAAATATTAATAAAATATAATAAAATTTTAAAAATTTAAAATAATTAATAATAAATATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:7545:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 ATTTATTAAAAATAAAATTAAAATAATAAATTATAATTTTTTTTAAATATAATTAAAAAATATTTTAATTTTTACTAATTAATTAAAATAACTATTATAATTAAATTATTTAATTTTATATATTA I-IIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9I-III9IIIIII-IIIIIIIII9IIIIII--9IIIIIIIIIII9I--I9-IIIIII99II-I--9IIIIIIIIIIII9I- YT:Z:UP LH00652:104:22KG7JLT4:7:1101:7545:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 ATTTATTAAAAATAAAATTAAAATAATAAATTATAATTTTTTTTAAATATAATTAAAAAATATTTTAATTTTTTTTAAAAAAAATTTTTAAAAAAATAATTAAAATTAAAAAAATTTTAATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII-III9II9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:21128:1084_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 TATATTTATAATATTATTATATATAATTTTATATAAAATAAAAAAAATTTATTAATATATATAATTAATTTTTTATATTTATAAATAATTAAATATATAAAAAAAAATTTAAAAAATAAATATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:21128:1084_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 TTATTTATTTTATTATTATTTATTTATTTATTTTTTTATTTTTATAAAATATTATTTATTTTAAATTTAAAAAATTATAAATTATTTTAAAAAAATATTTATTTTTTATATTTATTTTTTAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:8467:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 TTTTATGTATTGTATGGTGGGTGGTGTGTTGGAGTTTTGTTTTAGTTAAATGTTTGTTGTGATTAGATTTGTTTTGATTAGATTTGGTAGAGTGGTGTTTTGTGTATGGGTAGGGGGTAAAAATT IIIIIIIIIIIIIII9IIIIIIIIII9III9IIIIIII9III-I-9I-II-9II99II-II--I-9I--9-999I99-II9I9II9II99I9III-I-9--9------99-99--9999999--- YT:Z:UP LH00652:104:22KG7JLT4:7:1101:8467:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 CAAAAATTAATTAAACATATTATTCACACTAAACTATAAAAAATTTCCATCCCTTTTCACACTTAACCTAATAACCAATTAAATTCCAAACCTTATAAATAATTTTACCACCTACCCATACACCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:7545:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 ATTTATTAAAAATAAAATTAAAATAATAAATTATAATTTTTTTTAAATATAATTAAAAAATATTTTAATTTTTACTAATTAATTAAAATAACTATTATAATTAAATTATTTAATTTTATATATTA I-IIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9I-III9IIIIII-IIIIIIIII9IIIIII--9IIIIIIIIIII9I--I9-IIIIII99II-I--9IIIIIIIIIIII9I- YT:Z:UP LH00652:104:22KG7JLT4:7:1101:7545:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 ATTTATTAAAAATAAAATTAAAATAATAAATTATAATTTTTTTTAAATATAATTAAAAAATATTTTAATTTTTTTTAAAAAAAATTTTTAAAAAAATAATTAAAATTAAAAAAATTTTAATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII-III9II9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:7545:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 ATTTGTTAAAAATAAAATTGAGGTAATAAATTGTGGTTTTTTTTAGATATAATTGAAAGGTATTTTAATTTTTATTGGTTGGTTAAAATAGTTATTATAATTAAATTATTTAGTTTTGTATGTTA I-IIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9I-III9IIIIII-IIIIIIIII9IIIIII--9IIIIIIIIIII9I--I9-IIIIII99II-I--9IIIIIIIIIIII9I- YT:Z:UP LH00652:104:22KG7JLT4:7:1101:7545:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 ATTTACCAAAAACAAAACCAAAACAATAAATTATAATTCCTTCTAAATACAACTAAAAAATATTTTAACTTCCTCTAAAAAAAACTTCCAAAAAAATAATTAAAACTAAAAAAATCTCAACAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIII-III9II9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIII YT:Z:UP Found first alignment: LH00652:104:22KG7JLT4:7:1101:8467:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 TTTTATATATTATATAATAAATAATATATTAAAATTTTATTTCAATTAAATATTTATTATAATTAAATTTATTTTAATTAAATTTAATAAAATAATATTTTATATATAAATAAAAAATAAAAATC IIIIIIIIIIIIIII9IIIIIIIIII9III9IIIIIII9III-I-9I-II-9II99II-II--I-9I--9-999I99-II9I9II9II99I9III-I-9--9------99-99--9999999--- YT:Z:UP LH00652:104:22KG7JLT4:7:1101:8467:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 TAAAAATTAATTAAATATATTATTTATATTAAATTATAAAAAATTTTTATTTTTTTTTATATTTAATTTAATAATTAATTAAATTTTAAATTTTATAAATAATTTTATTATTTATTTATATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2G2_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)) >>> Writing bisulfite mapping results to 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:21128:1084_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 TATATTTATAATATTATTATATATAATTTTATATAAAATAAAAAAAATTTATTAATATATATAATTAATTTTTTATATTTATAAATAATTAAATATATAAAAAAAAATTTAAAAAATAAATATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:21128:1084_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 TTATTTATTTTATTATTATTTATTTATTTATTTTTTTATTTTTATAAAATATTATTTATTTTAAATTTAAAAAATTATAAATTATTTTAAAAAAATATTTATTTTTTATATTTATTTTTTAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:23531:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 AAATAAATAAATATATTAAAAAATTTTAATTAATAAAAAATAATTAATTATATATTATAATAAAATATTAATAAAATATAATAAAATTTTAAAAATTTAAAATAATTAATAATAAATATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:23531:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 AAATAAATAAATATATTAAAAAATTTTAATTAATAAAAAATAATTAATTATATATTATAATAAAATATTAATAAAATATAATAAAATTTTAAAAATTTAAAATAATTAATAATAAATATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:21128:1084_1:N:0:CCGCTTAA+ACGATGAC/1 83 ptg000035l_GA_converted 9038303 42 125M = 9038198 -230 CTACACCTATCCCCTAAATCCTCCCCTACATATTTAATTATTCATAAATATAAAAAACCAATCATACATATTAACAAACTCTTTCCACTTCATACAAAATCATATATAATAACACCATAAATATA 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 LH00652:104:22KG7JLT4:7:1101:21128:1084_2:N:0:CCGCTTAA+ACGATGAC/2 163 ptg000035l_GA_converted 9038198 42 125M = 9038303 230 TTATTTATTTTATTATTATTTATTTATTTATTTCTTTATTTTTACAAAATACTACTTATTTTAAATTTAAAAAACTACAAATCACCTCAAAAAAATACCCACCCCCTACACCTATCCCCTAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:42A82 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00652:104:22KG7JLT4:7:1101:23531:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 AAATAAATAAATATATTAAAGAGTTTTAATTGATAAGGGATGATTAATTATATATTGTGATAAGGTATTAATAAGGTGTGGTGGAGTTTTAAGAATTTGGAGTAATTGATGATAAATATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:23531:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 AAATAAATAAATATATTAAAAAACCCCAATTAACAAAAAATAACTAATTATATACTATAATAAAATATTAATAAAACATAATAAAATTTCAAAAATTCAAAACAACCAATAACAAACATCCATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:8467:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 TTTTATATATTATATAATAAATAATATATTAAAATTTTATTTCAATTAAATATTTATTATAATTAAATTTATTTTAATTAAATTTAATAAAATAATATTTTATATATAAATAAAAAATAAAAATC IIIIIIIIIIIIIII9IIIIIIIIII9III9IIIIIII9III-I-9I-II-9II99II-II--I-9I--9-999I99-II9I9II9II99I9III-I-9--9------99-99--9999999--- YT:Z:UP LH00652:104:22KG7JLT4:7:1101:8467:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 TAAAAATTAATTAAATATATTATTTATATTAAATTATAAAAAATTTTTATTTTTTTTTATATTTAATTTAATAATTAATTAAATTTTAAATTTTATAAATAATTTTATTATTTATTTATATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz Found first alignment: LH00652:104:22KG7JLT4:7:1101:8467:1098_1:N:0:CCGCTTAA+ACGATGAC/1 83 ptg000025l_GA_converted 8965343 24 2M1I100M1I21M = 8965243 -223 AATTTTTACCCCCTACCCATACACAAAACACCACTCTACCAAATCTAATCAAAACAAATCTAATCACAACAAACATTTAACTAAAACAAAACTCCAACACACCACCCACCATACAATACATAAAA ---9999999--99-99------9--9-I-III9I99II9II9I9II-99I999-9--I9-I--II-II99II9-II-I9-I-III9IIIIIII9III9IIIIIIIIII9IIIIIIIIIIIIIII AS:i:-34 XN:i:0 XM:i:3 XO:i:2 XG:i:2 NM:i:5 MD:Z:9A13C57T41 YS:i:-24 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:8467:1098_2:N:0:CCGCTTAA+ACGATGAC/2 163 ptg000025l_GA_converted 8965243 24 125M = 8965343 223 CAAAAATTAATTAAACATATTATTCACACTAAACTATAAAAAATTTCCATCCCTTTTCACACTTAACCTAATAACCAATTAAATTCCAAACCTTATAAATAATTTTACCACCTACCCATACACCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:44A17C12A8A40 YS:i:-34 YT:Z:CP >>> Writing bisulfite mapping results to 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz (8726002 sequences in total) Input files are 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2G2_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 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:17350:1098_1:N:0:CCGCTTAA+ACGATGAC/1 99 ptg000023l_CT_converted 32115021 0 125M = 32115035 131 GGAGTAAAAAGAGATATTTGTAAATAGTAAATAGTATTTTTTTTGTTATATAGGGTAATTGTTTATGTTTTAAAATGGGTTTGATTGGAAAGATGTGATTTTTGTTATAGTATTATTTTAAGGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII9IIIII9I AS:i:-42 XS:i:-36 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:3A1G14A33T2T65A0A0 YS:i:-52 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:17350:1098_2:N:0:CCGCTTAA+ACGATGAC/2 147 ptg000023l_CT_converted 32115035 0 109M5I3M3I5M = 32115021 -131 TATTTGTAAATAGTAAATAGTATTTTTTTTGTTATATAGGGTAATTGTTTATGTTTTAAAATGGGTTTGATTGGAAAGATGTGATTTTTGTTATAGTATTATTTTAAGGTTTTTAAAGATGTAAG IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-52 XS:i:-58 XN:i:0 XM:i:3 XO:i:2 XG:i:8 NM:i:11 MD:Z:6A33T2T73 YS:i:-42 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:17350:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 AAAATAAAAAAAAATATTTATAAATAATAAATAATATTTTTTTTATTATATAAAATAATTATTTATATTTTAAAATAAATTCAATTAAAAAAATATAATTTTCATTATAATATTATTTTAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII9IIIII9I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:17350:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 TTTATATTTTTAAAAATTTTAAAATAATATTATAATGAAAATTATATTTTTTTAATTGAATTTATTTTAAAATATAAATAATTATTTTATATAATAAAAAAAATATTATTTATTATTTATAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:17350:1098_1:N:0:CCGCTTAA+ACGATGAC/1 77 * 0 0 * * 0 0 AAAATAAAAAAAAATATTTATAAATAATAAATAATATTTTTTTTATTATATAAAATAATTATTTATATTTTAAAATAAATTCAATTAAAAAAATATAATTTTCATTATAATATTATTTTAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII9IIIII9I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:17350:1098_2:N:0:CCGCTTAA+ACGATGAC/2 141 * 0 0 * * 0 0 TTTATATTTTTAAAAATTTTAAAATAATATTATAATGAAAATTATATTTTTTTAATTGAATTTATTTTAAAATATAAATAATTATTTTATATAATAAAAAAAATATTATTTATTATTTATAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2G2_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: LH00652:104:22KG7JLT4:7:1101:17350:1098_1:N:0:CCGCTTAA+ACGATGAC/1 83 ptg000002l_GA_converted 8366364 25 125M = 8366350 -139 AACCTTAAAATAATACTATAACAAAAATCACATCTTTCCAATCAAACCCATTTTAAAACATAAACAATTACCCTATATAACAAAAAAAATACTATTTACTATTTACAAATATCTCTTTTTACTCC I9IIIII9IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-30 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:70A54 YS:i:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:17350:1098_2:N:0:CCGCTTAA+ACGATGAC/2 163 ptg000002l_GA_converted 8366350 25 125M = 8366364 139 CTTACATCTTTAAAAACCTTAAAATAATACTATAACAAAAATCACATCTTTCCAATCAAACCCATTTTAAAACATAAACAATTACCCTATATAACAAAAAAAATACTATTTACTATTTACAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII AS:i:-6 XS:i:-62 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:84A40 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1229:19510:15124_1:N:0:CCGCTTAA+ACGATGAC ptg000146l 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 LH00652:104:22KG7JLT4:7:1278:5183:22201_1:N:0:CCGCTTAA+ACGATGAC ptg000135l 25311 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1311:8143:14242_1:N:0:CCGCTTAA+ACGATGAC ptg000006l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1323:37259:1448_1:N:0:CCGCTTAA+ACGATGAC ptg000048l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1352:5951:1813_1:N:0:CCGCTTAA+ACGATGAC ptg000109l 39600 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1352:5959:1827_1:N:0:CCGCTTAA+ACGATGAC ptg000109l 39600 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1388:46401:11425_1:N:0:CCGCTTAA+ACGATGAC ptg000115l 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 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2116:28344:21038_1:N:0:CCGCTTAA+ACGATGAC ptg000185l 34486 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 LH00652:104:22KG7JLT4:7:2269:23701:5456_1:N:0:CCGCTTAA+ACGATGAC ptg000159l 1 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2336:21977:10206_1:N:0:CCGCTTAA+ACGATGAC ptg000031l 15849141 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2298:7456:2906_1:N:0:CCGCTTAA+ACGATGAC ptg000048l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2417:30812:28478_1:N:0:CCGCTTAA+ACGATGAC ptg000174l 27224 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2481:28741:24919_1:N:0:CCGCTTAA+ACGATGAC ptg000065l 49672 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2481:28773:24919_1:N:0:CCGCTTAA+ACGATGAC ptg000065l 49672 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1102:5538:1462_1:N:0:CCGCTTAA+ACGATGAC ptg000046l 39583 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2481:28749:24933_1:N:0:CCGCTTAA+ACGATGAC ptg000065l 49672 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1102:5547:1448_1:N:0:CCGCTTAA+ACGATGAC ptg000046l 39583 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1184:17123:15671_1:N:0:CCGCTTAA+ACGATGAC ptg000094l 36816 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1308:24607:15349_1:N:0:CCGCTTAA+ACGATGAC ptg000025l 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1291:5385:10865_1:N:0:CCGCTTAA+ACGATGAC ntLink_0 96471 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1346:12706:14101_1:N:0:CCGCTTAA+ACGATGAC ptg000002l 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 LH00652:104:22KG7JLT4:8:1370:25618:25760_1:N:0:CCGCTTAA+ACGATGAC ptg000092l 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2149:33465:16736_1:N:0:CCGCTTAA+ACGATGAC ptg000022l 9976728 Processed 7000000 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 LH00652:104:22KG7JLT4:8:2162:6445:5190_1:N:0:CCGCTTAA+ACGATGAC ptg000052l 52605 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2276:35528:15321_1:N:0:CCGCTTAA+ACGATGAC ptg000108l 1 Processed 7000000 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 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2447:32858:17338_1:N:0:CCGCTTAA+ACGATGAC ptg000048l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2427:13370:21444_1:N:0:CCGCTTAA+ACGATGAC ptg000027l 1 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 8704332 (99.75%) aligned concordantly 0 times 8418 (0.10%) aligned concordantly exactly 1 time 13253 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 3901625 (44.71%) aligned concordantly 0 times 1909037 (21.88%) aligned concordantly exactly 1 time 2915341 (33.41%) aligned concordantly >1 times 55.29% overall alignment rate 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 8705145 (99.76%) aligned concordantly 0 times 8548 (0.10%) aligned concordantly exactly 1 time 12310 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 3895538 (44.64%) aligned concordantly 0 times 1908494 (21.87%) aligned concordantly exactly 1 time 2921971 (33.49%) aligned concordantly >1 times 55.36% overall alignment rate Processed 8726003 sequences in total Successfully deleted the temporary files 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8726003 Final Cytosine Methylation Report ================================= Total number of C's analysed: 247764730 Total methylated C's in CpG context: 4050119 Total methylated C's in CHG context: 218210 Total methylated C's in CHH context: 952240 Total methylated C's in Unknown context: 7505 Total unmethylated C's in CpG context: 34322176 Total unmethylated C's in CHG context: 41895972 Total unmethylated C's in CHH context: 166326013 Total unmethylated C's in Unknown context: 362956 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 8000000 sequence pairs so far 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 8703974 (99.75%) aligned concordantly 0 times 8543 (0.10%) aligned concordantly exactly 1 time 13485 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 3901904 (44.72%) aligned concordantly 0 times 1908469 (21.87%) aligned concordantly exactly 1 time 2915629 (33.41%) aligned concordantly >1 times 55.28% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 8705029 (99.76%) aligned concordantly 0 times 8537 (0.10%) aligned concordantly exactly 1 time 12436 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 3894906 (44.64%) aligned concordantly 0 times 1911039 (21.90%) aligned concordantly exactly 1 time 2920057 (33.46%) aligned concordantly >1 times 55.36% overall alignment rate Processed 8726002 sequences in total Successfully deleted the temporary files 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8726002 Final Cytosine Methylation Report ================================= Total number of C's analysed: 247691086 Total methylated C's in CpG context: 4049735 Total methylated C's in CHG context: 217549 Total methylated C's in CHH context: 954331 Total methylated C's in Unknown context: 7341 Total unmethylated C's in CpG context: 34278782 Total unmethylated C's in CHG context: 41883156 Total unmethylated C's in CHH context: 166307533 Total unmethylated C's in Unknown context: 362104 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Now waiting for all child processes to complete 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 3901255 (44.71%) aligned concordantly 0 times 1908715 (21.87%) aligned concordantly exactly 1 time 2916033 (33.42%) aligned concordantly >1 times 55.29% overall alignment rate 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 3897996 (44.67%) aligned concordantly 0 times 1909209 (21.88%) aligned concordantly exactly 1 time 2918798 (33.45%) aligned concordantly >1 times 55.33% overall alignment rate 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 8705229 (99.76%) aligned concordantly 0 times 8482 (0.10%) aligned concordantly exactly 1 time 12292 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8726003 reads; of these: 8726003 (100.00%) were paired; of these: 8704147 (99.75%) aligned concordantly 0 times 8506 (0.10%) aligned concordantly exactly 1 time 13350 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate Processed 8726003 sequences in total Successfully deleted the temporary files 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8726003 Final Cytosine Methylation Report ================================= Total number of C's analysed: 247628790 Total methylated C's in CpG context: 4051687 Total methylated C's in CHG context: 217684 Total methylated C's in CHH context: 956934 Total methylated C's in Unknown context: 7537 Total unmethylated C's in CpG context: 34269515 Total unmethylated C's in CHG context: 41866620 Total unmethylated C's in CHH context: 166266350 Total unmethylated C's in Unknown context: 363597 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 8704176 (99.75%) aligned concordantly 0 times 8603 (0.10%) aligned concordantly exactly 1 time 13223 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 3899363 (44.69%) aligned concordantly 0 times 1910119 (21.89%) aligned concordantly exactly 1 time 2916520 (33.42%) aligned concordantly >1 times 55.31% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 8705439 (99.76%) aligned concordantly 0 times 8360 (0.10%) aligned concordantly exactly 1 time 12203 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 3897114 (44.66%) aligned concordantly 0 times 1906041 (21.84%) aligned concordantly exactly 1 time 2922847 (33.50%) aligned concordantly >1 times 55.34% overall alignment rate Processed 8726002 sequences in total Successfully deleted the temporary files 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8726002 Final Cytosine Methylation Report ================================= Total number of C's analysed: 247586528 Total methylated C's in CpG context: 4040689 Total methylated C's in CHG context: 216783 Total methylated C's in CHH context: 954393 Total methylated C's in Unknown context: 7504 Total unmethylated C's in CpG context: 34288715 Total unmethylated C's in CHG context: 41862033 Total unmethylated C's in CHH context: 166223915 Total unmethylated C's in Unknown context: 363194 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2415:1704:16624_1:N:0:CCGCTTAA+ACGATGAC ptg000048l 76428 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 3895088 (44.64%) aligned concordantly 0 times 1910274 (21.89%) aligned concordantly exactly 1 time 2920640 (33.47%) aligned concordantly >1 times 55.36% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 8705071 (99.76%) aligned concordantly 0 times 8660 (0.10%) aligned concordantly exactly 1 time 12271 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 8704346 (99.75%) aligned concordantly 0 times 8379 (0.10%) aligned concordantly exactly 1 time 13277 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8726002 reads; of these: 8726002 (100.00%) were paired; of these: 3900667 (44.70%) aligned concordantly 0 times 1908629 (21.87%) aligned concordantly exactly 1 time 2916706 (33.43%) aligned concordantly >1 times 55.30% overall alignment rate Processed 8726002 sequences in total Successfully deleted the temporary files 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2G2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8726002 Final Cytosine Methylation Report ================================= Total number of C's analysed: 247697885 Total methylated C's in CpG context: 4056376 Total methylated C's in CHG context: 218147 Total methylated C's in CHH context: 962775 Total methylated C's in Unknown context: 7588 Total unmethylated C's in CpG context: 34300923 Total unmethylated C's in CHG context: 41890242 Total unmethylated C's in CHH context: 166269422 Total unmethylated C's in Unknown context: 363217 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 2G2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 2G2_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 2G2_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/2G2_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 2G2_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/2G2_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 2G2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 2G2_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: 43630012 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1238369019 Total methylated C's in CpG context: 20248606 Total methylated C's in CHG context: 1088373 Total methylated C's in CHH context: 4780673 Total methylated C's in Unknown context: 37475 Total unmethylated C's in CpG context: 171460111 Total unmethylated C's in CHG context: 209398023 Total unmethylated C's in CHH context: 831393233 Total unmethylated C's in Unknown context: 1815068 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Deleting temporary report files... Bismark completed in 0d 8h 14m 46s ==================== Bismark run complete ====================