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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_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/1B1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8059367) Using the subset file >1B1_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/1B1_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/1B1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8059366) Using the subset file >1B1_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/1B1_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/1B1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8059367) Using the subset file >1B1_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/1B1_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/1B1_R1_001.fastp-trim.fq.gz for PID: 82846 and offset 5 (sequences written out: 8059366) Using the subset file >1B1_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/1B1_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/1B1_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8059367) Using the subset file >1B1_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/1B1_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/1B1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8059367) Using the subset file >1B1_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/1B1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B1_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/1B1_R2_001.fastp-trim.fq.gz for PID: 82846 and offset 5 (sequences written out: 8059366) Using the subset file >1B1_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/1B1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B1_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/1B1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8059367) Using the subset file >1B1_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/1B1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B1_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/1B1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8059366) Using the subset file >1B1_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/1B1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B1_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/1B1_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8059367) Using the subset file >1B1_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/1B1_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B1_R1_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 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz (8059367 sequences in total) Writing a C -> T converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz (8059367 sequences in total) Writing a C -> T converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz (8059366 sequences in total) Writing a C -> T converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz (8059366 sequences in total) Writing a C -> T converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz (8059367 sequences in total) Writing a C -> T converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B1_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 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz (8059367 sequences in total) Input files are 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz (8059366 sequences in total) Input files are 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45710:1070_1:N:0:TTGCGAGA+GTGCCATA/1 99 ptg000020l_CT_converted 15598844 24 125M = 15598890 171 TATTAAAAGTTGGATAAAAAAAAAAAGAAAAATGTAGTTTTTTATAAGATAGAATTTTTATTTAGAGATATATTTAGTTATATTAATGTTTTTTTGGTTAGTTATTAAATAAAGTTATAATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:58A15A45G4 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45710:1070_2:N:0:TTGCGAGA+GTGCCATA/2 147 ptg000020l_CT_converted 15598890 24 125M = 15598844 -171 AGATAGAATTTTTATTTAGAGATATATTTAGTTATATTAATGTTTTTTTGGTTAGTTATTAAATAAAGTTATAATTTATATGAAAAGTTGTATTGTTTTTGTTTTTTGTTAATATTTATTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:12A15A45G20G13A15 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:51504:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAAAATAATTATTGATGTGAATATAGTTATTTTGTATTTTGTATTTAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51504:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 CTATATTCACATCAATAATTATTTTATATATACTAAACCAAATATAATTCAAAATCAAAAAAACATCATAAAAAAAAAAAAAATATATCCTAATATAAACTTCTATTATATTCATATCCCTCCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIII99IIII--II--9-9-------------9--99----9--------9-9-99-I9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B1_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 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz (8059367 sequences in total) Input files are 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43023:1070_1:N:0:TTGCGAGA+GTGCCATA/1 99 ptg000016l_CT_converted 7771137 2 125M = 7771161 149 TGATTTAAAGTGAGGATTTTGTATGGGTTATAGTTTTTGTATGATTGTTGATTTTTAAAATGTTTTTATTTTTTGAATATTTGGTTTTTTTTTGAGTGGTTTTTTGTATAGAATAATTGTAAATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII--IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-36 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:3G53G27G6G0A31 YS:i:-48 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43023:1070_2:N:0:TTGCGAGA+GTGCCATA/2 147 ptg000016l_CT_converted 7771161 2 125M = 7771137 -149 GGGTTATAGTTTTTGTATGATTGTTGATTTTTAAAATGTTTTTATTTTTTGAATATTTGGTTTTTTTTTGAGTGGTTTTTTGTATAGAATAATTGTAAATGATGTGTTAAATGGATTTTGATATA IIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIIIIIIIIIIII-I9IIII-IIIIIIIIII9II-III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-48 XS:i:-54 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:33G27G6G0A33T3A0G15G0 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:51504:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAAAATAATTATTAATATAAATATAATTATTTTATATTTTATATTTAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51504:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TTATATTTATATTAATAATTATTTTATATATATTAAATTAAATATAATTTAAGATTGGAAGAGTGTTGTGGAGGGGAAAAGGGTGTGTTTTAATGTGGGTTTTTGTTGTGTTTATATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIII99IIII--II--9-9-------------9--99----9--------9-9-99-I9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:45710:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TATTAAAAATTAAATAAAAAAAAAAAAAAAAATATAATTTTTTATAAAATAAAATTTTTATTTAAAAATATATTTAATTATATTAATATTTTTTTAATTAATTATTAAATAAAATTATAATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45710:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TTTAAAATAAATATTAATAAAAAATAAAAATGATATAATTTTTTATATAAATTATAATTTTATTTAATAATTAATTAAAAAAATATTAATATAATTAAATATATTTTTAAATAAAAATTTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B1_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz (8059367 sequences in total) Input files are 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45710:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TATTAAAAATTAAATAAAAAAAAAAAAAAAAATATAATTTTTTATAAAATAAAATTTTTATTTAAAAATATATTTAATTATATTAATATTTTTTTAATTAATTATTAAATAAAATTATAATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45710:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TTTAAAATAAATATTAATAAAAAATAAAAATGATATAATTTTTTATATAAATTATAATTTTATTTAATAATTAATTAAAAAAATATTAATATAATTAAATATATTTTTAAATAAAAATTTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:51504:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAAAATAATTATTAATATAAATATAATTATTTTATATTTTATATTTAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51504:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TTATATTTATATTAATAATTATTTTATATATATTAAATTAAATATAATTTAAGATTGGAAGAGTGTTGTGGAGGGGAAAAGGGTGTGTTTTAATGTGGGTTTTTGTTGTGTTTATATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIII99IIII--II--9-9-------------9--99----9--------9-9-99-I9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:43023:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAATTTAAAATAAAAATTTTATATAAATTATAATTTTTATATAATTATTAATTTTTAAAATATTTTTATTTTTTAAATATTTAATTTTTTTTTAAATAATTTTTTATATAAAATAATTATAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII--IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43023:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TATATTAAAATTTATTTAATATATTATTTATAATTATTTTATATAAAAAATTATTTAAAAAAAAATTAAATATTTAAAAAATAAAAATATTTTAAAAATTAATAATTATATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-II9IIIIIIIIII-IIII9I-IIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:43039:1070_1:N:0:TTGCGAGA+GTGCCATA/1 99 ptg000016l_CT_converted 7768474 0 13M1I111M = 7768497 148 TGATTTAAAGTGAGGATTTTGTATGGGTTATAGTTTTTGTATGATTGTTGATTTTTAAAATGTTTTTATTTTTTGAATATTTGGTTTTTTTTTGAGTGGTTTTTTGTATAGAATAATTGTAAATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-32 XS:i:-36 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:2T81G6G25T6 YS:i:-42 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43039:1070_2:N:0:TTGCGAGA+GTGCCATA/2 147 ptg000016l_CT_converted 7768497 0 125M = 7768474 -148 GGGTTATAGTTTTTGTATGATTGTTGATTTTTAAAATGTTTTTATTTTTTGAATATTTGGTTTTTTTTTGAGTGGTTTTTTGTATAGAATAATTGTAAATGATGTGTTAAATGGATTTTGATATA IIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-42 XS:i:-54 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:61G6G25T8T3A0G15G0 YS:i:-32 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45710:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TATTAAAAGTTGGATAAAAAAAAAAAGAAAAATGTAGTTTTTTATAAGATAGAATTTTTATTTAGAGATATATTTAGTTATATTAATGTTTTTTTGGTTAGTTATTAAATAAAGTTATAATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45710:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 CTCAAAATAAATATTAACAAAAAACAAAAACAATACAACTTTTCATATAAATTATAACTTTATTTAATAACTAACCAAAAAAACATTAATATAACTAAATATATCTCTAAATAAAAATTCTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:51504:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAAAATAATTATTGATGTGAATATAGTTATTTTGTATTTTGTATTTAAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51504:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 CTATATTCACATCAATAATTATTTTATATATACTAAACCAAATATAATTCAAAATCAAAAAAACATCATAAAAAAAAAAAAAATATATCCTAATATAAACTTCTATTATATTCATATCCCTCCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIII99IIII--II--9-9-------------9--99----9--------9-9-99-I9 YT:Z:UP >>> Writing bisulfite mapping results to 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:43039:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAATTTAAAATAAAAATTTTATATAAATTATAATTTTTATATAATTATTAATTTTTAAAATATTTTTATTTTTTAAATATTTAATTTTTTTTTAAATAATTTTTTATATAAAATAATTATAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43039:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TATATTAAAATTTATTTAATATATTATTTATAATTATTTTATATAAAAAATTATTTAAAAAAAAATTAAATATTTAAAAAATAAAAATATTTTAAAAATTAATAATTATATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:43023:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAATTTAAAATAAAAATTTTATATAAATTATAATTTTTATATAATTATTAATTTTTAAAATATTTTTATTTTTTAAATATTTAATTTTTTTTTAAATAATTTTTTATATAAAATAATTATAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII--IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43023:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TATATTAAAATTTATTTAATATATTATTTATAATTATTTTATATAAAAAATTATTTAAAAAAAAATTAAATATTTAAAAAATAAAAATATTTTAAAAATTAATAATTATATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-II9IIIIIIIIII-IIII9I-IIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B1_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)) Reading in the sequence files 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:43039:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 TAATTTAAAATAAAAATTTTATATAAATTATAATTTTTATATAATTATTAATTTTTAAAATATTTTTATTTTTTAAATATTTAATTTTTTTTTAAATAATTTTTTATATAAAATAATTATAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43039:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TATATTAAAATTTATTTAATATATTATTTATAATTATTTTATATAAAAAATTATTTAAAAAAAAATTAAATATTTAAAAAATAAAAATATTTTAAAAATTAATAATTATATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:43023:1070_1:N:0:TTGCGAGA+GTGCCATA/1 83 ptg000004l_GA_converted 1626150 1 125M = 1626126 -149 CATTTACAATTATTCTATACAAAAAACCACTCAAAAAAAAACCAAATATTCAAAAAATAAAAACATTTTAAAAATCAACAATCATACAAAAACTATAACCCATACAAAATCCTCACTTTAAATCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII--IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:39C85 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43023:1070_2:N:0:TTGCGAGA+GTGCCATA/2 163 ptg000004l_GA_converted 1626126 1 125M = 1626150 149 TATATCAAAATCCATTTAACACATCATTTACAATTATTCTATACAAAAAACCACTCAAAAAAAAACCAAATATTCAAAAAATAAAAACATTTTAAAAATCAACAATCATACAAAAACTATAACCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-II9IIIIIIIIII-IIII9I-IIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C15C0T3A41C61 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz (8059366 sequences in total) Input files are 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B1_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 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:43039:1070_1:N:0:TTGCGAGA+GTGCCATA/1 83 ptg000004l_GA_converted 1626150 1 125M = 1626126 -149 CATTTACAATTATTCTATACAAAAAACCACTCAAAAAAAAACCAAATATTCAAAAAATAAAAACATTTTAAAAATCAACAATCATACAAAAACTATAACCCATACAAAATCCTCACTTTAAATCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:39C85 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43039:1070_2:N:0:TTGCGAGA+GTGCCATA/2 163 ptg000004l_GA_converted 1626126 1 125M = 1626150 149 TATATCAAAATCCATTTAACACATCATTTACAATTATTCTATACAAAAAACCACTCAAAAAAAAACCAAATATTCAAAAAATAAAAACATTTTAAAAATCAACAATCATACAAAAACTATAACCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C15C0T3A41C61 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:49642:1070_1:N:0:TTGCGAGA+GTGCCATA/1 99 ptg000018l_CT_converted 7195140 11 125M = 7195252 237 GGTAAAGAAGATTTTAGGTTTATAGTTTTTTAAAGTATTAGTTGGTAATTTAGTATTTGTTTTAAATATATTGTTTGGTTTTGTAATAAGTTATTGTTATAGGTATGAAAAATATAATGTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-36 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:16A78T29 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49642:1070_2:N:0:TTGCGAGA+GTGCCATA/2 147 ptg000018l_CT_converted 7195252 11 125M = 7195140 -237 TATAATGTTTTTTTTTGTTATGTTTTTGATGGTAATATATATTAAAGATTTATTATTTTTTTATTTAAGTTTTTGTGTAGTTTTTTATTTTTATTAATATTTAAAGGAAAAATATGTATGAAGAA IIII9IIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:24G26T73 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B1_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)) Reading in the sequence files 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:49642:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 AATAAAAAAAATTTTAAATTTATAATTTTTTAAAATATTAATTAATAATTTAATATTTATTTTAAATATATTATTTAATTTTATAATAAATTATTATTATAAATATAAAAAATATAATATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49642:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TTTTTTATATATATTTTTTTTTTAAATATTAATAAAAATAAAAAATTATATAAAAATTTAAATAAAAAAATAATAAATTTTTAATATATATTATTATTAAAAATATAATAAAAAAAAATATTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:49642:1070_1:N:0:TTGCGAGA+GTGCCATA/1 77 * 0 0 * * 0 0 AATAAAAAAAATTTTAAATTTATAATTTTTTAAAATATTAATTAATAATTTAATATTTATTTTAAATATATTATTTAATTTTATAATAAATTATTATTATAAATATAAAAAATATAATATTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49642:1070_2:N:0:TTGCGAGA+GTGCCATA/2 141 * 0 0 * * 0 0 TTTTTTATATATATTTTTTTTTTAAATATTAATAAAAATAAAAAATTATATAAAAATTTAAATAAAAAAATAATAAATTTTTAATATATATTATTATTAAAAATATAATAAAAAAAAATATTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B1_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: LH00526:197:22KFKVLT4:3:1101:49642:1070_1:N:0:TTGCGAGA+GTGCCATA/1 83 ntLink_8_GA_converted 4276949 7 125M = 4276837 -237 AAAAAACATTATATTTTTCATACCTATAACAATAACTTATTACAAAACCAAACAATATATTTAAAACAAATACTAAATTACCAACTAATACTTTAAAAAACTATAAACCTAAAATCTTCTTTACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-36 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:16A12A5A17C54T16 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49642:1070_2:N:0:TTGCGAGA+GTGCCATA/2 163 ntLink_8_GA_converted 4276837 7 125M = 4276949 237 TTCTTCATACATATTTTTCCTTTAAATATTAATAAAAATAAAAAACTACACAAAAACTTAAATAAAAAAATAATAAATCTTTAATATATATTACCATCAAAAACATAACAAAAAAAAACATTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIIIII9IIII AS:i:-12 XS:i:-32 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:78A21C24 YS:i:-30 YT:Z:CP >>> Writing bisulfite mapping results to 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1262:28473:3535_1:N:0:TTGCGAGA+GTGCCATA ptg000026l 14741924 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1412:5103:18075_1:N:0:TTGCGAGA+GTGCCATA ptg000118l 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 LH00526:197:22KFKVLT4:3:2168:7288:10819_1:N:0:TTGCGAGA+GTGCCATA ptg000083l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2198:17055:21872_1:N:0:TTGCGAGA+GTGCCATA ptg000015l 14997092 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2415:6503:24197_1:N:0:TTGCGAGA+GTGCCATA ptg000007l 12295912 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2485:20737:15974_1:N:0:TTGCGAGA+GTGCCATA ptg000006l 3 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1453:23043:17669_1:N:0:TTGCGAGA+GTGCCATA ptg000174l 27225 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1493:9473:24435_1:N:0:TTGCGAGA+GTGCCATA ptg000083l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1392:6681:23356_1:N:0:TTGCGAGA+GTGCCATA ptg000056l 59103 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2133:47482:8060_1:N:0:TTGCGAGA+GTGCCATA ptg000039l 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2146:47846:20373_1:N:0:TTGCGAGA+GTGCCATA ptg000025l 21443081 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 3553459 (44.09%) aligned concordantly 0 times 1706585 (21.18%) aligned concordantly exactly 1 time 2799322 (34.73%) aligned concordantly >1 times 55.91% overall alignment rate 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 8037740 (99.73%) aligned concordantly 0 times 8415 (0.10%) aligned concordantly exactly 1 time 13211 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 3548316 (44.03%) aligned concordantly 0 times 1708069 (21.19%) aligned concordantly exactly 1 time 2802981 (34.78%) aligned concordantly >1 times 55.97% overall alignment rate 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 8035764 (99.71%) aligned concordantly 0 times 8533 (0.11%) aligned concordantly exactly 1 time 15069 (0.19%) aligned concordantly >1 times 0.29% overall alignment rate Processed 8059366 sequences in total Successfully deleted the temporary files 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8059366 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221492434 Total methylated C's in CpG context: 4130865 Total methylated C's in CHG context: 227224 Total methylated C's in CHH context: 999674 Total methylated C's in Unknown context: 7046 Total unmethylated C's in CpG context: 30403044 Total unmethylated C's in CHG context: 37253459 Total unmethylated C's in CHH context: 148478168 Total unmethylated C's in Unknown context: 312607 C methylated in CpG context: 12.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Now waiting for all child processes to complete Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2484:5046:22516_1:N:0:TTGCGAGA+GTGCCATA ptg000057l 39942 Processed 8000000 sequence pairs so far 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 3551187 (44.06%) aligned concordantly 0 times 1709551 (21.21%) aligned concordantly exactly 1 time 2798628 (34.73%) aligned concordantly >1 times 55.94% overall alignment rate 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 8037459 (99.73%) aligned concordantly 0 times 8606 (0.11%) aligned concordantly exactly 1 time 13301 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 3547332 (44.02%) aligned concordantly 0 times 1709085 (21.21%) aligned concordantly exactly 1 time 2802949 (34.78%) aligned concordantly >1 times 55.98% overall alignment rate 8059366 reads; of these: 8059366 (100.00%) were paired; of these: 8035453 (99.70%) aligned concordantly 0 times 8636 (0.11%) aligned concordantly exactly 1 time 15277 (0.19%) aligned concordantly >1 times 0.30% overall alignment rate Processed 8059366 sequences in total Successfully deleted the temporary files 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8059366 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221612520 Total methylated C's in CpG context: 4132723 Total methylated C's in CHG context: 226943 Total methylated C's in CHH context: 1001726 Total methylated C's in Unknown context: 6958 Total unmethylated C's in CpG context: 30414688 Total unmethylated C's in CHG context: 37253521 Total unmethylated C's in CHH context: 148582919 Total unmethylated C's in Unknown context: 313706 C methylated in CpG context: 12.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2350:11358:20919_1:N:0:TTGCGAGA+GTGCCATA ptg000018l 1 Processed 8000000 sequence pairs so far 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 8035714 (99.71%) aligned concordantly 0 times 8592 (0.11%) aligned concordantly exactly 1 time 15061 (0.19%) aligned concordantly >1 times 0.29% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 8038066 (99.74%) aligned concordantly 0 times 8365 (0.10%) aligned concordantly exactly 1 time 12936 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 3554235 (44.10%) aligned concordantly 0 times 1706805 (21.18%) aligned concordantly exactly 1 time 2798327 (34.72%) aligned concordantly >1 times 55.90% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 3547703 (44.02%) aligned concordantly 0 times 1709136 (21.21%) aligned concordantly exactly 1 time 2802528 (34.77%) aligned concordantly >1 times 55.98% overall alignment rate Processed 8059367 sequences in total Successfully deleted the temporary files 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8059367 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221569367 Total methylated C's in CpG context: 4141855 Total methylated C's in CHG context: 226122 Total methylated C's in CHH context: 1003922 Total methylated C's in Unknown context: 7160 Total unmethylated C's in CpG context: 30378976 Total unmethylated C's in CHG context: 37252972 Total unmethylated C's in CHH context: 148565520 Total unmethylated C's in Unknown context: 314746 C methylated in CpG context: 12.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Processed 8000000 sequence pairs so far 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 8037739 (99.73%) aligned concordantly 0 times 8473 (0.11%) aligned concordantly exactly 1 time 13155 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 3554912 (44.11%) aligned concordantly 0 times 1707958 (21.19%) aligned concordantly exactly 1 time 2796497 (34.70%) aligned concordantly >1 times 55.89% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 8035715 (99.71%) aligned concordantly 0 times 8722 (0.11%) aligned concordantly exactly 1 time 14930 (0.19%) aligned concordantly >1 times 0.29% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 3550124 (44.05%) aligned concordantly 0 times 1709056 (21.21%) aligned concordantly exactly 1 time 2800187 (34.74%) aligned concordantly >1 times 55.95% overall alignment rate Processed 8059367 sequences in total Successfully deleted the temporary files 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8059367 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221613012 Total methylated C's in CpG context: 4124589 Total methylated C's in CHG context: 226242 Total methylated C's in CHH context: 999303 Total methylated C's in Unknown context: 7033 Total unmethylated C's in CpG context: 30414180 Total unmethylated C's in CHG context: 37266512 Total unmethylated C's in CHH context: 148582186 Total unmethylated C's in Unknown context: 315858 C methylated in CpG context: 11.9% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Processed 8000000 sequence pairs so far 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 8037453 (99.73%) aligned concordantly 0 times 8713 (0.11%) aligned concordantly exactly 1 time 13201 (0.16%) aligned concordantly >1 times 0.27% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 8035552 (99.70%) aligned concordantly 0 times 8516 (0.11%) aligned concordantly exactly 1 time 15299 (0.19%) aligned concordantly >1 times 0.30% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 3545988 (44.00%) aligned concordantly 0 times 1709733 (21.21%) aligned concordantly exactly 1 time 2803646 (34.79%) aligned concordantly >1 times 56.00% overall alignment rate 8059367 reads; of these: 8059367 (100.00%) were paired; of these: 3551779 (44.07%) aligned concordantly 0 times 1708443 (21.20%) aligned concordantly exactly 1 time 2799145 (34.73%) aligned concordantly >1 times 55.93% overall alignment rate Processed 8059367 sequences in total Successfully deleted the temporary files 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B1_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8059367 Final Cytosine Methylation Report ================================= Total number of C's analysed: 221581970 Total methylated C's in CpG context: 4129159 Total methylated C's in CHG context: 224586 Total methylated C's in CHH context: 996308 Total methylated C's in Unknown context: 7236 Total unmethylated C's in CpG context: 30394023 Total unmethylated C's in CHG context: 37264244 Total unmethylated C's in CHH context: 148573650 Total unmethylated C's in Unknown context: 314234 C methylated in CpG context: 12.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1B1_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1B1_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1B1_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/1B1_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1B1_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/1B1_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B1_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B1_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: 40296833 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1107869303 Total methylated C's in CpG context: 20659191 Total methylated C's in CHG context: 1131117 Total methylated C's in CHH context: 5000933 Total methylated C's in Unknown context: 35433 Total unmethylated C's in CpG context: 152004911 Total unmethylated C's in CHG context: 186290708 Total unmethylated C's in CHH context: 742782443 Total unmethylated C's in Unknown context: 1571151 C methylated in CpG context: 12.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Deleting temporary report files... Bismark completed in 0d 6h 50m 22s ==================== Bismark run complete ====================