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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_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/1C6_R1_001.fastp-trim.fq.gz for PID: 53882 and offset 5 (sequences written out: 7388243) Using the subset file >1C6_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/1C6_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/1C6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7388244) Using the subset file >1C6_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/1C6_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/1C6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7388243) Using the subset file >1C6_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/1C6_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/1C6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7388244) Using the subset file >1C6_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/1C6_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/1C6_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7388244) Using the subset file >1C6_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/1C6_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/1C6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7388244) Using the subset file >1C6_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/1C6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz to 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz to 1C6_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/1C6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7388243) Using the subset file >1C6_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/1C6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz to 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz to 1C6_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/1C6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7388244) Using the subset file >1C6_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/1C6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz to 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz to 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1C6_R2_001.fastp-trim.fq.gz for PID: 53882 and offset 5 (sequences written out: 7388243) Using the subset file >1C6_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/1C6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz to 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz to 1C6_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/1C6_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7388244) Using the subset file >1C6_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/1C6_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz to 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz to 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz (7388243 sequences in total) Writing a C -> T converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz to 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz to 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz (7388244 sequences in total) Writing a C -> T converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz to 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz to 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz (7388244 sequences in total) Writing a C -> T converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz to 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz to 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz (7388243 sequences in total) Writing a C -> T converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz to 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz to 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz (7388244 sequences in total) Writing a C -> T converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz to 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz to 1C6_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 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz (7388244 sequences in total) Input files are 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz (7388244 sequences in total) Input files are 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:36784:1084_1:N:0:CATGAGCA+GCAAGATC/1 99 ptg000027l_CT_converted 15334818 1 125M = 15334879 186 GTGGATGGTAAGATGGAGTAAGTAAAGTTTTAGAGTTTAATAATGTGATTAAAGTATGAGGTTTGAAAAGTAGTGGTTTTATAAATAGGTATTTTTAGGTTAAGAGAATTATTAAGTTTGGAATG I9IIIIIIIIIIIIIIIIIIIIII-IIIIII9I9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:36784:1084_2:N:0:CATGAGCA+GCAAGATC/2 147 ptg000027l_CT_converted 15334879 1 125M = 15334818 -186 TTTGAAAAGTAGTGGTTTTATAAATAGGTATTTTTAGGTTAAGAGAATTATTAAGTTTGGAATGGTTATGGGAGATAAAGTTAATAAAATAGTGTATATTAAGGTTAATATGGTTGTATAGATAT IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:39203:1070_1:N:0:CATGAGCA+GCAAGATC/1 99 ptg000025l_CT_converted 48529 1 125M = 48792 388 TTTTAAAGTTTATGTTAGGGGTGGGTTTTGATATGATGTTGGGTGGTTGTGTTGGTAATTGGATGTTTTATAAGTTTAAAAGGAAAGAAAATTAATTTTGGTTTATTTTTGTTTGTTTAATGTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIIIIIIIII9IIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39203:1070_2:N:0:CATGAGCA+GCAAGATC/2 147 ptg000025l_CT_converted 48792 1 125M = 48529 -388 TAATTGATTGATTATGGGAAAGAAGTATTTTAGTTTTTTTAGTAAGGTATTTTGAAGATATATTTTTTGGAAGAGAAATTTTGTTTTGTAGTTGTAGTAAATATTATTATTATGGTGGATTATAT IIII9IIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C6_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 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz (7388243 sequences in total) Input files are 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C6_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz (7388244 sequences in total) Input files are 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:41445:1084_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 GGATTGTTGTTAGTGATTGATGTTTTGATAATTTGTGGATGGTAAGAGGAATTGTTTTGTGTTTTTGAGATGGTTAATGTTATTTGTTTAGTGATTTTAAGTTGTATATTTTGAGAGGTATATTA III9II9IIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIII-IIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIII9I9IIIIIIIIIIIIII-9IIIIIIII-I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41445:1084_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 AATACCACAATACTCAACTTCATCACAACTCAACACATACACACTATATTAATTAACACATAATATACCTCTCAAAATATACAACTTAAAATCACTAAACAAATAACATTAACCATCTCAAAAAC IIIIIIIIIIII9IIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-IIIIIIIII9I9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:39203:1070_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 TTTTAAAATTTATATTAAAAATAAATTTTAATACAATATCAAATAATCATATTAATAATTAAATATTTTATAAATTTAAAAAAAAAAAAAATTAATTTTAATTTATTTTTATTTATTTAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39203:1070_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 ATATAATTTATTGTAATAATAATATTTATTATAATTATAAAATAAAATTTTTTTTTTAAAAAATATATTTTTAAAATATTTTATTAAAAAAATTAAAATATTTTTTTTTTATAATTAATTAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:36784:1084_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 ATAAATAATAAAATAAAATAAATAAAATTTTAAAATTTAATAATATAATTAAAATATAAAATTTAAAAAATAATAATTTTATAAATAAATATTTTTAAATTAAAAAAATTATTAAATTTAAAATA I9IIIIIIIIIIIIIIIIIIIIII-IIIIII9I9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:36784:1084_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 ATATTTATATAATTATATTAATTTTAATATATATTATTTTATTAATTTTATTTTTTATAATTATTTTAAATTTAATAATTTTTTTAATTTAAAAATATTTATTTATAAAATTATTATTTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C6_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 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz (7388243 sequences in total) Input files are 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C6_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 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:39203:1070_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 TTTTAAAATTTATATTAAAAATAAATTTTAATACAATATCAAATAATCATATTAATAATTAAATATTTTATAAATTTAAAAAAAAAAAAAATTAATTTTAATTTATTTTTATTTATTTAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39203:1070_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 ATATAATTTATTGTAATAATAATATTTATTATAATTATAAAATAAAATTTTTTTTTTAAAAAATATATTTTTAAAATATTTTATTAAAAAAATTAAAATATTTTTTTTTTATAATTAATTAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43622:1070_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 AATTTTTTTTTTGAAAGTTATAATTAAATAGTATATTTTTGTAATATAGTTATTATATTTGTTTTTGTTAAGTTATTTTTTATTTAATATTTTTTTTATATTAATAAGATATGTTGAATAAATTT IIIIIIIIIIIIIIIIIIII-II9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9III9IIIIIIII-9III99I9II9IIII99IIII9IIIIIII-IIIIII-II9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43622:1070_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 ACATTTTTCCTTTACTAACTTTTTTTATATTAACCCAAATTTATTCAACATATCTTATTAATATAAAAAAAATATTAAATAAAAAATAACTTAACAAAAACAAATATAATAACTATATTACAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:21918:1098_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 TGAATTTTTTTTTAAAAATTGATTTATGTGAGAATAATGGATGAGATTTAATTGTAATTTTAGGTAATGAAAGATATTTATTTGGTAATAATTATTTTTTTGTGTAGGGTTTAAGAAAAGTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:21918:1098_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 CAAATTTTTTCTTAAAAATTAACTTACACAAAAACAATAAATAAAATTCAATTACAATTTTAAACAACAAAAAATACCCATTTAACAATAATTATTTTTTTACACAAAATTTAAAAAAAACTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:36784:1084_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 ATAAATAATAAAATAAAATAAATAAAATTTTAAAATTTAATAATATAATTAAAATATAAAATTTAAAAAATAATAATTTTATAAATAAATATTTTTAAATTAAAAAAATTATTAAATTTAAAATA I9IIIIIIIIIIIIIIIIIIIIII-IIIIII9I9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:36784:1084_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 ATATTTATATAATTATATTAATTTTAATATATATTATTTTATTAATTTTATTTTTTATAATTATTTTAAATTTAATAATTTTTTTAATTTAAAAATATTTATTTATAAAATTATTATTTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:41445:1084_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 AAATTATTATTAATAATTAATATTTTAATAATTTATAAATAATAAAAAAAATTATTTTATATTTTTAAAATAATTAATATTATTTATTTAATAATTTTAAATTATATATTTTAAAAAATATATTA III9II9IIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIII-IIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIII9I9IIIIIIIIIIIIII-9IIIIIIII-I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41445:1084_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 AATATTATAATATTTAATTTTATTATAATTTAATATATATATATTATATTAATTAATATATAATATATTTTTTAAAATATATAATTTAAAATTATTAAATAAATAATATTGATTATTTTAAAAAT IIIIIIIIIIII9IIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-IIIIIIIII9I9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:43622:1070_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 AATTTTTTTTTTAAAAATTATAATTAAATAATATATTTTTATAATATAATTATTATATTTATTTTTATTAAATTATTTTTTATTTAATATTTTTTTTATATTAATAAAATATATTAAATAAATTT IIIIIIIIIIIIIIIIIIII-II9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9III9IIIIIIII-9III99I9II9IIII99IIII9IIIIIII-IIIIII-II9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43622:1070_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 ATATTTTTTTTTTATTAATTTTTTTTATATTAATTTAAATTTATTTAATATATTTTATTAATATAAAAAAAATATTAAATAAAAAATAATTTAATAAAAATAAATATAATAATTATATTATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:21918:1098_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 TAAATTTTTTTTTAAAAATTAATTTATATAAAAATAATAAATAAAATTTAATTATAATTTTAAATAATAAAAAATATTTATTTAATAATAATTATTTTTTTATATAAAATTTAAAAAAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:21918:1098_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 TAAATTTTTTTTTAAAAATTAATTTATATAAAAATAATAAATAAAATTTAATTATAATTTTAAATAATAAAAAATATTTATTTAATAATAATTATTTTTTTATATAAAATTTAAAAAAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:36784:1084_1:N:0:CATGAGCA+GCAAGATC/1 83 ptg000034l_GA_converted 683766 17 125M = 683705 -186 CATTCCAAACTTAATAATTCTCTTAACCTAAAAATACCTATTTATAAAACCACTACTTTTCAAACCTCATACTTTAATCACATTATTAAACTCTAAAACTTTACTTACTCCATCTTACCATCCAC IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9I9IIIIII-IIIIIIIIIIIIIIIIIIIIII9I AS:i:-6 XS:i:-30 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:110T14 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:36784:1084_2:N:0:CATGAGCA+GCAAGATC/2 163 ptg000034l_GA_converted 683705 17 125M = 683766 186 ATATCTATACAACCATATTAACCTTAATATACACTATTTTATTAACTTTATCTCCCATAACCATTCCAAACTTAATAATTCTCTTAACCTAAAAATACCTATTTATAAAACCACTACTTTTCAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-18 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:39203:1070_1:N:0:CATGAGCA+GCAAGATC/1 83 ptg000001l_GA_converted 21452937 1 125M = 21452674 -388 AAACATTAAACAAACAAAAATAAACCAAAATTAATTTTCTTTCCTTTTAAACTTATAAAACATCCAATTACCAACACAACCACCCAACATCATATCAAAACCCACCCCTAACATAAACTTTAAAA IIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39203:1070_2:N:0:CATGAGCA+GCAAGATC/2 163 ptg000001l_GA_converted 21452674 1 125M = 21452937 388 ATATAATCCACCATAATAATAATATTTACTACAACTACAAAACAAAATTTCTCTTCCAAAAAATATATCTTCAAAATACCTTACTAAAAAAACTAAAATACTTCTTTCCCATAATCAATCAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIII9IIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:41445:1084_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 AAATTATTATTAATAATTAATATTTTAATAATTTATAAATAATAAAAAAAATTATTTTATATTTTTAAAATAATTAATATTATTTATTTAATAATTTTAAATTATATATTTTAAAAAATATATTA III9II9IIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIII-IIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIII9I9IIIIIIIIIIIIII-9IIIIIIII-I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41445:1084_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 AATATTATAATATTTAATTTTATTATAATTTAATATATATATATTATATTAATTAATATATAATATATTTTTTAAAATATATAATTTAAAATTATTAAATAAATAATATTGATTATTTTAAAAAT IIIIIIIIIIII9IIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-IIIIIIIII9I9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:43622:1070_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 AATTTTTTTTTTAAAAATTATAATTAAATAATATATTTTTATAATATAATTATTATATTTATTTTTATTAAATTATTTTTTATTTAATATTTTTTTTATATTAATAAAATATATTAAATAAATTT IIIIIIIIIIIIIIIIIIII-II9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9III9IIIIIIII-9III99I9II9IIII99IIII9IIIIIII-IIIIII-II9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43622:1070_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 ATATTTTTTTTTTATTAATTTTTTTTATATTAATTTAAATTTATTTAATATATTTTATTAATATAAAAAAAATATTAAATAAAAAATAATTTAATAAAAATAAATATAATAATTATATTATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C6_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: LH00526:197:22KFKVLT4:3:1101:21918:1098_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 TAAATTTTTTTTTAAAAATTAATTTATATAAAAATAATAAATAAAATTTAATTATAATTTTAAATAATAAAAAATATTTATTTAATAATAATTATTTTTTTATATAAAATTTAAAAAAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:21918:1098_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 TAAATTTTTTTTTAAAAATTAATTTATATAAAAATAATAAATAAAATTTAATTATAATTTTAAATAATAAAAAATATTTATTTAATAATAATTATTTTTTTATATAAAATTTAAAAAAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:21918:1098_1:N:0:CATGAGCA+GCAAGATC/1 77 * 0 0 * * 0 0 TGAATTTTTTTTTAAAAATTGATTTATGTGAGAATAATGGATGAGATTTAATTGTAATTTTAGGTAATGAAAGATATTTATTTGGTAATAATTATTTTTTTGTGTAGGGTTTAAGAAAAGTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:21918:1098_2:N:0:CATGAGCA+GCAAGATC/2 141 * 0 0 * * 0 0 CAAATTTTTTCTTAAAAATTAACTTACACAAAAACAATAAATAAAATTCAATTACAATTTTAAACAACAAAAAATACCCATTTAACAATAATTATTTTTTTACACAAAATTTAAAAAAAACTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII-IIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:41445:1084_1:N:0:CATGAGCA+GCAAGATC/1 83 ptg000022l_GA_converted 3439464 42 125M = 3439404 -185 TAATATACCTCTCAAAATATACAACTTAAAATCACTAAACAAATAACATTAACCATCTCAAAAACACAAAACAATTCCTCTTACCATCCACAAATTATCAAAACATCAATCACTAACAACAATCC I-IIIIIIII9-IIIIIIIIIIIIII9I9IIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIII-IIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIIII9II9III AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:53A42T28 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41445:1084_2:N:0:CATGAGCA+GCAAGATC/2 163 ptg000022l_GA_converted 3439404 42 125M = 3439464 185 AATACCACAATACTCAACTTCATCACAACTCAACACATACACACTATATTAATTAACACATAATATACCTCTCAAAATATACAACTTAAAATCACTAAACAAATAACATTAACCATCTCAAAAAC IIIIIIIIIIII9IIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-IIIIIIIII9I9II AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:48A64A11 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:43622:1070_1:N:0:CATGAGCA+GCAAGATC/1 83 ptg000020l_GA_converted 13959269 2 65M2D60M = 13959231 -165 AAATTTATTCAACATATCTTATTAATATAAAAAAAATATTAAATAAAAAATAACTTAACAAAAACAAATATAATAACTATATTACAAAAATATACTATTTAATTATAACTTTCAAAAAAAAAATT III9II-IIIIII-IIIIIII9IIII99IIII9II9I99III9-IIIIIIII9III9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9II-IIIIIIIIIIIIIIIIIIII AS:i:-23 XS:i:-29 XN:i:0 XM:i:2 XO:i:1 XG:i:2 NM:i:4 MD:Z:65^AA9T43C6 YS:i:-28 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43622:1070_2:N:0:CATGAGCA+GCAAGATC/2 163 ptg000020l_GA_converted 13959231 2 31M2D70M2D24M = 13959269 165 ACATTTTTCCTTTACTAACTTTTTTTATATTAACCCAAATTTATTCAACATATCTTATTAATATAAAAAAAATATTAAATAAAAAATAACTTAACAAAAACAAATATAATAACTATATTACAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-28 XS:i:-28 XN:i:0 XM:i:1 XO:i:2 XG:i:4 NM:i:5 MD:Z:31^AA70^AA9T14 YS:i:-23 YT:Z:CP >>> Writing bisulfite mapping results to 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1304:38329:18972_1:N:0:CATGAGCA+GCAAGATC ptg000174l 27262 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 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1267:3395:26998_1:N:0:CATGAGCA+GCAAGATC ptg000097l 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1156:23545:8088_1:N:0:CATGAGCA+GCAAGATC ptg000077l 42461 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1223:8769:13523_1:N:0:CATGAGCA+GCAAGATC ptg000039l 1 Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1450:47393:4040_1:N:0:CATGAGCA+GCAAGATC ptg000133l 37099 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2376:38637:22306_1:N:0:CATGAGCA+GCAAGATC ptg000025l 21443080 Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1450:47377:4068_1:N:0:CATGAGCA+GCAAGATC ptg000133l 37099 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2220:40765:5146_1:N:0:CATGAGCA+GCAAGATC ptg000033l 2625597 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 3049617 (41.28%) aligned concordantly 0 times 1500565 (20.31%) aligned concordantly exactly 1 time 2838061 (38.41%) aligned concordantly >1 times 58.72% overall alignment rate 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 7363351 (99.66%) aligned concordantly 0 times 8807 (0.12%) aligned concordantly exactly 1 time 16085 (0.22%) aligned concordantly >1 times 0.34% overall alignment rate 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 7364404 (99.68%) aligned concordantly 0 times 8887 (0.12%) aligned concordantly exactly 1 time 14952 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 3053821 (41.33%) aligned concordantly 0 times 1499696 (20.30%) aligned concordantly exactly 1 time 2834726 (38.37%) aligned concordantly >1 times 58.67% overall alignment rate Processed 7388243 sequences in total Successfully deleted the temporary files 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7388243 Final Cytosine Methylation Report ================================= Total number of C's analysed: 200455658 Total methylated C's in CpG context: 3096891 Total methylated C's in CHG context: 217860 Total methylated C's in CHH context: 936565 Total methylated C's in Unknown context: 6387 Total unmethylated C's in CpG context: 29416845 Total unmethylated C's in CHG context: 34337781 Total unmethylated C's in CHH context: 132449716 Total unmethylated C's in Unknown context: 273833 C methylated in CpG context: 9.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 7364585 (99.68%) aligned concordantly 0 times 8813 (0.12%) aligned concordantly exactly 1 time 14846 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 3054046 (41.34%) aligned concordantly 0 times 1499240 (20.29%) aligned concordantly exactly 1 time 2834958 (38.37%) aligned concordantly >1 times 58.66% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 7363339 (99.66%) aligned concordantly 0 times 9085 (0.12%) aligned concordantly exactly 1 time 15820 (0.21%) aligned concordantly >1 times 0.34% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 3050702 (41.29%) aligned concordantly 0 times 1499526 (20.30%) aligned concordantly exactly 1 time 2838016 (38.41%) aligned concordantly >1 times 58.71% overall alignment rate Processed 7388244 sequences in total Successfully deleted the temporary files 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7388244 Final Cytosine Methylation Report ================================= Total number of C's analysed: 200342343 Total methylated C's in CpG context: 3101743 Total methylated C's in CHG context: 217696 Total methylated C's in CHH context: 940879 Total methylated C's in Unknown context: 6079 Total unmethylated C's in CpG context: 29408497 Total unmethylated C's in CHG context: 34313228 Total unmethylated C's in CHH context: 132360300 Total unmethylated C's in Unknown context: 273481 C methylated in CpG context: 9.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 7364765 (99.68%) aligned concordantly 0 times 8759 (0.12%) aligned concordantly exactly 1 time 14719 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 3054321 (41.34%) aligned concordantly 0 times 1499581 (20.30%) aligned concordantly exactly 1 time 2834341 (38.36%) aligned concordantly >1 times 58.66% overall alignment rate 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 3049330 (41.27%) aligned concordantly 0 times 1499767 (20.30%) aligned concordantly exactly 1 time 2839146 (38.43%) aligned concordantly >1 times 58.73% overall alignment rate 7388243 reads; of these: 7388243 (100.00%) were paired; of these: 7363420 (99.66%) aligned concordantly 0 times 8793 (0.12%) aligned concordantly exactly 1 time 16030 (0.22%) aligned concordantly >1 times 0.34% overall alignment rate Processed 7388243 sequences in total Successfully deleted the temporary files 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7388243 Final Cytosine Methylation Report ================================= Total number of C's analysed: 200364516 Total methylated C's in CpG context: 3097274 Total methylated C's in CHG context: 216427 Total methylated C's in CHH context: 935001 Total methylated C's in Unknown context: 6183 Total unmethylated C's in CpG context: 29393475 Total unmethylated C's in CHG context: 34318946 Total unmethylated C's in CHH context: 132403393 Total unmethylated C's in Unknown context: 274308 C methylated in CpG context: 9.5% 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 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 3052946 (41.32%) aligned concordantly 0 times 1499916 (20.30%) aligned concordantly exactly 1 time 2835382 (38.38%) aligned concordantly >1 times 58.68% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 7362825 (99.66%) aligned concordantly 0 times 8811 (0.12%) aligned concordantly exactly 1 time 16608 (0.22%) aligned concordantly >1 times 0.34% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 7364269 (99.68%) aligned concordantly 0 times 8786 (0.12%) aligned concordantly exactly 1 time 15189 (0.21%) aligned concordantly >1 times 0.32% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 3050205 (41.28%) aligned concordantly 0 times 1500424 (20.31%) aligned concordantly exactly 1 time 2837615 (38.41%) aligned concordantly >1 times 58.72% overall alignment rate Processed 7388244 sequences in total Successfully deleted the temporary files 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7388244 Final Cytosine Methylation Report ================================= Total number of C's analysed: 200515268 Total methylated C's in CpG context: 3108503 Total methylated C's in CHG context: 219590 Total methylated C's in CHH context: 948278 Total methylated C's in Unknown context: 6478 Total unmethylated C's in CpG context: 29400796 Total unmethylated C's in CHG context: 34350249 Total unmethylated C's in CHH context: 132487852 Total unmethylated C's in Unknown context: 274752 C methylated in CpG context: 9.6% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Processed 7000000 sequence pairs so far 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 7364274 (99.68%) aligned concordantly 0 times 8878 (0.12%) aligned concordantly exactly 1 time 15092 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 3051732 (41.31%) aligned concordantly 0 times 1500943 (20.32%) aligned concordantly exactly 1 time 2835569 (38.38%) aligned concordantly >1 times 58.69% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 7363192 (99.66%) aligned concordantly 0 times 8805 (0.12%) aligned concordantly exactly 1 time 16247 (0.22%) aligned concordantly >1 times 0.34% overall alignment rate 7388244 reads; of these: 7388244 (100.00%) were paired; of these: 3048719 (41.26%) aligned concordantly 0 times 1501020 (20.32%) aligned concordantly exactly 1 time 2838505 (38.42%) aligned concordantly >1 times 58.74% overall alignment rate Processed 7388244 sequences in total Successfully deleted the temporary files 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C6_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7388244 Final Cytosine Methylation Report ================================= Total number of C's analysed: 200398956 Total methylated C's in CpG context: 3106796 Total methylated C's in CHG context: 219723 Total methylated C's in CHH context: 939650 Total methylated C's in Unknown context: 6193 Total unmethylated C's in CpG context: 29417193 Total unmethylated C's in CHG context: 34311837 Total unmethylated C's in CHH context: 132403757 Total unmethylated C's in Unknown context: 274550 C methylated in CpG context: 9.6% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1C6_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1C6_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1C6_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/1C6_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1C6_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/1C6_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C6_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C6_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: 36941218 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1002076741 Total methylated C's in CpG context: 15511207 Total methylated C's in CHG context: 1091296 Total methylated C's in CHH context: 4700373 Total methylated C's in Unknown context: 31320 Total unmethylated C's in CpG context: 147036806 Total unmethylated C's in CHG context: 171632041 Total unmethylated C's in CHH context: 662105018 Total unmethylated C's in Unknown context: 1370924 C methylated in CpG context: 9.5% 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 5h 31m 35s ==================== Bismark run complete ====================