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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_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/1B2_R1_001.fastp-trim.fq.gz for PID: 33124 and offset 5 (sequences written out: 10155510) Using the subset file >1B2_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/1B2_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/1B2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_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/1B2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_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/1B2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_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/1B2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_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/1B2_R2_001.fastp-trim.fq.gz for PID: 33124 and offset 5 (sequences written out: 10155510) Using the subset file >1B2_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/1B2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B2_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/1B2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B2_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/1B2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B2_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/1B2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B2_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/1B2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 10155511) Using the subset file >1B2_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/1B2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz (10155511 sequences in total) Writing a C -> T converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz (10155511 sequences in total) Writing a C -> T converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz (10155511 sequences in total) Writing a C -> T converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz (10155511 sequences in total) Writing a C -> T converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz (10155510 sequences in total) Writing a C -> T converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B2_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 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz (10155511 sequences in total) Input files are 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz (10155511 sequences in total) Input files are 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:51237:1056_1:N:0:GAACGAAG+GGTGATTC/1 99 ntLink_8_CT_converted 7291194 7 125M = 7291170 -149 TAGAAAATGATTTGTTTTGGTTTTGGGTTTTTTGTTTTGAGTTAAATTATGGTAATTAAGTATTTTGTTGTGTTTTTTTTTTTTTTTTTGATAAGATAAATGTATAGTGGTATTTTATTGGTGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII----99I---9--9-9-9-99I-9--99-99--I-99 AS:i:-18 XS:i:-26 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:88A10T20T4 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51237:1056_2:N:0:GAACGAAG+GGTGATTC/2 147 ntLink_8_CT_converted 7291170 7 125M = 7291194 149 GTTTTGTGTGTAATAAAAGTTTAATAGAAAATGATTTGTTTTGGTTTTGGGTTTTTTGTTTTGAGTTAAATTATGGTAATTAAGTGTTTTGTTGTGTTTTTTTTTTTTTTTTAGATAAGATAATT 9IIIIII99I9-I9IIIII9II9III9IIIIII-9II-IIII9IIIII9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII-IIII-II9I-IIIIII9IIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-14 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:85A39 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43250:1070_1:N:0:GAACGAAG+GGTGATTC/1 99 ntLink_6_CT_converted 20233994 2 4M9I74M3I35M = 20234134 265 ATAAAAAAAAAGATATTAAATATTTATTTTTGAAATATGATTATTTGGGGTGTGTATTGTTAGGGTTTTTTTTTTATATTTTTTATAAAGAAATTGAAATTAGTTTGTATTTTTTGTGGATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII AS:i:-70 XS:i:-73 XN:i:0 XM:i:4 XO:i:2 XG:i:12 NM:i:16 MD:Z:0T1T0T1T107 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43250:1070_2:N:0:GAACGAAG+GGTGATTC/2 147 ntLink_6_CT_converted 20234134 2 125M = 20233994 -265 TTGTGTATTATTAATTTGATTTTTAGTTGGGTTTTAAGTGGAGTTATAGGTTTTTTTATTTTGTTATTTTGAAAGAAAAGTTTTTTGGGAGGTTTATGTTTTGATTATGTGAATTATTTTTTTGA IIIIIII9IIIIII-IIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:102A22 YS:i:-70 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B2_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz (10155511 sequences in total) Input files are 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43250:1070_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 ATAAAAAAAAAAATATTAAATATTTATTTTTAAAATATAATTATTTAAAATATATATTATTAAAATTTTTTTTTTATATTTTTTATAAAAAAATTAAAATTAATTTATATTTTTTATAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43250:1070_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 TTAAAAAAATAATTTATATAATTAAAATATAAATTTTTTAAAAAATTTTTTTTTTAAAATAATAAAATAAAAAAATTTATAATTTTATTTAAAATTTAATTAAAAATTAAATTAATAATATATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIII-IIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:51237:1056_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 TAAAAAATAATTTATTTTAATTTTAAATTTTTTATTTTAAATTAAATTATAATAATTAAATATTTTATTATATTTTTTTTTTTTTTTTCAACAAAATAAATATATAATAATATTTTATTAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII----99I---9--9-9-9-99I-9--99-99--I-99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51237:1056_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 AATTATTTTATTTAAAAAAAAAAAAAAAATATAATAAAATATTTAATTATTATAATTTAATTTAAAATAAAAAATTTAAAATTAAAATAAATTATTTTTTATTAAATTTTTATTATATATAAAAT IIIIIIIIIIIIIIIIIIIIII9IIIIII-I9II-IIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIII9IIII-II9-IIIIII9III9II9IIIII9I-9I99IIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:51237:1056_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 TAAAAAATAATTTATTTTAATTTTAAATTTTTTATTTTAAATTAAATTATAATAATTAAATATTTTATTATATTTTTTTTTTTTTTTTCAACAAAATAAATATATAATAATATTTTATTAATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII----99I---9--9-9-9-99I-9--99-99--I-99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51237:1056_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 AATTATTTTATTTAAAAAAAAAAAAAAAATATAATAAAATATTTAATTATTATAATTTAATTTAAAATAAAAAATTTAAAATTAAAATAAATTATTTTTTATTAAATTTTTATTATATATAAAAT IIIIIIIIIIIIIIIIIIIIII9IIIIII-I9II-IIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIII9IIII-II9-IIIIII9III9II9IIIII9I-9I99IIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:49019:1056_1:N:0:GAACGAAG+GGTGATTC/1 99 ptg000007l_CT_converted 10647036 1 125M = 10647216 305 GAAAATTGTAAATTTTTTTGATGTTATTTTTAATTTGTTTGATGGGAAGTATATGGTTTATATTAAATTTGGAAATATTTTATTTTATGTAAATAGGAAATTGAATTATTTATTTTGTATTATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:49019:1056_2:N:0:GAACGAAG+GGTGATTC/2 147 ptg000007l_CT_converted 10647216 1 125M = 10647036 -305 TTTGTTTAATTATTTAGTATTTATTTATTAGAAAGTTTTAGATGATAGTGGATATTATTATTGTTTTATATTTATATTAAGTTTTATGTAGTTTTTAAATTTTATAAGAATGAATTGTTGTTGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43250:1070_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 ATAAAAAAAAAAATATTAAATATTTATTTTTAAAATATAATTATTTAAAATATATATTATTAAAATTTTTTTTTTATATTTTTTATAAAAAAATTAAAATTAATTTATATTTTTTATAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43250:1070_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 TTAAAAAAATAATTTATATAATTAAAATATAAATTTTTTAAAAAATTTTTTTTTTAAAATAATAAAATAAAAAAATTTATAATTTTATTTAAAATTTAATTAAAAATTAAATTAATAATATATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIII-IIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:49019:1056_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 AAAAATTATAAATTTTTTTAATATTATTTTTAATTTATTTAATAAAAAATATATAATTTATATTAAATTTAAAAATATTTTATTTTATATAAATAAAAAATTAAATTATTTATTTTATATTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49019:1056_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 TATAATAATAATTTATTTTTATAAAATTTAAAAATTATATAAAATTTAATATAAATATAAAATAATAATAATATTTATTATTATTTAAAATTTTTTAATAAATAAATATTAAATAATTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:51237:1056_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 TAGAAAATGATTTGTTTTGGTTTTGGGTTTTTTGTTTTGAGTTAAATTATGGTAATTAAGTATTTTGTTGTGTTTTTTTTTTTTTTTTTGATAAGATAAATGTATAGTGGTATTTTATTGGTGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII----99I---9--9-9-9-99I-9--99-99--I-99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51237:1056_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 AATTATCTTATCTAAAAAAAAAAAAAAAACACAACAAAACACTTAATTACCATAATTTAACTCAAAACAAAAAACCCAAAACCAAAACAAATCATTTTCTATTAAACTTTTATTACACACAAAAC IIIIIIIIIIIIIIIIIIIIII9IIIIII-I9II-IIII-IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9IIIII9IIII-II9-IIIIII9III9II9IIIII9I-9I99IIIIII9 YT:Z:UP >>> Writing bisulfite mapping results to 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:43250:1070_1:N:0:GAACGAAG+GGTGATTC/1 83 ptg000023l_GA_converted 14152438 35 125M = 14152286 -277 AAAAATCCACAAAAAATACAAACTAATTTCAATTTCTTTATAAAAAATATAAAAAAAAAACCCTAACAATACACACCCCAAATAATCATATTTCAAAAATAAATATTTAATATCTTTTTTTTTAT IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-73 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43250:1070_2:N:0:GAACGAAG+GGTGATTC/2 163 ptg000023l_GA_converted 14152286 35 125M = 14152438 277 TCAAAAAAATAATTCACATAATCAAAACATAAACCTCCCAAAAAACTTTTCTTTCAAAATAACAAAATAAAAAAACCTATAACTCCACTTAAAACCCAACTAAAAATCAAATTAATAATACACAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIII-IIIIII9IIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Created C -> T as well as G -> A converted versions of the FastQ file 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz (10155511 sequences in total) Input files are 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B2_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)) Reading in the sequence files 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:49019:1056_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 AAAAATTATAAATTTTTTTAATATTATTTTTAATTTATTTAATAAAAAATATATAATTTATATTAAATTTAAAAATATTTTATTTTATATAAATAAAAAATTAAATTATTTATTTTATATTATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49019:1056_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 TATAATAATAATTTATTTTTATAAAATTTAAAAATTATATAAAATTTAATATAAATATAAAATAATAATAATATTTATTATTATTTAAAATTTTTTAATAAATAAATATTAAATAATTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43444:1070_1:N:0:GAACGAAG+GGTGATTC/1 99 ntLink_8_CT_converted 8599609 6 125M = 8599659 175 GGTATTGAGTGTGAAATTTTTTTTGATTTAATTATATTATAGTATTAGTATATAGATATAATTTAAATAAAATATTGTATTTAAAATAATAGTATTATATTAATTGAGTATAGTTATTTGTAATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43444:1070_2:N:0:GAACGAAG+GGTGATTC/2 147 ntLink_8_CT_converted 8599659 6 125M = 8599609 -175 TATAGATATAATTTAAATAAAATATTGTATTTAAAATAATAGTATTATATTAATTGAGTATAGTTATTTGTAATGTTTTTGTTAATAGGTTTTAGTTTATGATGTTTTTTTATTTATGTTTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:88T36 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B2_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz (10155510 sequences in total) Input files are 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B2_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 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43460:1070_1:N:0:GAACGAAG+GGTGATTC/1 99 ntLink_8_CT_converted 8599609 6 125M = 8599659 175 GGTATTGAGTGTGAAATTTTTTTTGATTTAATTATATTATAGTATTAGTATATAGATATAATTTAAATAAAATATTGTATTTAAAATAATAGTATTATATTAATTGAGTATAGTTATTTGTAATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43460:1070_2:N:0:GAACGAAG+GGTGATTC/2 147 ntLink_8_CT_converted 8599659 6 125M = 8599609 -175 TATAGATATAATTTAAATAAAATATTGTATTTAAAATAATAGTATTATATTAATTGAGTATAGTTATTTGTAATGTTTTTGTTAATAGGTTTTAGTTTATGATGTTTTTTTATTTATGTTTATAT II9IIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIII-IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:88T36 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43444:1070_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 AATATTAAATATAAAATTTTTTTTAATTTAATTATATTATAATATTAATATATAAATATAATTTAAATAAAATATTATATTTAAAATAATAATATTATACTAATTAAATATAATTATTTATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43444:1070_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 ATATAAATATAAATAAAAAAATATTATAAATTAAAATTTATTAATAAAAATATTATAAATAATTATATTTAATTAGTATAATATTATTATTTTAAATATAATATTTTATTTAAATTATATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:49019:1056_1:N:0:GAACGAAG+GGTGATTC/1 83 ptg000016l_GA_converted 2039871 1 125M = 2039691 -305 CAATAATACAAAATAAATAATTCAATTTCCTATTTACATAAAATAAAATATTTCCAAATTTAATATAAACCATATACTTCCCATCAAACAAATTAAAAATAACATCAAAAAAATTTACAATTTTC IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:49019:1056_2:N:0:GAACGAAG+GGTGATTC/2 163 ptg000016l_GA_converted 2039691 1 125M = 2039871 305 TACAACAACAATTCATTCTTATAAAATTTAAAAACTACATAAAACTTAATATAAATATAAAACAATAATAATATCCACTATCATCTAAAACTTTCTAATAAATAAATACTAAATAATTAAACAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:43460:1070_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 AATATTAAATATAAAATTTTTTTTAATTTAATTATATTATAATATTAATATATAAATATAATTTAAATAAAATATTATATTTAAAATAATAATATTATATTAATTAAATATAATTATTTATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43460:1070_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 ATATAAATATAAATAAAAAAATATTATAAATTAAAATTTATTAATAAAAATATTATAAATAATTATATTTAATTAATATAATATTATTATTTTAAATATAATATTTTATTTAAATTATATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII-IIIIIIIIIIIIIIIIIIIIIIIIII-IIII9IIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43444:1070_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 AATATTAAATATAAAATTTTTTTTAATTTAATTATATTATAATATTAATATATAAATATAATTTAAATAAAATATTATATTTAAAATAATAATATTATACTAATTAAATATAATTATTTATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43444:1070_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 ATATAAATATAAATAAAAAAATATTATAAATTAAAATTTATTAATAAAAATATTATAAATAATTATATTTAATTAGTATAATATTATTATTTTAAATATAATATTTTATTTAAATTATATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43460:1070_1:N:0:GAACGAAG+GGTGATTC/1 77 * 0 0 * * 0 0 AATATTAAATATAAAATTTTTTTTAATTTAATTATATTATAATATTAATATATAAATATAATTTAAATAAAATATTATATTTAAAATAATAATATTATATTAATTAAATATAATTATTTATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43460:1070_2:N:0:GAACGAAG+GGTGATTC/2 141 * 0 0 * * 0 0 ATATAAATATAAATAAAAAAATATTATAAATTAAAATTTATTAATAAAAATATTATAAATAATTATATTTAATTAATATAATATTATTATTTTAAATATAATATTTTATTTAAATTATATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII-IIIIIIIIIIIIIIIIIIIIIIIIII-IIII9IIIIIIIII9II YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B2_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: LH00526:197:22KFKVLT4:3:1101:43444:1070_1:N:0:GAACGAAG+GGTGATTC/1 83 ptg000012l_GA_converted 16057508 1 125M = 16057458 -175 CATTACAAATAACTATACTCAATTAATATAATACTATTATTTTAAATACAATATTTTATTTAAATTATATCTATATACTAATACTATAATATAATTAAATCAAAAAAAATTTCACACTCAATACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:43444:1070_2:N:0:GAACGAAG+GGTGATTC/2 163 ptg000012l_GA_converted 16057458 1 125M = 16057508 175 ATATAAACATAAATAAAAAAACATCATAAACTAAAACCTATTAACAAAAACATTACAAATAACTATACTCAATTAATATAATACTATTATTTTAAATACAATATTTTATTTAAATTATATCTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:43460:1070_1:N:0:GAACGAAG+GGTGATTC/1 83 ptg000012l_GA_converted 16057508 1 125M = 16057458 -175 CATTACAAATAACTATACTCAATTAATATAATACTATTATTTTAAATACAATATTTTATTTAAATTATATCTATATACTAATACTATAATATAATTAAATCAAAAAAAATTTCACACTCAATACC IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:43460:1070_2:N:0:GAACGAAG+GGTGATTC/2 163 ptg000012l_GA_converted 16057458 1 125M = 16057508 175 ATATAAACATAAATAAAAAAACATCATAAACTAAAACCTATTAACAAAAACATTACAAATAACTATACTCAATTAATATAATACTATTATTTTAAATACAATATTTTATTTAAATTATATCTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII-IIIIIIIIIIIIIIIIIIIIIIIIII-IIII9IIIIIIIII9II 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 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1154:16804:5272_1:N:0:GAACGAAG+GGTGATTC ptg000174l 27225 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 LH00526:197:22KFKVLT4:3:1342:43937:7864_1:N:0:GAACGAAG+GGTGATTC ptg000090l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1360:50144:4320_1:N:0:GAACGAAG+GGTGATTC ptg000020l 1 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 LH00526:197:22KFKVLT4:3:1360:50160:4320_1:N:0:GAACGAAG+GGTGATTC ptg000020l 1 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1467:42165:24379_1:N:0:GAACGAAG+GGTGATTC ptg000006l 3 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 LH00526:197:22KFKVLT4:3:2194:25115:18986_1:N:0:GAACGAAG+GGTGATTC ptg000015l 14997091 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2319:48922:20947_1:N:0:GAACGAAG+GGTGATTC ptg000026l 14741926 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2395:38872:20163_1:N:0:GAACGAAG+GGTGATTC ptg000060c 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2394:5564:5398_1:N:0:GAACGAAG+GGTGATTC ptg000033l 2625597 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2476:34122:18664_1:N:0:GAACGAAG+GGTGATTC ptg000117l 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2476:34113:18678_1:N:0:GAACGAAG+GGTGATTC ptg000117l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2123:15218:14826_1:N:0:GAACGAAG+GGTGATTC ptg000039l 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2190:30294:8508_1:N:0:GAACGAAG+GGTGATTC ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2234:19458:21465_1:N:0:GAACGAAG+GGTGATTC ptg000060c 1 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2294:48874:16128_1:N:0:GAACGAAG+GGTGATTC ptg000155l 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2391:6948:26312_1:N:0:GAACGAAG+GGTGATTC ptg000083l 2 Processed 10000000 sequence pairs so far 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4623473 (45.53%) aligned concordantly 0 times 2096994 (20.65%) aligned concordantly exactly 1 time 3435044 (33.82%) aligned concordantly >1 times 54.47% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10131695 (99.77%) aligned concordantly 0 times 8493 (0.08%) aligned concordantly exactly 1 time 15323 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10134781 (99.80%) aligned concordantly 0 times 8187 (0.08%) aligned concordantly exactly 1 time 12543 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4631729 (45.61%) aligned concordantly 0 times 2094099 (20.62%) aligned concordantly exactly 1 time 3429683 (33.77%) aligned concordantly >1 times 54.39% overall alignment rate Processed 10155511 sequences in total Successfully deleted the temporary files 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 10155511 Final Cytosine Methylation Report ================================= Total number of C's analysed: 274101703 Total methylated C's in CpG context: 4172153 Total methylated C's in CHG context: 244308 Total methylated C's in CHH context: 1081218 Total methylated C's in Unknown context: 8055 Total unmethylated C's in CpG context: 38117702 Total unmethylated C's in CHG context: 45875169 Total unmethylated C's in CHH context: 184611153 Total unmethylated C's in Unknown context: 402881 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 10000000 sequence pairs so far 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10134849 (99.80%) aligned concordantly 0 times 8278 (0.08%) aligned concordantly exactly 1 time 12384 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate Processed 10000000 sequence pairs so far 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4623442 (45.53%) aligned concordantly 0 times 2094738 (20.63%) aligned concordantly exactly 1 time 3437331 (33.85%) aligned concordantly >1 times 54.47% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10132139 (99.77%) aligned concordantly 0 times 8338 (0.08%) aligned concordantly exactly 1 time 15034 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4628267 (45.57%) aligned concordantly 0 times 2094665 (20.63%) aligned concordantly exactly 1 time 3432579 (33.80%) aligned concordantly >1 times 54.43% overall alignment rate Processed 10155511 sequences in total Successfully deleted the temporary files 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 10155511 Final Cytosine Methylation Report ================================= Total number of C's analysed: 273978206 Total methylated C's in CpG context: 4180952 Total methylated C's in CHG context: 243291 Total methylated C's in CHH context: 1071779 Total methylated C's in Unknown context: 7945 Total unmethylated C's in CpG context: 38097537 Total unmethylated C's in CHG context: 45875420 Total unmethylated C's in CHH context: 184509227 Total unmethylated C's in Unknown context: 403734 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4626095 (45.55%) aligned concordantly 0 times 2096082 (20.64%) aligned concordantly exactly 1 time 3433334 (33.81%) aligned concordantly >1 times 54.45% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10132022 (99.77%) aligned concordantly 0 times 8363 (0.08%) aligned concordantly exactly 1 time 15126 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4622181 (45.51%) aligned concordantly 0 times 2096259 (20.64%) aligned concordantly exactly 1 time 3437071 (33.84%) aligned concordantly >1 times 54.49% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10134997 (99.80%) aligned concordantly 0 times 8287 (0.08%) aligned concordantly exactly 1 time 12227 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate Processed 10155511 sequences in total Successfully deleted the temporary files 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 10155511 Final Cytosine Methylation Report ================================= Total number of C's analysed: 274139306 Total methylated C's in CpG context: 4168693 Total methylated C's in CHG context: 241910 Total methylated C's in CHH context: 1072563 Total methylated C's in Unknown context: 7941 Total unmethylated C's in CpG context: 38127906 Total unmethylated C's in CHG context: 45892100 Total unmethylated C's in CHH context: 184636134 Total unmethylated C's in Unknown context: 403285 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Processed 10000000 sequence pairs so far 10155510 reads; of these: 10155510 (100.00%) were paired; of these: 4626227 (45.55%) aligned concordantly 0 times 2095866 (20.64%) aligned concordantly exactly 1 time 3433417 (33.81%) aligned concordantly >1 times 54.45% overall alignment rate 10155510 reads; of these: 10155510 (100.00%) were paired; of these: 4631468 (45.61%) aligned concordantly 0 times 2094482 (20.62%) aligned concordantly exactly 1 time 3429560 (33.77%) aligned concordantly >1 times 54.39% overall alignment rate 10155510 reads; of these: 10155510 (100.00%) were paired; of these: 10132133 (99.77%) aligned concordantly 0 times 8360 (0.08%) aligned concordantly exactly 1 time 15017 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 10155510 reads; of these: 10155510 (100.00%) were paired; of these: 10134773 (99.80%) aligned concordantly 0 times 8272 (0.08%) aligned concordantly exactly 1 time 12465 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate Processed 10155510 sequences in total Successfully deleted the temporary files 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 10155510 Final Cytosine Methylation Report ================================= Total number of C's analysed: 274008180 Total methylated C's in CpG context: 4171846 Total methylated C's in CHG context: 242118 Total methylated C's in CHH context: 1077720 Total methylated C's in Unknown context: 8037 Total unmethylated C's in CpG context: 38097865 Total unmethylated C's in CHG context: 45881156 Total unmethylated C's in CHH context: 184537475 Total unmethylated C's in Unknown context: 404232 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Now waiting for all child processes to complete Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2477:26353:22362_1:N:0:GAACGAAG+GGTGATTC ptg000048l 1 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10135130 (99.80%) aligned concordantly 0 times 8088 (0.08%) aligned concordantly exactly 1 time 12293 (0.12%) aligned concordantly >1 times 0.20% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 10132258 (99.77%) aligned concordantly 0 times 8233 (0.08%) aligned concordantly exactly 1 time 15020 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4623022 (45.52%) aligned concordantly 0 times 2094789 (20.63%) aligned concordantly exactly 1 time 3437700 (33.85%) aligned concordantly >1 times 54.48% overall alignment rate 10155511 reads; of these: 10155511 (100.00%) were paired; of these: 4628531 (45.58%) aligned concordantly 0 times 2093936 (20.62%) aligned concordantly exactly 1 time 3433044 (33.80%) aligned concordantly >1 times 54.42% overall alignment rate Processed 10155511 sequences in total Successfully deleted the temporary files 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 10155511 Final Cytosine Methylation Report ================================= Total number of C's analysed: 274009469 Total methylated C's in CpG context: 4170329 Total methylated C's in CHG context: 242987 Total methylated C's in CHH context: 1074923 Total methylated C's in Unknown context: 8030 Total unmethylated C's in CpG context: 38104690 Total unmethylated C's in CHG context: 45858458 Total unmethylated C's in CHH context: 184558082 Total unmethylated C's in Unknown context: 405113 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1B2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1B2_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1B2_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/1B2_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1B2_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/1B2_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B2_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: 50777554 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1370236864 Total methylated C's in CpG context: 20863973 Total methylated C's in CHG context: 1214614 Total methylated C's in CHH context: 5378203 Total methylated C's in Unknown context: 40008 Total unmethylated C's in CpG context: 190545700 Total unmethylated C's in CHG context: 229382303 Total unmethylated C's in CHH context: 922852071 Total unmethylated C's in Unknown context: 2019245 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Deleting temporary report files... Bismark completed in 0d 6h 10m 38s ==================== Bismark run complete ====================