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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_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/1B10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 11376595) Using the subset file >1B10_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/1B10_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/1B10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 11376594) Using the subset file >1B10_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/1B10_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/1B10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 11376595) Using the subset file >1B10_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/1B10_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/1B10_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 11376594) Using the subset file >1B10_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/1B10_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/1B10_R1_001.fastp-trim.fq.gz for PID: 31420 and offset 5 (sequences written out: 11376594) Using the subset file >1B10_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/1B10_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/1B10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 11376594) Using the subset file >1B10_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/1B10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B10_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/1B10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 11376595) Using the subset file >1B10_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/1B10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B10_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/1B10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 11376595) Using the subset file >1B10_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/1B10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B10_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/1B10_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 11376594) Using the subset file >1B10_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/1B10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B10_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/1B10_R2_001.fastp-trim.fq.gz for PID: 31420 and offset 5 (sequences written out: 11376594) Using the subset file >1B10_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/1B10_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B10_R1_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 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz (11376595 sequences in total) Writing a C -> T converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz (11376594 sequences in total) Writing a C -> T converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz (11376595 sequences in total) Writing a C -> T converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz (11376594 sequences in total) Writing a C -> T converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz (11376594 sequences in total) Writing a C -> T converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B10_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 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz (11376594 sequences in total) Input files are 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B10_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 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz (11376594 sequences in total) Found first alignment: LH00526:197:22KFKVLT4:3:1101:40935:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 GTAGAGAAGTGGTGTAGGTGGATAAAATATATAGTTTTTTGGATAAGTATAAATTGTAGTGGGAAGGGTTTTTTTTATAAGTGTTTGTTTTTTTGATGATGTGTTATTTAAGATTGTATTTTGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII-III-I-IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40935:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 ACATCATCAAAAAAACAAACACTTATAAAAAAAACCCTTCCCACTACAATTTATACTTATCCAAAAAACTATATATTTTATCCACCTACACCACTTCTCTACTAAACATATTTATATACCCATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B10_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)) Input files are 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:38653:1070_1:N:0:CTCAGAAG+AACTTGCC/1 99 ptg000020l_CT_converted 4442072 0 4M2D73M2D31M = 4442047 -137 AAATAAAAAAATATTTAATTTTTAAAAATAAAGTATTTAGTTTTTAAAGTTTAGTTATTTTTATTTTGATTGTTTTTTGTGGATAAAAGATGTATGTATTATGAAGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-40 XS:i:-40 XN:i:0 XM:i:3 XO:i:2 XG:i:4 NM:i:7 MD:Z:4^AA49T5G5G11^AA31 YS:i:-40 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:38653:1070_2:N:0:CTCAGAAG+AACTTGCC/2 147 ptg000020l_CT_converted 4442047 0 29M2D73M2D6M = 4442072 137 GTTAATTTGAGATTATTATGTTTTAAAATAAAAAAATATTTAATTTTTAAAAATAAAGTATTTAGTTTTTAAAGTTTAGTTATTTTTATTTTGATTGTTTTTTGTGGA IIIIIIIIIIII9IIIIIIIII9IIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII AS:i:-40 XS:i:-40 XN:i:0 XM:i:3 XO:i:2 XG:i:4 NM:i:7 MD:Z:29^AA49T5G5G11^AA6 YS:i:-40 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B10_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 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz (11376595 sequences in total) Input files are 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:40935:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 ATAAAAAAATAATATAAATAAATAAAATATATAATTTTTTAAATAAATATAAATTATAATAAAAAAAATTTTTTTTATAAATATTTATTTTTTTAATAATATATTATTTAAAATTATATTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII-III-I-IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40935:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 ATATTATTAAAAAAATAAATATTTATAAAAAAAATTTTTTTTATTATAATTTATATTTATTTAAAAAATTATATATTTTATTTATTTATATTATTTTTTTATTAAATATATTTATATATTTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:38653:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 AAATAAAAAAATATTTAATTTTTAAAAATAAAATATTTAATTTTTAAAATTTAATTATTTTTATTTTAATTATTTTTTATAAATAAAAAATATATATATTATAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38653:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TTTATAAAAAATAATTAAAATAAAAATAATTAAATTTTAAAAATTAAATATTTTATTTTTAAAAATTAAATATTTTTTTATTTTAAAATATAATAATTTTAAATTAAT IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B10_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 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz (11376594 sequences in total) Input files are 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz (11376595 sequences in total) Input files are 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B10_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 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:40935:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 ATAAAAAAATAATATAAATAAATAAAATATATAATTTTTTAAATAAATATAAATTATAATAAAAAAAATTTTTTTTATAAATATTTATTTTTTTAATAATATATTATTTAAAATTATATTTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII-III-I-IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40935:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 ATATTATTAAAAAAATAAATATTTATAAAAAAAATTTTTTTTATTATAATTTATATTTATTTAAAAAATTATATATTTTATTTATTTATATTATTTTTTTATTAAATATATTTATATATTTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:38653:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 AAATAAAAAAATATTTAATTTTTAAAAATAAAATATTTAATTTTTAAAATTTAATTATTTTTATTTTAATTATTTTTTATAAATAAAAAATATATATATTATAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38653:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TTTATAAAAAATAATTAAAATAAAAATAATTAAATTTTAAAAATTAAATATTTTATTTTTAAAAATTAAATATTTTTTTATTTTAAAATATAATAATTTTAAATTAAT IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:51512:1056_1:N:0:CTCAGAAG+AACTTGCC/1 99 ptg000016l_CT_converted 9858894 6 125M = 9858948 179 TTTAAGAGTTTTAATGTAATTTGTTTATTGATAGAAGAAAATGTTAGATTTTTAATTTAAGGTTTTTATTATGGATAAAAAAATATAAAGTTAAATAATTGAAGGTTTTAATTTAAAGGTTGTGT III9IIIIIII9IIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:41A74T8 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51512:1056_2:N:0:CTCAGAAG+AACTTGCC/2 147 ptg000016l_CT_converted 9858948 6 125M = 9858894 -179 ATTTAAGGTTTTTATTATGGATAAAAAAATATAAAGTTAAATAATTGAAGGTTTTAATTTAAAGGTTGTGTGAGATATTTATTGATGTTTTGTTGTTATGTTGTTAATAATTGTTGTGAGTTGTT IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:62T62 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:44091:1070_1:N:0:CTCAGAAG+AACTTGCC/1 99 ptg000047l_CT_converted 4435238 26 112M = 4435240 127 AGGTTATTAAAGTTTGATTAAGTTAATTTTGGATTAGTGGAAAATTTTAATTGTTATTTTTTTATTATTAAAGAAGGGTTTTAATAAAATTGTGGTTTAAAAAGGTTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-46 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:112 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44091:1070_2:N:0:CTCAGAAG+AACTTGCC/2 147 ptg000047l_CT_converted 4435240 26 125M = 4435238 -127 GTTATTAAAGTTTGATTAAGTTAATTTTGGATTAGTGGAAAATTTTAATTGTTATTTTTTTATTATTAAAGAAGGGTTTTAATAAAATTGTGGTTTAAAAAGGTTATAAATTATTTTTTTTTTAA IIII9IIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIII AS:i:-6 XS:i:-67 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:122A2 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:52030:1056_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 TTAAATATTTTTTTGTTAAATAGGTTAGATTATTTGGATATGATAAAGAGTGAATTGTTAAGTTGGTTAGATGATGTAAAGGATTTATTAGATAATAGGGTTTAGTGGGATTGTTTGAAATTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52030:1056_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TAATTTATTAAAACATATAATTAAACTTATTTTAATTTTAAATTTCAAACAATCCCACTAAACCCTATTATCTAATAAATCCTTTACATCATCTAACCAACTTAACAATTCACTCTTTATCATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:38653:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 AAATAAAAAAATATTTAATTTTTAAAAATAAAGTATTTAGTTTTTAAAGTTTAGTTATTTTTATTTTGATTGTTTTTTGTGGATAAAAGATGTATGTATTATGAAGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38653:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TCCACAAAAAACAATCAAAATAAAAATAACTAAACTTTAAAAACTAAATACTTTATTTTTAAAAATTAAATATTTTTTTATTTTAAAACATAATAATCTCAAATTAAC IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:51512:1056_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 TTTAAAAATTTTAATATAATTTATTTATTAATAAAAAAAAATATTAAATTTTTAATTTAAAATTTTTATTATAAATAAAAAAATATAAAATTAAATAATTAAAAATTTTAATTTAAAAATTATAT III9IIIIIII9IIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51512:1056_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 AATAATTTATAATAATTATTAATAATATAATAATAAAATATTAATAAATATTTTATATAATTTTTAAATTAAAATTTTTAATTATTTAATTTTATATTTTTTTATTTATAATAAAAATTTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B10_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)) >>> Writing bisulfite mapping results to 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:40935:1070_1:N:0:CTCAGAAG+AACTTGCC/1 83 ptg000009l_GA_converted 1424074 42 125M = 1424097 148 CACAAAATACAATCTTAAATAACACATCATCAAAAAAACAAACACTTATAAAAAAAACCCTTCCCACTACAATTTATACTTATCCAAAAAACTATATATTTTATCCACCTACACCACTTCTCTAC IIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII-I-III-IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40935:1070_2:N:0:CTCAGAAG+AACTTGCC/2 163 ptg000009l_GA_converted 1424097 42 125M = 1424074 -148 ACATCATCAAAAAAACAAACACTTATAAAAAAAACCCTTCCCACTACAATTTATACTTATCCAAAAAACTATATATTTTATCCACCTACACCACTTCTCTACTAAACATATTTATATACCCATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:52030:1056_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 TTAAATATTTTTTTATTAAATAAATTAAATTATTTAAATATAATAAAAAATAAATTATTAAATTAATTAAATAATATAAAAAATTTATTAAATAATAAAATTTAATAAAATTATTTAAAATTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52030:1056_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TAATTTATTAAAATATATAATTAAATTTATTTTAATTTTAAATTTTAAATAATTTTATTAAATTTTATTATTTAATAAATTTTTTATATTATTTAATTAATTTAATAATTTATTTTTTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B10_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)) >>> Writing bisulfite mapping results to 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:44091:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 AAATTATTAAAATTTAATTAAATTAATTTTAAATTAATAAAAAATTTTAATTATTATTTTTTTATTATTAAAAAAAAATTTTAATAAAATTATAATTTAAAAAAATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44091:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TTAAAAAAAAAATAATTTATAATTTTTTTAAATTATAATTTTATTAAAATTTTTTTTTAATAATAAAAAAATAATAATTAAAATTTTTTATTAATTTAAAATTAATTTAATTAAATTTTAATAAT IIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B10_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)) Reading in the sequence files 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:51512:1056_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 TTTAAAAATTTTAATATAATTTATTTATTAATAAAAAAAAATATTAAATTTTTAATTTAAAATTTTTATTATAAATAAAAAAATATAAAATTAAATAATTAAAAATTTTAATTTAAAAATTATAT III9IIIIIII9IIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51512:1056_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 AATAATTTATAATAATTATTAATAATATAATAATAAAATATTAATAAATATTTTATATAATTTTTAAATTAAAATTTTTAATTATTTAATTTTATATTTTTTTATTTATAATAAAAATTTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:52030:1056_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 TTAAATATTTTTTTATTAAATAAATTAAATTATTTAAATATAATAAAAAATAAATTATTAAATTAATTAAATAATATAAAAAATTTATTAAATAATAAAATTTAATAAAATTATTTAAAATTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52030:1056_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TAATTTATTAAAATATATAATTAAATTTATTTTAATTTTAAATTTTAAATAATTTTATTAAATTTTATTATTTAATAAATTTTTTATATTATTTAATTAATTTAATAATTTATTTTTTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B10_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)) Reading in the sequence files 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:52030:1056_1:N:0:CTCAGAAG+AACTTGCC/1 83 ptg000008l_GA_converted 10301783 7 103M2D22M = 10301746 -164 TTAAATTTCAAACAATCCCACTAAACCCTATTATCTAATAAATCCTTTACATCATCTAACCAACTTAACAATTCACTCTTTATCATATCCAAATAATCTAACCTATTTAACAAAAAAATATTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-23 XS:i:-30 XN:i:0 XM:i:2 XO:i:1 XG:i:2 NM:i:4 MD:Z:20A42T39^TA22 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:52030:1056_2:N:0:CTCAGAAG+AACTTGCC/2 163 ptg000008l_GA_converted 10301746 7 125M = 10301783 164 TAATTTATTAAAACATATAATTAAACTTATTTTAATTTTAAATTTCAAACAATCCCACTAAACCCTATTATCTAATAAATCCTTTACATCATCTAACCAACTTAACAATTCACTCTTTATCATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-36 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:13T43A42T24 YS:i:-23 YT:Z:CP >>> Writing bisulfite mapping results to 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:44091:1070_1:N:0:CTCAGAAG+AACTTGCC/1 77 * 0 0 * * 0 0 AAATTATTAAAATTTAATTAAATTAATTTTAAATTAATAAAAAATTTTAATTATTATTTTTTTATTATTAAAAAAAAATTTTAATAAAATTATAATTTAAAAAAATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44091:1070_2:N:0:CTCAGAAG+AACTTGCC/2 141 * 0 0 * * 0 0 TTAAAAAAAAAATAATTTATAATTTTTTTAAATTATAATTTTATTAAAATTTTTTTTTAATAATAAAAAAATAATAATTAAAATTTTTTATTAATTTAAAATTAATTTAATTAAATTTTAATAAT IIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B10_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: LH00526:197:22KFKVLT4:3:1101:51512:1056_1:N:0:CTCAGAAG+AACTTGCC/1 83 ptg000002l_GA_converted 8626720 0 42M1D83M = 8626666 -180 ACACAACCTTTAAATTAAAACCTTCAATTATTTAACTTTATATTTTTTTATCCATAATAAAAACCTTAAATTAAAAATCTAACATTTTCTTCTATCAATAAACAAATTACATTAAAACTCTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII9IIIIIII9III AS:i:-32 XS:i:-30 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:3A4A33^T41T28C12 YS:i:-20 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51512:1056_2:N:0:CTCAGAAG+AACTTGCC/2 163 ptg000002l_GA_converted 8626666 0 96M1D29M = 8626720 180 AACAACTCACAACAATTATTAACAACATAACAACAAAACATCAATAAATATCTCACACAACCTTTAAATTAAAACCTTCAATTATTTAACTTTATATTTTTTTATCCATAATAAAAACCTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII AS:i:-20 XS:i:-38 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:57A4A33^T29 YS:i:-32 YT:Z:CP >>> Writing bisulfite mapping results to 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:44091:1070_1:N:0:CTCAGAAG+AACTTGCC/1 83 ntLink_8_GA_converted 20188989 2 112M = 20188974 -127 TTTATAACCTTTTTAAACCACAATTTTATTAAAACCCTTCTTTAATAATAAAAAAATAACAATTAAAATTTTCCACTAATCCAAAATTAACTTAATCAAACTTTAATAACCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-18 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:45C43C16A2A2 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44091:1070_2:N:0:CTCAGAAG+AACTTGCC/2 163 ntLink_8_GA_converted 20188974 2 125M = 20188989 127 TTAAAAAAAAAATAATTTATAACCTTTTTAAACCACAATTTTATTAAAACCCTTCTTTAATAATAAAAAAATAACAATTAAAATTTTCCACTAATCCAAAATTAACTTAATCAAACTTTAATAAC IIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIII AS:i:-30 XS:i:-41 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T57C43C16A2A0 YS:i:-24 YT:Z:CP >>> Writing bisulfite mapping results to 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1110:43080:7360_1:N:0:CTCAGAAG+AACTTGCC ptg000015l 14997129 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1140:45159:27237_1:N:0:CTCAGAAG+AACTTGCC ptg000039l 1 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 LH00526:197:22KFKVLT4:3:1262:31386:20681_1:N:0:CTCAGAAG+AACTTGCC ptg000066l 66348 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1345:37091:5707_1:N:0:CTCAGAAG+AACTTGCC ptg000083l 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1314:38758:9237_1:N:0:CTCAGAAG+AACTTGCC ptg000105l 1 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1459:50735:15512_1:N:0:CTCAGAAG+AACTTGCC ptg000015l 14997092 Processed 3000000 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 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2293:17929:6799_1:N:0:CTCAGAAG+AACTTGCC ptg000149l 81044 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1175:12467:8466_1:N:0:CTCAGAAG+AACTTGCC ptg000009l 19096021 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1257:18253:24449_1:N:0:CTCAGAAG+AACTTGCC ptg000012l 2 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 LH00526:197:22KFKVLT4:4:1472:5548:10609_1:N:0:CTCAGAAG+AACTTGCC ptg000006l 1 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2197:33668:3984_1:N:0:CTCAGAAG+AACTTGCC ptg000083l 2 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1472:5556:10623_1:N:0:CTCAGAAG+AACTTGCC ptg000006l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2111:47466:24001_1:N:0:CTCAGAAG+AACTTGCC ptg000015l 14997117 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2222:15695:6491_1:N:0:CTCAGAAG+AACTTGCC ptg000092l 28970 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2222:15687:6505_1:N:0:CTCAGAAG+AACTTGCC ptg000092l 28970 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2135:31038:15148_1:N:0:CTCAGAAG+AACTTGCC ptg000098l 55079 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2201:7765:18146_1:N:0:CTCAGAAG+AACTTGCC ptg000080l 40112 Processed 10000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2364:33288:17529_1:N:0:CTCAGAAG+AACTTGCC ptg000017l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2308:46988:10735_1:N:0:CTCAGAAG+AACTTGCC ptg000025l 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 11326108 (99.56%) aligned concordantly 0 times 17712 (0.16%) aligned concordantly exactly 1 time 32774 (0.29%) aligned concordantly >1 times 0.44% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 4891598 (43.00%) aligned concordantly 0 times 2192370 (19.27%) aligned concordantly exactly 1 time 4292626 (37.73%) aligned concordantly >1 times 57.00% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 4885451 (42.94%) aligned concordantly 0 times 2194311 (19.29%) aligned concordantly exactly 1 time 4296832 (37.77%) aligned concordantly >1 times 57.06% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 11327488 (99.57%) aligned concordantly 0 times 17816 (0.16%) aligned concordantly exactly 1 time 31290 (0.28%) aligned concordantly >1 times 0.43% overall alignment rate Processed 11376594 sequences in total Successfully deleted the temporary files 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 11376594 Final Cytosine Methylation Report ================================= Total number of C's analysed: 283369672 Total methylated C's in CpG context: 4198764 Total methylated C's in CHG context: 340858 Total methylated C's in CHH context: 1522536 Total methylated C's in Unknown context: 9606 Total unmethylated C's in CpG context: 43963123 Total unmethylated C's in CHG context: 48831385 Total unmethylated C's in CHH context: 184513006 Total unmethylated C's in Unknown context: 373401 C methylated in CpG context: 8.7% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.5% Processed 11000000 sequence pairs so far 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 11327463 (99.57%) aligned concordantly 0 times 17690 (0.16%) aligned concordantly exactly 1 time 31441 (0.28%) aligned concordantly >1 times 0.43% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 4885299 (42.94%) aligned concordantly 0 times 2193708 (19.28%) aligned concordantly exactly 1 time 4297587 (37.78%) aligned concordantly >1 times 57.06% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 11325630 (99.55%) aligned concordantly 0 times 17981 (0.16%) aligned concordantly exactly 1 time 32983 (0.29%) aligned concordantly >1 times 0.45% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 4890458 (42.99%) aligned concordantly 0 times 2193885 (19.28%) aligned concordantly exactly 1 time 4292251 (37.73%) aligned concordantly >1 times 57.01% overall alignment rate Processed 11376594 sequences in total Successfully deleted the temporary files 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 11376594 Final Cytosine Methylation Report ================================= Total number of C's analysed: 283302927 Total methylated C's in CpG context: 4206737 Total methylated C's in CHG context: 340922 Total methylated C's in CHH context: 1525941 Total methylated C's in Unknown context: 9546 Total unmethylated C's in CpG context: 43949369 Total unmethylated C's in CHG context: 48796274 Total unmethylated C's in CHH context: 184483684 Total unmethylated C's in Unknown context: 374249 C methylated in CpG context: 8.7% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.5% 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 11325775 (99.55%) aligned concordantly 0 times 17833 (0.16%) aligned concordantly exactly 1 time 32987 (0.29%) aligned concordantly >1 times 0.45% overall alignment rate 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 11327367 (99.57%) aligned concordantly 0 times 17731 (0.16%) aligned concordantly exactly 1 time 31497 (0.28%) aligned concordantly >1 times 0.43% overall alignment rate 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 4892741 (43.01%) aligned concordantly 0 times 2192590 (19.27%) aligned concordantly exactly 1 time 4291264 (37.72%) aligned concordantly >1 times 56.99% overall alignment rate 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 4884362 (42.93%) aligned concordantly 0 times 2196759 (19.31%) aligned concordantly exactly 1 time 4295474 (37.76%) aligned concordantly >1 times 57.07% overall alignment rate Processed 11376595 sequences in total Successfully deleted the temporary files 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 11376595 Final Cytosine Methylation Report ================================= Total number of C's analysed: 283323744 Total methylated C's in CpG context: 4205609 Total methylated C's in CHG context: 342839 Total methylated C's in CHH context: 1538742 Total methylated C's in Unknown context: 9940 Total unmethylated C's in CpG context: 43935594 Total unmethylated C's in CHG context: 48797798 Total unmethylated C's in CHH context: 184503162 Total unmethylated C's in Unknown context: 374369 C methylated in CpG context: 8.7% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.6% Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 11326214 (99.56%) aligned concordantly 0 times 18001 (0.16%) aligned concordantly exactly 1 time 32379 (0.28%) aligned concordantly >1 times 0.44% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 11327767 (99.57%) aligned concordantly 0 times 17686 (0.16%) aligned concordantly exactly 1 time 31141 (0.27%) aligned concordantly >1 times 0.43% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 4884222 (42.93%) aligned concordantly 0 times 2195055 (19.29%) aligned concordantly exactly 1 time 4297317 (37.77%) aligned concordantly >1 times 57.07% overall alignment rate 11376594 reads; of these: 11376594 (100.00%) were paired; of these: 4892176 (43.00%) aligned concordantly 0 times 2192106 (19.27%) aligned concordantly exactly 1 time 4292312 (37.73%) aligned concordantly >1 times 57.00% overall alignment rate Processed 11376594 sequences in total Successfully deleted the temporary files 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 11376594 Final Cytosine Methylation Report ================================= Total number of C's analysed: 283291077 Total methylated C's in CpG context: 4201317 Total methylated C's in CHG context: 339142 Total methylated C's in CHH context: 1521606 Total methylated C's in Unknown context: 9595 Total unmethylated C's in CpG context: 43955637 Total unmethylated C's in CHG context: 48794055 Total unmethylated C's in CHH context: 184479320 Total unmethylated C's in Unknown context: 374132 C methylated in CpG context: 8.7% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.5% Now waiting for all child processes to complete 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 11326162 (99.56%) aligned concordantly 0 times 17781 (0.16%) aligned concordantly exactly 1 time 32652 (0.29%) aligned concordantly >1 times 0.44% overall alignment rate 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 4885754 (42.95%) aligned concordantly 0 times 2192751 (19.27%) aligned concordantly exactly 1 time 4298090 (37.78%) aligned concordantly >1 times 57.05% overall alignment rate 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 11327461 (99.57%) aligned concordantly 0 times 17824 (0.16%) aligned concordantly exactly 1 time 31310 (0.28%) aligned concordantly >1 times 0.43% overall alignment rate 11376595 reads; of these: 11376595 (100.00%) were paired; of these: 4892379 (43.00%) aligned concordantly 0 times 2190055 (19.25%) aligned concordantly exactly 1 time 4294161 (37.75%) aligned concordantly >1 times 57.00% overall alignment rate Processed 11376595 sequences in total Successfully deleted the temporary files 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B10_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 11376595 Final Cytosine Methylation Report ================================= Total number of C's analysed: 283168812 Total methylated C's in CpG context: 4206738 Total methylated C's in CHG context: 341092 Total methylated C's in CHH context: 1529867 Total methylated C's in Unknown context: 9783 Total unmethylated C's in CpG context: 43930685 Total unmethylated C's in CHG context: 48789414 Total unmethylated C's in CHH context: 184371016 Total unmethylated C's in Unknown context: 374576 C methylated in CpG context: 8.7% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.5% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1B10_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1B10_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1B10_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/1B10_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1B10_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/1B10_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B10_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B10_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: 56882972 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1416456232 Total methylated C's in CpG context: 21019165 Total methylated C's in CHG context: 1704853 Total methylated C's in CHH context: 7638692 Total methylated C's in Unknown context: 48470 Total unmethylated C's in CpG context: 219734408 Total unmethylated C's in CHG context: 244008926 Total unmethylated C's in CHH context: 922350188 Total unmethylated C's in Unknown context: 1870727 C methylated in CpG context: 8.7% C methylated in CHG context: 0.7% C methylated in CHH context: 0.8% C methylated in Unknown context (CN or CHN): 2.5% Deleting temporary report files... Bismark completed in 0d 8h 18m 30s ==================== Bismark run complete ====================