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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_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/1A12_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8418698) Using the subset file >1A12_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/1A12_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/1A12_R1_001.fastp-trim.fq.gz for PID: 80725 and offset 5 (sequences written out: 8418697) Using the subset file >1A12_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/1A12_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/1A12_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8418698) Using the subset file >1A12_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/1A12_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/1A12_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8418697) Using the subset file >1A12_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/1A12_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/1A12_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8418698) Using the subset file >1A12_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/1A12_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/1A12_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8418698) Using the subset file >1A12_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/1A12_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A12_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/1A12_R2_001.fastp-trim.fq.gz for PID: 80725 and offset 5 (sequences written out: 8418697) Using the subset file >1A12_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/1A12_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A12_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/1A12_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8418698) Using the subset file >1A12_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/1A12_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A12_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/1A12_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8418698) Using the subset file >1A12_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/1A12_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A12_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/1A12_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8418697) Using the subset file >1A12_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/1A12_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz (8418697 sequences in total) Writing a C -> T converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz (8418698 sequences in total) Writing a C -> T converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz (8418698 sequences in total) Writing a C -> T converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz (8418698 sequences in total) Writing a C -> T converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz (8418697 sequences in total) Writing a C -> T converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A12_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 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz (8418697 sequences in total) Input files are 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A12_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 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz (8418698 sequences in total) Input files are 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:48089:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TTAGATAAAGTATAGAAAAGGTGAATTTTTTAGTGTAGAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48089:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TTTTCTATACTTTATCTAAATTTCACCATCATCTAACATATAAAAAATCAAAAAAACATCATATAAAAAAAAAAAATCTCTTACTTTATAAAACTTAATAATTACTATTTCCTTCAAAAAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII--IIII9II---I-9--9-9I9-I-9-----------9-I--9-9-I99-99-I-----9-9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:51431:1056_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 AGGTTTTAGGGATTTAATTAGATATATAGTTGGTAGGTATTATTTGATTATTAATTTAAATTTTTGATAAGGTGATTAGGGATTTTTTTGGAAGTAGTTGTTGTGGTTGTGTTAATGTGAGAGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51431:1056_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TAACCTAACAACACTTATCTTCATCAATACACTCTATCTTACACTCAACAAATTATCCTAACTTATATTCTAAAACCAACTCTCACATTAACACAACCACAACAACTACTTCCAAAAAAATCCCT IIIIIIIIIIIIII9IIIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9I9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A12_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz (8418698 sequences in total) Input files are 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:48089:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TTAAATAAAATATAAAAAAAATAAATTTTTTAATATAAAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48089:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TTTTTTATATTTTATTTAAATTTTATTATTATTTAATATATAAAAGATTGGAAGAGTGTTGTGTGGGGGAAGAGGGTTTTTTGTTTTGTGGAGTTTGGTGGTTGTTGTTTTTTTTAAAAAGGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII--IIII9II---I-9--9-9I9-I-9-----------9-I--9-9-I99-99-I-----9-9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A12_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz (8418698 sequences in total) Input files are 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz (8418697 sequences in total) Input files are 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A12_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 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:51431:1056_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 AAATTTTAAAAATTTAATTAAATATATAATTAATAAATATTATTTAATTATTAATTTAAATTTTTAATAAAATAATTAAAAATTTTTTTAAAAATAATTATTATAATTACATTAATATAAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51431:1056_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TAATTTAATAATATTTATTTTTATTAATATATTTTATTTTATATTTGATAAATTATTTTAATTTATATTTTAAAATTAATTTTTATATTAATGTAATTATAATAATTATTTTTAAAAAAATTTTT IIIIIIIIIIIIII9IIIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9I9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:38961:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TAAAGTATAATAGGAATTTATTATGAGGGTATTAGGTTTTGTTTTTGTGGTTAGTAAAAATTTTTTTTGTTGAAATGAGAAATTGAAATTGATTTATTATTTTTTTTGTTAGTTATTATATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38961:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TATCTTACATAATTACTATAAAATTCATAAAAAAACACTCTCAAAAAAAAACCCCAAAACCCCCCCACCCTACAAAAAAAACTTCCAACCCCCCCCCTACCAAACCTACAACATAACACCCCACA IIIIIIIIIIIIIIIIIIIIII99IIIIIIIII-IIIIIIIIIIIIIIII9---9IIII9II9999I-9III-IIII99I--I-----99-----9I--99-9---9--99----9----999-9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:48089:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TTAAATAAAATATAAAAAAAATAAATTTTTTAATATAAAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48089:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TTTTTTATATTTTATTTAAATTTTATTATTATTTAATATATAAAAGATTGGAAGAGTGTTGTGTGGGGGAAGAGGGTTTTTTGTTTTGTGGAGTTTGGTGGTTGTTGTTTTTTTTAAAAAGGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII--IIII9II---I-9--9-9I9-I-9-----------9-I--9-9-I99-99-I-----9-9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:51431:1056_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 AAATTTTAAAAATTTAATTAAATATATAATTAATAAATATTATTTAATTATTAATTTAAATTTTTAATAAAATAATTAAAAATTTTTTTAAAAATAATTATTATAATTACATTAATATAAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51431:1056_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TAATTTAATAATATTTATTTTTATTAATATATTTTATTTTATATTTGATAAATTATTTTAATTTATATTTTAAAATTAATTTTTATATTAATGTAATTATAATAATTATTTTTAAAAAAATTTTT IIIIIIIIIIIIII9IIIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9I9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:38961:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TAAAATATAATAAAAATTTATTATAAAAATATTAAATTTTATTTTTATAATTAATAAAAATTTTTTTTATTAAAATAAAAAATTAAAATTAATTTATTATTTTTTTTATTAATTATTATATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38961:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TATTTTATATAATTATTATAAAATTTATAAAAAAATATTTTTAAAAAAAAATTTTAAAATTTTTTTATTTTATAAAAAAAATTTTTAATTTTTTTTTTATTAAATTTATAATATAATATTTTATA IIIIIIIIIIIIIIIIIIIIII99IIIIIIIII-IIIIIIIIIIIIIIII9---9IIII9II9999I-9III-IIII99I--I-----99-----9I--99-9---9--99----9----999-9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:48089:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TTAGATAAAGTATAGAAAAGGTGAATTTTTTAGTGTAGAAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48089:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TTTTCTATACTTTATCTAAATTTCACCATCATCTAACATATAAAAAATCAAAAAAACATCATATAAAAAAAAAAAATCTCTTACTTTATAAAACTTAATAATTACTATTTCCTTCAAAAAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII--IIII9II---I-9--9-9I9-I-9-----------9-I--9-9-I99-99-I-----9-9 YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:45548:1070_1:N:0:CCAGTATC+ATCTCGCT/1 99 ptg000017l_CT_converted 6223600 2 125M = 6223631 156 TTGAGTATATTTTAGAAAAATTGTTATTTTTTAGTTAATTTTTGTTGTTTTATAGAGATGTTGGTATTAATAGAAATTAGAATAAATTTTGTATTTATTTATATTAATTAGGTTAAAATTTGATT II9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-36 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:28A30T0G55T8 YS:i:-30 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45548:1070_2:N:0:CCAGTATC+ATCTCGCT/2 147 ptg000017l_CT_converted 6223631 2 125M = 6223600 -156 TAGTTAATTTTTGTTGTTTTATAGAGATGTTGGTATTAATAGAAATTAGAATAAATTTTGTATTTATTTATATTAATTAGGTTAAAATTTGATTAGTATTAATGATTTTATAGTTTTTTGAAATT III9IIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIII-IIIIII9IIIIII9IIIIIIIIIIIIIIIIIIIIII-IIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-32 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:28T0G55T33A2G2 YS:i:-24 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A12_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)) >>> Writing bisulfite mapping results to 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:49926:1056_1:N:0:CCAGTATC+ATCTCGCT/1 99 ptg000031l_CT_converted 7909857 42 125M = 7909896 164 GTTATTAGTTAATTGTTAATTATTTTGAAATTAATTGTTAATTAAAGGTTGAAGGATAATAAGTGTATGTTAATTGTTTGATGATTAGTTTGTGTTTTTATTTTTGTTTATGGTGGTTAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:92A32 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49926:1056_2:N:0:CCAGTATC+ATCTCGCT/2 147 ptg000031l_CT_converted 7909896 42 125M = 7909857 -164 AATTAAAGGTTGAAGGATAATAAGTGTATGTTAATTGTTTGATGATTAGTTTGTGTTTTTATTTTTGTTTATGGTGGTTAATTATTAAAATGAATTAATTTTAGATGTTAATGTTAGAATAATGA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:53A69T1 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:38961:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TAAAATATAATAAAAATTTATTATAAAAATATTAAATTTTATTTTTATAATTAATAAAAATTTTTTTTATTAAAATAAAAAATTAAAATTAATTTATTATTTTTTTTATTAATTATTATATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38961:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TATTTTATATAATTATTATAAAATTTATAAAAAAATATTTTTAAAAAAAAATTTTAAAATTTTTTTATTTTATAAAAAAAATTTTTAATTTTTTTTTTATTAAATTTATAATATAATATTTTATA IIIIIIIIIIIIIIIIIIIIII99IIIIIIIII-IIIIIIIIIIIIIIII9---9IIII9II9999I-9III-IIII99I--I-----99-----9I--99-9---9--99----9----999-9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:49926:1056_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 ATTATTAATTAATTATTAATTATTTTAAAATTAATTATTAATTAAAAATTAAAAAATAATAAATATATATTAATTATTTAATAATTAATTTATATTTTTATTTTTATTTATAATAATTAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49926:1056_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TTATTATTTTAATATTAATATTTAAAATTAATTTATTTTAATAATTAATTATTATAAATAAAAATAAAAATATAAATTAATTATTAAATAATTAATATATATTTATTATTTTTTAATTTTTAATT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A12_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: LH00526:197:22KFKVLT4:3:1101:45548:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TTAAATATATTTTAAAAAAATTATTATTTTTTAATTAATTTTTATTATTTTATAAAAATATTAATATTAATAAAAATTAAAATAAATTTTATATTTATTTATATTAATTAAATTAAAATTTAATT II9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45548:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 AATTTTAAAAAATTATAAAATTATTAATATTAATTAAATTTTAATTTAATTAATATAAATAAATATAAAATTTATTTTAATTTTTATTAATATTAATATTTTTATAAAATAATAAAAATTAATTA IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A12_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)) Reading in the sequence files 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:38961:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TAAAGTATAATAGGAATTTATTATGAGGGTATTAGGTTTTGTTTTTGTGGTTAGTAAAAATTTTTTTTGTTGAAATGAGAAATTGAAATTGATTTATTATTTTTTTTGTTAGTTATTATATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38961:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TATCTTACATAATTACTATAAAATTCATAAAAAAACACTCTCAAAAAAAAACCCCAAAACCCCCCCACCCTACAAAAAAAACTTCCAACCCCCCCCCTACCAAACCTACAACATAACACCCCACA IIIIIIIIIIIIIIIIIIIIII99IIIIIIIII-IIIIIIIIIIIIIIII9---9IIII9II9999I-9III-IIII99I--I-----99-----9I--99-9---9--99----9----999-9 YT:Z:UP >>> Writing bisulfite mapping results to 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:51431:1056_1:N:0:CCAGTATC+ATCTCGCT/1 83 ptg000001l_GA_converted 3394488 42 125M = 3394411 -202 AACTCTCACATTAACACAACCACAACAACTACTTCCAAAAAAATCCCTAATCACCTTATCAAAAATTTAAATTAATAATCAAATAATACCTACCAACTATATATCTAATTAAATCCCTAAAACCT III9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:51431:1056_2:N:0:CCAGTATC+ATCTCGCT/2 163 ptg000001l_GA_converted 3394411 42 125M = 3394488 202 TAACCTAACAACACTTATCTTCATCAATACACTCTATCTTACACTCAACAAATTATCCTAACTTATATTCTAAAACCAACTCTCACATTAACACAACCACAACAACTACTTCCAAAAAAATCCCT IIIIIIIIIIIIII9IIIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9I9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 >>> Writing bisulfite mapping results to 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:49926:1056_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 ATTATTAATTAATTATTAATTATTTTAAAATTAATTATTAATTAAAAATTAAAAAATAATAAATATATATTAATTATTTAATAATTAATTTATATTTTTATTTTTATTTATAATAATTAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49926:1056_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TTATTATTTTAATATTAATATTTAAAATTAATTTATTTTAATAATTAATTATTATAAATAAAAATAAAAATATAAATTAATTATTAAATAATTAATATATATTTATTATTTTTTAATTTTTAATT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:49926:1056_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 GTTATTAGTTAATTGTTAATTATTTTGAAATTAATTGTTAATTAAAGGTTGAAGGATAATAAGTGTATGTTAATTGTTTGATGATTAGTTTGTGTTTTTATTTTTGTTTATGGTGGTTAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49926:1056_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TCATTATTCTAACATTAACATCTAAAATTAATTCATTTTAATAATTAACCACCATAAACAAAAATAAAAACACAAACTAATCATCAAACAATTAACATACACTTATTATCCTTCAACCTTTAATT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:45548:1070_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 TTAAATATATTTTAAAAAAATTATTATTTTTTAATTAATTTTTATTATTTTATAAAAATATTAATATTAATAAAAATTAAAATAAATTTTATATTTATTTATATTAATTAAATTAAAATTTAATT II9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45548:1070_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 AATTTTAAAAAATTATAAAATTATTAATATTAATTAAATTTTAATTTAATTAATATAAATAAATATAAAATTTATTTTAATTTTTATTAATATTAATATTTTTATAAAATAATAAAAATTAATTA IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A12_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)) Reading in the sequence files 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:45548:1070_1:N:0:CCAGTATC+ATCTCGCT/1 83 ptg000008l_GA_converted 2902293 1 125M = 2902262 -156 AATCAAATTTTAACCTAATTAATATAAATAAATACAAAATTTATTCTAATTTCTATTAATACCAACATCTCTATAAAACAACAAAAATTAACTAAAAAATAACAATTTTTCTAAAATATACTCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9II 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 LH00526:197:22KFKVLT4:3:1101:45548:1070_2:N:0:CCAGTATC+ATCTCGCT/2 163 ptg000008l_GA_converted 2902262 1 125M = 2902293 156 AATTTCAAAAAACTATAAAATCATTAATACTAATCAAATTTTAACCTAATTAATATAAATAAATACAAAATTTATTCTAATTTCTATTAATACCAACATCTCTATAAAACAACAAAAATTAACTA IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII-IIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII9III 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 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1225:4795:11352_1:N:0:CCAGTATC+ATCTCGCT ptg000127l 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 LH00526:197:22KFKVLT4:3:1342:46843:1098_1:N:0:CCAGTATC+ATCTCGCT ptg000025l 21443081 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1392:3096:29506_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1425:21239:19953_1:N:0:CCAGTATC+ATCTCGCT ntLink_7 182805 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2104:22995:28875_1:N:0:CCAGTATC+ATCTCGCT ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2129:27721:15232_1:N:0:CCAGTATC+ATCTCGCT ptg000082l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2154:18560:11254_1:N:0:CCAGTATC+ATCTCGCT ptg000066l 1 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 LH00526:197:22KFKVLT4:3:2354:42861:20177_1:N:0:CCAGTATC+ATCTCGCT ptg000135l 25310 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2368:40425:8984_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2427:3824:3423_1:N:0:CCAGTATC+ATCTCGCT ptg000056l 59095 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2436:42902:26326_1:N:0:CCAGTATC+ATCTCGCT ptg000094l 36817 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2494:20308:16801_1:N:0:CCAGTATC+ATCTCGCT ptg000155l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2427:3840:3395_1:N:0:CCAGTATC+ATCTCGCT ptg000056l 59095 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2436:42893:26340_1:N:0:CCAGTATC+ATCTCGCT ptg000094l 36817 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2427:3832:3409_1:N:0:CCAGTATC+ATCTCGCT ptg000056l 59095 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1113:1736:19112_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1113:1720:19112_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1153:21668:1700_1:N:0:CCAGTATC+ATCTCGCT ptg000102l 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1212:36315:5931_1:N:0:CCAGTATC+ATCTCGCT ptg000004l 15492348 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1284:36347:8984_1:N:0:CCAGTATC+ATCTCGCT ptg000082l 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1234:45086:14840_1:N:0:CCAGTATC+ATCTCGCT ptg000006l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1373:3711:19812_1:N:0:CCAGTATC+ATCTCGCT ptg000097l 1 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2115:24338:4250_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1490:36800:22292_1:N:0:CCAGTATC+ATCTCGCT ptg000160l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2234:27534:16927_1:N:0:CCAGTATC+ATCTCGCT ptg000098l 1 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2234:27526:16913_1:N:0:CCAGTATC+ATCTCGCT ptg000098l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2234:45386:5104_1:N:0:CCAGTATC+ATCTCGCT ptg000006l 2 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 8396548 (99.74%) aligned concordantly 0 times 7826 (0.09%) aligned concordantly exactly 1 time 14323 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 8398891 (99.76%) aligned concordantly 0 times 7792 (0.09%) aligned concordantly exactly 1 time 12014 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 3609620 (42.88%) aligned concordantly 0 times 1845485 (21.92%) aligned concordantly exactly 1 time 2963592 (35.20%) aligned concordantly >1 times 57.12% overall alignment rate 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 3616965 (42.96%) aligned concordantly 0 times 1843133 (21.89%) aligned concordantly exactly 1 time 2958599 (35.14%) aligned concordantly >1 times 57.04% overall alignment rate Processed 8418697 sequences in total Successfully deleted the temporary files 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8418697 Final Cytosine Methylation Report ================================= Total number of C's analysed: 238699878 Total methylated C's in CpG context: 3676677 Total methylated C's in CHG context: 221385 Total methylated C's in CHH context: 970562 Total methylated C's in Unknown context: 6887 Total unmethylated C's in CpG context: 33319191 Total unmethylated C's in CHG context: 40303313 Total unmethylated C's in CHH context: 160208750 Total unmethylated C's in Unknown context: 328266 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): 2.1% Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2305:49424:15148_1:N:0:CCAGTATC+ATCTCGCT ptg000002l 2 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 8398611 (99.76%) aligned concordantly 0 times 7804 (0.09%) aligned concordantly exactly 1 time 12282 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 8396353 (99.73%) aligned concordantly 0 times 7719 (0.09%) aligned concordantly exactly 1 time 14625 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 3609494 (42.87%) aligned concordantly 0 times 1845950 (21.93%) aligned concordantly exactly 1 time 2963253 (35.20%) aligned concordantly >1 times 57.13% overall alignment rate 8418697 reads; of these: 8418697 (100.00%) were paired; of these: 3615977 (42.95%) aligned concordantly 0 times 1843088 (21.89%) aligned concordantly exactly 1 time 2959632 (35.16%) aligned concordantly >1 times 57.05% overall alignment rate Processed 8418697 sequences in total Successfully deleted the temporary files 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8418697 Final Cytosine Methylation Report ================================= Total number of C's analysed: 238654174 Total methylated C's in CpG context: 3670326 Total methylated C's in CHG context: 221230 Total methylated C's in CHH context: 970660 Total methylated C's in Unknown context: 6683 Total unmethylated C's in CpG context: 33316253 Total unmethylated C's in CHG context: 40303916 Total unmethylated C's in CHH context: 160171789 Total unmethylated C's in Unknown context: 328757 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% Now waiting for all child processes to complete 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 8398873 (99.76%) aligned concordantly 0 times 7695 (0.09%) aligned concordantly exactly 1 time 12130 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 8396551 (99.74%) aligned concordantly 0 times 7784 (0.09%) aligned concordantly exactly 1 time 14363 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 3616163 (42.95%) aligned concordantly 0 times 1843602 (21.90%) aligned concordantly exactly 1 time 2958933 (35.15%) aligned concordantly >1 times 57.05% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 3610611 (42.89%) aligned concordantly 0 times 1844283 (21.91%) aligned concordantly exactly 1 time 2963804 (35.21%) aligned concordantly >1 times 57.11% overall alignment rate Processed 8418698 sequences in total Successfully deleted the temporary files 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8418698 Final Cytosine Methylation Report ================================= Total number of C's analysed: 238554114 Total methylated C's in CpG context: 3681879 Total methylated C's in CHG context: 221109 Total methylated C's in CHH context: 970971 Total methylated C's in Unknown context: 6737 Total unmethylated C's in CpG context: 33280512 Total unmethylated C's in CHG context: 40295622 Total unmethylated C's in CHH context: 160104021 Total unmethylated C's in Unknown context: 329146 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 8398725 (99.76%) aligned concordantly 0 times 7858 (0.09%) aligned concordantly exactly 1 time 12115 (0.14%) aligned concordantly >1 times 0.24% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 3615459 (42.95%) aligned concordantly 0 times 1844424 (21.91%) aligned concordantly exactly 1 time 2958815 (35.15%) aligned concordantly >1 times 57.05% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 3611304 (42.90%) aligned concordantly 0 times 1845416 (21.92%) aligned concordantly exactly 1 time 2961978 (35.18%) aligned concordantly >1 times 57.10% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 8396214 (99.73%) aligned concordantly 0 times 7929 (0.09%) aligned concordantly exactly 1 time 14555 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate Processed 8418698 sequences in total Successfully deleted the temporary files 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8418698 Final Cytosine Methylation Report ================================= Total number of C's analysed: 238607940 Total methylated C's in CpG context: 3673872 Total methylated C's in CHG context: 219767 Total methylated C's in CHH context: 967775 Total methylated C's in Unknown context: 6811 Total unmethylated C's in CpG context: 33308420 Total unmethylated C's in CHG context: 40307463 Total unmethylated C's in CHH context: 160130643 Total unmethylated C's in Unknown context: 328641 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 8000000 sequence pairs so far 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 8396337 (99.73%) aligned concordantly 0 times 7735 (0.09%) aligned concordantly exactly 1 time 14626 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 8398636 (99.76%) aligned concordantly 0 times 7839 (0.09%) aligned concordantly exactly 1 time 12223 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 3609471 (42.87%) aligned concordantly 0 times 1844214 (21.91%) aligned concordantly exactly 1 time 2965013 (35.22%) aligned concordantly >1 times 57.13% overall alignment rate 8418698 reads; of these: 8418698 (100.00%) were paired; of these: 3615740 (42.95%) aligned concordantly 0 times 1843081 (21.89%) aligned concordantly exactly 1 time 2959877 (35.16%) aligned concordantly >1 times 57.05% overall alignment rate Processed 8418698 sequences in total Successfully deleted the temporary files 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A12_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8418698 Final Cytosine Methylation Report ================================= Total number of C's analysed: 238543262 Total methylated C's in CpG context: 3671143 Total methylated C's in CHG context: 220785 Total methylated C's in CHH context: 971762 Total methylated C's in Unknown context: 6913 Total unmethylated C's in CpG context: 33281660 Total unmethylated C's in CHG context: 40282477 Total unmethylated C's in CHH context: 160115435 Total unmethylated C's in Unknown context: 328888 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): 2.1% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1A12_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1A12_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1A12_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/1A12_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1A12_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/1A12_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A12_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A12_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: 42093488 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1193059368 Total methylated C's in CpG context: 18373897 Total methylated C's in CHG context: 1104276 Total methylated C's in CHH context: 4851730 Total methylated C's in Unknown context: 34031 Total unmethylated C's in CpG context: 166506036 Total unmethylated C's in CHG context: 201492791 Total unmethylated C's in CHH context: 800730638 Total unmethylated C's in Unknown context: 1643698 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% Deleting temporary report files... Bismark completed in 0d 7h 15m 3s ==================== Bismark run complete ====================