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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_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/1H2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8838460) Using the subset file >1H2_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/1H2_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/1H2_R1_001.fastp-trim.fq.gz for PID: 54434 and offset 5 (sequences written out: 8838459) Using the subset file >1H2_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/1H2_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/1H2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8838460) Using the subset file >1H2_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/1H2_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/1H2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8838459) Using the subset file >1H2_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/1H2_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/1H2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8838459) Using the subset file >1H2_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/1H2_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/1H2_R2_001.fastp-trim.fq.gz for PID: 54434 and offset 5 (sequences written out: 8838459) Using the subset file >1H2_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/1H2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H2_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/1H2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8838460) Using the subset file >1H2_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/1H2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H2_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/1H2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8838459) Using the subset file >1H2_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/1H2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H2_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/1H2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8838459) Using the subset file >1H2_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/1H2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H2_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/1H2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8838460) Using the subset file >1H2_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/1H2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz (8838460 sequences in total) Writing a C -> T converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz (8838459 sequences in total) Writing a C -> T converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz (8838459 sequences in total) Writing a C -> T converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz (8838459 sequences in total) Writing a C -> T converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz (8838460 sequences in total) Writing a C -> T converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H2_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 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz (8838460 sequences in total) Input files are 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz (8838460 sequences in total) Input files are 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:38750:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 TTGGGTTTTTATTTTTTTTTTTATGAGAGTTGAATTGGGGGATTTTGTTTTGGAAGTTTTAAGTTGTGAAGGATTATTTGGAAATTTGATTTTGATGTTTTAAGTTGGTGGGTTTGTGAGAAAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-III-9IIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38750:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTAAAAACTTAAATATACATATTAATATATAATATATATAAATAAACAACCCTTTCTCACAAACCCACCAACTTAAAACATCAAAATCAAATTTCCAAATAATCCTTCACAACTTAAAACTTCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:43266:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 ATTAAATTGAATTAGTAAAATATTGATTGTATTTGTAAATTTGTATGGTTTTTTATTTTGTGGTTGTTTTTTGTATAGTGTAAGTGTTTTTTTTGGTTTGATTTAATTTTGATGTTGTAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43266:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 AACTCAATCTCCACCAATAAATTTACAACATCAAAATTAAATCAAACCAAAAAAAACACTTACACTATACAAAAAACAACCACAAAATAAAAAACCATACAAATTTACAAATACAATCAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H2_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 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz (8838459 sequences in total) Input files are 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz (8838459 sequences in total) Input files are 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:49141:1070_1:N:0:CAATGCGA+AGTTCGTC/1 99 ntLink_6_CT_converted 20486830 17 125M = 20486806 -149 TAGAGATATTGGAAATAGTAGTTATGTAATATTTTTTGGTGAAATAAAGTGTATTAAGGGTAATGTTAGTGTATGTGGTAATTTTATAGTTAATAGTTTAAATATTAATAAGAAGTTTTTGAGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-18 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:17A107 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49141:1070_2:N:0:CAATGCGA+AGTTCGTC/2 147 ntLink_6_CT_converted 20486806 17 125M = 20486830 149 GTTTATAATGATGTATTTTTTTTATAGAGATATTGGAAATAGTAGTTATGTAATATTTTTTGGTGAAATAAAGTGTATTAAGGGTAATGTTAGTGTATGTGGTAATTTTATAGTTAATAGTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-38 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:41A83 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:38750:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 TTAAATTTTTATTTTTTTTTTTACAAAAATCAAATCAAAAAATTTCATTTTAAAAATTTTAAATCACAAAAAATTATTTAAAAATTCAATTTCAATATTTTAAATTAATAAATTCATAAAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-III-9IIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38750:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTAAAAATTTAAATATATATATTAATATATAATATATATAAATAAATAATTTTTTTTTATGAATTTATTAATTTAAAATATTGAAATTGAATTTTTAAATAATTTTTTGTGATTTAAAATTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:43266:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 ATTAAATTAAATTAATAAAATATTAATTATATTTATAAATTTATATAATTTTTTATTTTATAATTATTTTTTATATAATATAAATATTTTTTTTAATTTAACTTAATTTTAATATTATAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43266:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 AATTTAATTTTTATTAATAAATTTATAATATTAAAATTAAATTAAATTAAAAAAAATATTTATATTATATAAAAAATAATTATAAAATAAAAAATTATATAAATTTATAAATATAATTAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:49966:1070_1:N:0:CAATGCGA+AGTTCGTC/1 99 ntLink_8_CT_converted 32359338 6 94M = 32359313 -119 GTGATATTTTTTTTATTGATGATGTTGTGAAAAAAATTTTTTTGATTTTTAAAATTTTAGTGTAAGAAATTTATTATTAGTTTTTTTTTATTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9III99IIIIIIIIII-IIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:72G21 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49966:1070_2:N:0:CAATGCGA+AGTTCGTC/2 147 ntLink_8_CT_converted 32359313 6 94M = 32359338 119 TTTTTGGGTGAAATTTTTTTAAATTGTGATATTTTTTTTATTGATGATGTTGTGAAAAAAATTTTTTTGATTTTTAAAATTTTAGTGTAAGAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:94 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:38750:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 TTAAATTTTTATTTTTTTTTTTACAAAAATCAAATCAAAAAATTTCATTTTAAAAATTTTAAATCACAAAAAATTATTTAAAAATTCAATTTCAATATTTTAAATTAATAAATTCATAAAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-III-9IIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38750:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTAAAAATTTAAATATATATATTAATATATAATATATATAAATAAATAATTTTTTTTTATGAATTTATTAATTTAAAATATTGAAATTGAATTTTTAAATAATTTTTTGTGATTTAAAATTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H2_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz (8838459 sequences in total) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49141:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 TAAAAATATTAAAAATAATAATTATATAATATTTTTTAATAAAATAAAATATATTAAAAATAATATTAATATATATAATAATTTTATAATTAATAATTTAAATATTAATAAAAAATTTTTAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49141:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTAAATTATTAATTATAAAATTATTATATATATTAATATTATTTTTAATATATTTTATTTTATTAAAAAATATTATATAATTATTATTTTTAATATTTTTATAAAAAAAATATATTATTATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H2_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)) Input files are 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43266:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 ATTAAATTAAATTAATAAAATATTAATTATATTTATAAATTTATATAATTTTTTATTTTATAATTATTTTTTATATAATATAAATATTTTTTTTAATTTAACTTAATTTTAATATTATAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43266:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 AATTTAATTTTTATTAATAAATTTATAATATTAAAATTAAATTAAATTAAAAAAAATATTTATATTATATAAAAAATAATTATAAAATAAAAAATTATATAAATTTATAAATATAATTAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:49141:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 TAAAAATATTAAAAATAATAATTATATAATATTTTTTAATAAAATAAAATATATTAAAAATAATATTAATATATATAATAATTTTATAATTAATAATTTAAATATTAATAAAAAATTTTTAAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49141:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTAAATTATTAATTATAAAATTATTATATATATTAATATTATTTTTAATATATTTTATTTTATTAAAAAATATTATATAATTATTATTTTTAATATTTTTATAAAAAAAATATATTATTATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:38750:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 TTGGGTTTTTATTTTTTTTTTTATGAGAGTTGAATTGGGGGATTTTGTTTTGGAAGTTTTAAGTTGTGAAGGATTATTTGGAAATTTGATTTTGATGTTTTAAGTTGGTGGGTTTGTGAGAAAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-III-9IIIIIIIIIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:38750:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTAAAAACTTAAATATACATATTAATATATAATATATATAAATAAACAACCCTTTCTCACAAACCCACCAACTTAAAACATCAAAATCAAATTTCCAAATAATCCTTCACAACTTAAAACTTCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:49966:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 ATAATATTTTTTTTATTAATAATATTATAAAAAAAATTTTTTTAATTTTTAAAATTTTAATATAAAAAATTTATTATTAATTTTTTTTTATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9III99IIIIIIIIII-IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49966:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTTTTTATATTAAAATTTTAAAAATTAAAAAAATTTTTTTTATAATATTATTAATAAAAAAAATATTATAATTTAAAAAAATTTTATTTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:52005:1070_1:N:0:CAATGCGA+AGTTCGTC/1 99 ptg000008l_CT_converted 29086233 6 68M1I56M = 29086315 195 GGTGAGTAGTTTATTTATTTATTGATTAGAAAATTTTATTGATTATAGTAAAGTTATAAAAATAGAATAAAAAAAAAAAATAAGAAATTATGAGATTGTGAAGGGGTATGTGAATGGATTTTGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9I-IIIIII9-9I99IIIII-I-II9IIIIIIIIIIII999I9II-I-II9I9-I---9-9999-9--999-999I-999--9 AS:i:-20 XS:i:-20 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:100G20A2 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:52005:1070_2:N:0:CAATGCGA+AGTTCGTC/2 147 ptg000008l_CT_converted 29086315 6 113M = 29086233 -195 GAAGTTATGAGATTGTGAGGGGGTATGTGAGTGGATTTTAGGTTTTAAAGAGGTGATTTTTAGATAATTAGAAAAATGTATAAAAAAGATAATAATAAAGTAAATAAATAAAT III-IIIIIIIIIIIII-IIIIIIIII9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:3A26A82 YS:i:-20 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H2_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: LH00526:197:22KFKVLT4:3:1101:43266:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 ATTAAATTGAATTAGTAAAATATTGATTGTATTTGTAAATTTGTATGGTTTTTTATTTTGTGGTTGTTTTTTGTATAGTGTAAGTGTTTTTTTTGGTTTGATTTAATTTTGATGTTGTAAATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43266:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 AACTCAATCTCCACCAATAAATTTACAACATCAAAATTAAATCAAACCAAAAAAAACACTTACACTATACAAAAAACAACCACAAAATAAAAAACCATACAAATTTACAAATACAATCAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:49141:1070_1:N:0:CAATGCGA+AGTTCGTC/1 83 ptg000021l_GA_converted 5560412 0 125M = 5560436 150 AACTCAAAAACTTCTTATTAATATTTAAACTATTAACTATAAAATTACCACATACACTAACATTACCCTTAATACACTTTATTTCACCAAAAAATATTACATAACTACTATTTCCAATATCTCTA IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:54T39A0T7C21 YS:i:-32 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49141:1070_2:N:0:CAATGCGA+AGTTCGTC/2 163 ptg000021l_GA_converted 5560436 0 102M1D23M = 5560412 -150 TTAAACTATTAACTATAAAATTACCACATACACTAACATTACCCTTAATACACTTTATTTCACCAAAAAATATTACATAACTACTATTTCCAATATCTCTATAAAAAAAATACATCATTATAAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-32 XS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:30T39A0T7C22^A23 YS:i:-24 YT:Z:CP >>> Writing bisulfite mapping results to 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:49966:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 ATAATATTTTTTTTATTAATAATATTATAAAAAAAATTTTTTTAATTTTTAAAATTTTAATATAAAAAATTTATTATTAATTTTTTTTTATTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9III99IIIIIIIIII-IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49966:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 TTTTTTATATTAAAATTTTAAAAATTAAAAAAATTTTTTTTATAATATTATTAATAAAAAAAATATTATAATTTAAAAAAATTTTATTTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H2_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 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:52005:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 AATAAATAATTTATTTATTTATTAATTAAAAAATTTTATTAATTATAATAAAATTATAAAAATAAAATAAAAAAAAAAAATAAAAAATTATAAAATTATAAAAAAATATATAAACAAATTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9I-IIIIII9-9I99IIIII-I-II9IIIIIIIIIIII999I9II-I-II9I9-I---9-9999-9--999-999I-999--9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52005:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 ATTTATTTATTTATTTTATTATTATTTTTTTTATATATTTTTTTAATTATTTAAAAATTATTTTTTTAAAATTTAAAATTTATTTATATATTTTTTTATAATTTTATAATTTT IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9IIIIIIIII-IIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49966:1070_1:N:0:CAATGCGA+AGTTCGTC/1 83 ptg000031l_GA_converted 3943688 1 94M = 3943713 119 CAAATAAAAAAAAACTAATAATAAATTTCTTACACTAAAATTTTAAAAATCAAAAAAATTTTTTTCACAACATCATCAATAAAAAAAATATCAC IIIIIIIIIIIII-IIIIIIIIII99III9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:21C10T61 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49966:1070_2:N:0:CAATGCGA+AGTTCGTC/2 163 ptg000031l_GA_converted 3943713 1 94M = 3943688 -119 TTTCTTACACTAAAATTTTAAAAATCAAAAAAATTTTTTTCACAACATCATCAATAAAAAAAATATCACAATTTAAAAAAATTTCACCCAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7T86 YS:i:-12 YT:Z:CP Reading in the sequence files 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz >>> Writing bisulfite mapping results to 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:52005:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 AATAAATAATTTATTTATTTATTAATTAAAAAATTTTATTAATTATAATAAAATTATAAAAATAAAATAAAAAAAAAAAATAAAAAATTATAAAATTATAAAAAAATATATAAACAAATTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9I-IIIIII9-9I99IIIII-I-II9IIIIIIIIIIII999I9II-I-II9I9-I---9-9999-9--999-999I-999--9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52005:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 ATTTATTTATTTATTTTATTATTATTTTTTTTATATATTTTTTTAATTATTTAAAAATTATTTTTTTAAAATTTAAAATTTATTTATATATTTTTTTATAATTTTATAATTTT IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9IIIIIIIII-IIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:52005:1070_1:N:0:CAATGCGA+AGTTCGTC/1 77 * 0 0 * * 0 0 GGTGAGTAGTTTATTTATTTATTGATTAGAAAATTTTATTGATTATAGTAAAGTTATAAAAATAGAATAAAAAAAAAAAATAAGAAATTATGAGATTGTGAAGGGGTATGTGAATGGATTTTGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9I-IIIIII9-9I99IIIII-I-II9IIIIIIIIIIII999I9II-I-II9I9-I---9-9999-9--999-999I-999--9 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:52005:1070_2:N:0:CAATGCGA+AGTTCGTC/2 141 * 0 0 * * 0 0 ATTTATTTATTTACTTTATTATTATCTTTTTTATACATTTTTCTAATTATCTAAAAATCACCTCTTTAAAACCTAAAATCCACTCACATACCCCCTCACAATCTCATAACTTC IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9IIIIIIIII-IIIIIIIIIIIII-III YT:Z:UP >>> Writing bisulfite mapping results to 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1139:33021:10932_1:N:0:CAATGCGA+AGTTCGTC ptg000090l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1177:10622:13341_1:N:0:CAATGCGA+AGTTCGTC ptg000029c 1802544 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1196:2368:28441_1:N:0:CAATGCGA+AGTTCGTC ptg000018l 2 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 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2237:52013:16521_1:N:0:CAATGCGA+AGTTCGTC ptg000015l 14997091 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2287:42918:26046_1:N:0:CAATGCGA+AGTTCGTC ptg000093l 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2392:26612:3031_1:N:0:CAATGCGA+AGTTCGTC ptg000015l 14997111 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far 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 LH00526:197:22KFKVLT4:4:1385:34923:8704_1:N:0:CAATGCGA+AGTTCGTC ptg000059l 1573514 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2360:25293:12991_1:N:0:CAATGCGA+AGTTCGTC ptg000083l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2424:22720:27363_1:N:0:CAATGCGA+AGTTCGTC ptg000006l 3 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2302:12394:3830_1:N:0:CAATGCGA+AGTTCGTC ptg000059l 1573514 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 3925942 (44.42%) aligned concordantly 0 times 1670362 (18.90%) aligned concordantly exactly 1 time 3242155 (36.68%) aligned concordantly >1 times 55.58% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 8807021 (99.64%) aligned concordantly 0 times 10748 (0.12%) aligned concordantly exactly 1 time 20690 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 8807906 (99.65%) aligned concordantly 0 times 10853 (0.12%) aligned concordantly exactly 1 time 19700 (0.22%) aligned concordantly >1 times 0.35% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 3933499 (44.50%) aligned concordantly 0 times 1667255 (18.86%) aligned concordantly exactly 1 time 3237705 (36.63%) aligned concordantly >1 times 55.50% overall alignment rate Processed 8838459 sequences in total Successfully deleted the temporary files 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8838459 Final Cytosine Methylation Report ================================= Total number of C's analysed: 220576703 Total methylated C's in CpG context: 3072717 Total methylated C's in CHG context: 234500 Total methylated C's in CHH context: 1001291 Total methylated C's in Unknown context: 6681 Total unmethylated C's in CpG context: 34138849 Total unmethylated C's in CHG context: 38496444 Total unmethylated C's in CHH context: 143632902 Total unmethylated C's in Unknown context: 294372 C methylated in CpG context: 8.3% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Now waiting for all child processes to complete Processed 8000000 sequence pairs so far 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 3932821 (44.50%) aligned concordantly 0 times 1666561 (18.86%) aligned concordantly exactly 1 time 3239077 (36.65%) aligned concordantly >1 times 55.50% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 3926251 (44.42%) aligned concordantly 0 times 1668911 (18.88%) aligned concordantly exactly 1 time 3243297 (36.70%) aligned concordantly >1 times 55.58% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 8806251 (99.64%) aligned concordantly 0 times 10889 (0.12%) aligned concordantly exactly 1 time 21319 (0.24%) aligned concordantly >1 times 0.36% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 8806948 (99.64%) aligned concordantly 0 times 10943 (0.12%) aligned concordantly exactly 1 time 20568 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate Processed 8838459 sequences in total Successfully deleted the temporary files 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8838459 Final Cytosine Methylation Report ================================= Total number of C's analysed: 220492908 Total methylated C's in CpG context: 3073944 Total methylated C's in CHG context: 237232 Total methylated C's in CHH context: 1013126 Total methylated C's in Unknown context: 6640 Total unmethylated C's in CpG context: 34139912 Total unmethylated C's in CHG context: 38478298 Total unmethylated C's in CHH context: 143550396 Total unmethylated C's in Unknown context: 294794 C methylated in CpG context: 8.3% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2458:50168:20555_1:N:0:CAATGCGA+AGTTCGTC ptg000029c 1802552 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2470:3347:13271_1:N:0:CAATGCGA+AGTTCGTC ptg000006l 2 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 3928908 (44.45%) aligned concordantly 0 times 1668763 (18.88%) aligned concordantly exactly 1 time 3240788 (36.67%) aligned concordantly >1 times 55.55% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 3931233 (44.48%) aligned concordantly 0 times 1669509 (18.89%) aligned concordantly exactly 1 time 3237717 (36.63%) aligned concordantly >1 times 55.52% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 8807913 (99.65%) aligned concordantly 0 times 10777 (0.12%) aligned concordantly exactly 1 time 19769 (0.22%) aligned concordantly >1 times 0.35% overall alignment rate 8838459 reads; of these: 8838459 (100.00%) were paired; of these: 8806863 (99.64%) aligned concordantly 0 times 10941 (0.12%) aligned concordantly exactly 1 time 20655 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate Processed 8838459 sequences in total Successfully deleted the temporary files 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8838459 Final Cytosine Methylation Report ================================= Total number of C's analysed: 220489457 Total methylated C's in CpG context: 3074521 Total methylated C's in CHG context: 235056 Total methylated C's in CHH context: 1009124 Total methylated C's in Unknown context: 6569 Total unmethylated C's in CpG context: 34127598 Total unmethylated C's in CHG context: 38488632 Total unmethylated C's in CHH context: 143554526 Total unmethylated C's in Unknown context: 294352 C methylated in CpG context: 8.3% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 8807820 (99.65%) aligned concordantly 0 times 10937 (0.12%) aligned concordantly exactly 1 time 19703 (0.22%) aligned concordantly >1 times 0.35% overall alignment rate 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 3929599 (44.46%) aligned concordantly 0 times 1670033 (18.90%) aligned concordantly exactly 1 time 3238828 (36.64%) aligned concordantly >1 times 55.54% overall alignment rate 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 3927890 (44.44%) aligned concordantly 0 times 1668119 (18.87%) aligned concordantly exactly 1 time 3242451 (36.69%) aligned concordantly >1 times 55.56% overall alignment rate 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 3933421 (44.50%) aligned concordantly 0 times 1668100 (18.87%) aligned concordantly exactly 1 time 3236939 (36.62%) aligned concordantly >1 times 55.50% overall alignment rate 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 8807010 (99.64%) aligned concordantly 0 times 10762 (0.12%) aligned concordantly exactly 1 time 20688 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate Processed 8838460 sequences in total Successfully deleted the temporary files 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8838460 Final Cytosine Methylation Report ================================= Total number of C's analysed: 220537410 Total methylated C's in CpG context: 3066194 Total methylated C's in CHG context: 237786 Total methylated C's in CHH context: 1007974 Total methylated C's in Unknown context: 6768 Total unmethylated C's in CpG context: 34140043 Total unmethylated C's in CHG context: 38480117 Total unmethylated C's in CHH context: 143605296 Total unmethylated C's in Unknown context: 293545 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 3928431 (44.45%) aligned concordantly 0 times 1668292 (18.88%) aligned concordantly exactly 1 time 3241737 (36.68%) aligned concordantly >1 times 55.55% overall alignment rate 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 8807743 (99.65%) aligned concordantly 0 times 10837 (0.12%) aligned concordantly exactly 1 time 19880 (0.22%) aligned concordantly >1 times 0.35% overall alignment rate 8838460 reads; of these: 8838460 (100.00%) were paired; of these: 8806943 (99.64%) aligned concordantly 0 times 10787 (0.12%) aligned concordantly exactly 1 time 20730 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate Processed 8838460 sequences in total Successfully deleted the temporary files 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8838460 Final Cytosine Methylation Report ================================= Total number of C's analysed: 220496016 Total methylated C's in CpG context: 3067852 Total methylated C's in CHG context: 234872 Total methylated C's in CHH context: 1008028 Total methylated C's in Unknown context: 6537 Total unmethylated C's in CpG context: 34130764 Total unmethylated C's in CHG context: 38486234 Total unmethylated C's in CHH context: 143568266 Total unmethylated C's in Unknown context: 293664 C methylated in CpG context: 8.2% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1H2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1H2_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1H2_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/1H2_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1H2_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/1H2_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H2_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: 44192297 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1102592494 Total methylated C's in CpG context: 15355228 Total methylated C's in CHG context: 1179446 Total methylated C's in CHH context: 5039543 Total methylated C's in Unknown context: 33195 Total unmethylated C's in CpG context: 170677166 Total unmethylated C's in CHG context: 192429725 Total unmethylated C's in CHH context: 717911386 Total unmethylated C's in Unknown context: 1470727 C methylated in CpG context: 8.3% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Deleting temporary report files... Bismark completed in 0d 5h 50m 27s ==================== Bismark run complete ====================