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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_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/1H5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8179401) Using the subset file >1H5_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/1H5_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/1H5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8179401) Using the subset file >1H5_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/1H5_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/1H5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8179400) Using the subset file >1H5_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/1H5_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/1H5_R1_001.fastp-trim.fq.gz for PID: 68189 and offset 5 (sequences written out: 8179400) Using the subset file >1H5_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/1H5_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/1H5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8179401) Using the subset file >1H5_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/1H5_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/1H5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8179401) Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1H5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8179400) Using the subset file >1H5_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/1H5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Using the subset file >1H5_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/1H5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1H5_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/1H5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8179401) Using the subset file >1H5_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/1H5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1H5_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/1H5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8179401) Using the subset file >1H5_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/1H5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1H5_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/1H5_R2_001.fastp-trim.fq.gz for PID: 68189 and offset 5 (sequences written out: 8179400) Using the subset file >1H5_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/1H5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz (8179400 sequences in total) Writing a C -> T converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz (8179401 sequences in total) Writing a C -> T converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz (8179400 sequences in total) Writing a C -> T converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz (8179401 sequences in total) Writing a C -> T converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz (8179401 sequences in total) Writing a C -> T converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1H5_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 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz (8179400 sequences in total) Input files are 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:30634:1084_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 ATAAGTTATTTAGAGTTGTTTTGTGTAAAAAATTGTTTTAAAAAATATTAAATATTTGAGAAATGAGATGATTTTGAAAATGGGTTATTATGTAAAGGTTATAGTTTTTGTAAAATTGTTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30634:1084_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 ACAAATCATTTAAAATTATTTTACACAAAAAACCACTTCAAAAAACACCAAATATTCAAAAAATAAAACAATTTTACAAAAACTATAACCTTTACATAATAACCCATTTTCAAAATCATCTCATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H5_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz (8179401 sequences in total) Input files are 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H5_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 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz (8179400 sequences in total) Input files are 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz (8179401 sequences in total) Input files are 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:48914:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 TGGGAATAGTTTATATGTAGATTTAGATATTTTTGGTTTAAATAATTATTGTAAATAGGTTGTTGTATATGGAATTTGATGATTTATTTATGATTAGTATTTTTTTTGAAAAGGAGTTGGTTATG IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48914:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 AATCAACATCAAAAAATATTCCATAACCAACTCCTTTTCAAAAAAAATACTAATCATAAATAAATCATCAAATTCCATATACAACAACCTATTTACAATAATTATTTAAACCAAAAATATCTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:39786:1070_1:N:0:CGGCATTA+TGACTGAC/1 99 ptg000045l_CT_converted 50968 1 125M = 51034 191 TTTTATTGTTTGTGAAATTATAATGTATGTTTAAAGTAAGGATTGTTTTGATTTAGTAAATGGAAAATATTGGTGAAAGTAATTGTTTTTAAGGATAGTGGTAGAAGATATTTTTATTATTATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:39786:1070_2:N:0:CGGCATTA+TGACTGAC/2 147 ptg000045l_CT_converted 51034 1 125M = 50968 -191 ATATTGGTGAAAGTAATTGTTTTTAAGGATAGTGGTAGAAGATATTTTTATTATTATGTATTTATTAATAGGATTGTATTAGTTATGTTAAGGTGTTTTATTTTTTTGAATAATGTATTATATAG IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:45807:1070_1:N:0:CGGCATTA+TGACTGAC/1 99 ptg000007l_CT_converted 2567057 1 125M = 2567110 178 AAATAGTTAATATTTGAAAAATGAGAGTATTTTGAAAATGGTTAAAAATGGTTATTAAGTAAAGGTTATAGATTTTGTAAAATTGTTATTTTGGGTTAAAAATTAAAAATGTATAAAAATATGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45807:1070_2:N:0:CGGCATTA+TGACTGAC/2 147 ptg000007l_CT_converted 2567110 1 125M = 2567057 -178 ATTAAGTAAAGGTTATAGATTTTGTAAAATTGTTATTTTGGGTTAAAAATTAAAAATGTATAAAAATATGTTAAAAATGTTTTTATAATATATTGTAGTTGTTTTATGTAAAAAATGGTTGGAAA IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:0 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:120T4 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:39786:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 TTTTATTATTTATAAAATTATAACATATATTTAAAATAAAAATTATTTTAATTTAATAAATAAAAAATATTAATAAAAATAATTATTTTTAAAAATAATAATAAAAAATATTTTTATTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39786:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 TTATATAATATATTATTTAAAAAAATAAAATATTTTAATATAATTAATATAATTTTATTAATAAATATATAATAATAAAAATATTTTTTATTATTATTTTTAAAAATAATTATTTTTATTAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:48914:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 TAAAAATAATTTATACATAAATTTAAATATTTTTAATTTAAATAATTATTATAAATAAATTATCATATATAAAATTTAATAATTTATTTATAATTAATATTTTTTTTAAAAAAAAATCAATTATA IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48914:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 AATTAATATTAAAAAATATTTTATAATTGATTTTTTTTTAAAAAAAATATTAATTATAAATAAATTATTAAATTTTATATATGATAATTTATTTATAATAATTATTTAAATTAAAAATATTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:30634:1084_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 ATAAATTATTTAAAATTATTTTATATAAAAAATTATTTTAAAAAATATTAAATATTTAAAAAATAAAATAATTTTAAAAATAAATTATTATATAAAAATTATAATTTTTATAAAATTATTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30634:1084_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 ATAAATTATTTAAAATTATTTTATATAAAAAATTATTTTAAAAAATATTAAATATTTAAAAAATAAAATAATTTTATAAAAATTATAATTTTTATATAATAATTTATTTTTAAAATTATTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1H5_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 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz (8179401 sequences in total) Input files are 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H5_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 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:30634:1084_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 ATAAATTATTTAAAATTATTTTATATAAAAAATTATTTTAAAAAATATTAAATATTTAAAAAATAAAATAATTTTAAAAATAAATTATTATATAAAAATTATAATTTTTATAAAATTATTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30634:1084_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 ATAAATTATTTAAAATTATTTTATATAAAAAATTATTTTAAAAAATATTAAATATTTAAAAAATAAAATAATTTTATAAAAATTATAATTTTTATATAATAATTTATTTTTAAAATTATTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:39786:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 TTTTATTATTTATAAAATTATAACATATATTTAAAATAAAAATTATTTTAATTTAATAAATAAAAAATATTAATAAAAATAATTATTTTTAAAAATAATAATAAAAAATATTTTTATTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39786:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 TTATATAATATATTATTTAAAAAAATAAAATATTTTAATATAATTAATATAATTTTATTAATAAATATATAATAATAAAAATATTTTTTATTATTATTTTTAAAAATAATTATTTTTATTAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:45807:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 AAATAATTAATATTTAAAAAATAAAAATATTTTAAAAATAATTAAAAATAATTATTAAATAAAAATTATAAATTTTATAAAATTATTATTTTAAATTAAAAATTAAAAATATATAAAAATATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45807:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 TTTTTAATTATTTTTTATATAAAATAATTATAATATATTATAAAAATATTTTTAATATATTTTTATATATTTTTAATTTTTAATTTAAAATAATAATTTTATAAAATTTATAATTTTTATTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:40417:1070_1:N:0:CGGCATTA+TGACTGAC/1 99 ptg000009l_CT_converted 13298368 1 64M = 13298343 -89 GGGGTGGGATTTTAAGATAATTTTATGTTGTTAGGGATGTTGTAAATAGTAGAGTTTATTTTTG III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII- AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:64 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40417:1070_2:N:0:CGGCATTA+TGACTGAC/2 147 ptg000009l_CT_converted 13298343 1 64M = 13298368 89 GAAGGTTTTTGTGTATAGGTTTTTAGGGGTGGGATTTTAAGATAATTTTATGTTGTTAGGGATG IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:64 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:48914:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 TAAAAATAATTTATACATAAATTTAAATATTTTTAATTTAAATAATTATTATAAATAAATTATCATATATAAAATTTAATAATTTATTTATAATTAATATTTTTTTTAAAAAAAAATCAATTATA IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48914:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 AATTAATATTAAAAAATATTTTATAATTGATTTTTTTTTAAAAAAAATATTAATTATAAATAAATTATTAAATTTTATATATGATAATTTATTTATAATAATTATTTAAATTAAAAATATTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:39786:1070_1:N:0:CGGCATTA+TGACTGAC/1 83 ptg000053l_GA_converted 49820 1 125M = 49754 -191 ACATAATAATAAAAATATCTTCTACCACTATCCTTAAAAACAATTACTTTCACCAATATTTTCCATTTACTAAATCAAAACAATCCTTACTTTAAACATACATTATAATTTCACAAACAATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:39786:1070_2:N:0:CGGCATTA+TGACTGAC/2 163 ptg000053l_GA_converted 49754 1 125M = 49820 191 CTATATAATACATTATTCAAAAAAATAAAACACCTTAACATAACTAATACAATCCTATTAATAAATACATAATAATAAAAATATCTTCTACCACTATCCTTAAAAACAATTACTTTCACCAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII 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 Found first alignment: LH00526:197:22KFKVLT4:3:1101:30634:1084_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 ATAAGTTATTTAGAGTTGTTTTGTGTAAAAAATTGTTTTAAAAAATATTAAATATTTGAGAAATGAGATGATTTTGAAAATGGGTTATTATGTAAAGGTTATAGTTTTTGTAAAATTGTTTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30634:1084_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 ACAAATCATTTAAAATTATTTTACACAAAAAACCACTTCAAAAAACACCAAATATTCAAAAAATAAAACAATTTTACAAAAACTATAACCTTTACATAATAACCCATTTTCAAAATCATCTCATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:45807:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 AAATAATTAATATTTAAAAAATAAAAATATTTTAAAAATAATTAAAAATAATTATTAAATAAAAATTATAAATTTTATAAAATTATTATTTTAAATTAAAAATTAAAAATATATAAAAATATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:45807:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 TTTTTAATTATTTTTTATATAAAATAATTATAATATATTATAAAAATATTTTTAATATATTTTTATATATTTTTAATTTTTAATTTAAAATAATAATTTTATAAAATTTATAATTTTTATTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H5_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: LH00526:197:22KFKVLT4:3:1101:48914:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 TGGGAATAGTTTATATGTAGATTTAGATATTTTTGGTTTAAATAATTATTGTAAATAGGTTGTTGTATATGGAATTTGATGATTTATTTATGATTAGTATTTTTTTTGAAAAGGAGTTGGTTATG IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48914:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 AATCAACATCAAAAAATATTCCATAACCAACTCCTTTTCAAAAAAAATACTAATCATAAATAAATCATCAAATTCCATATACAACAACCTATTTACAATAATTATTTAAACCAAAAATATCTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:40417:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 AAAATAAAATTTTAAAATAATTTTATATTATTAAAAATATTATAAATAATAAAATTTATTTTTA III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40417:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 TATTTTTAATAATATAAAATTATTTTAAAATTTTATTTTTAAAAATTTATATATAAAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) >>> Writing bisulfite mapping results to 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:45807:1070_1:N:0:CGGCATTA+TGACTGAC/1 83 ptg000007l_GA_converted 1920947 1 125M = 1920894 -178 AACATATTTTTATACATTTTTAATTTTTAACCCAAAATAACAATTTTACAAAATCTATAACCTTTACTTAATAACCATTTTTAACCATTTTCAAAATACTCTCATTTTTCAAATATTAACTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:45807:1070_2:N:0:CGGCATTA+TGACTGAC/2 163 ptg000007l_GA_converted 1920894 1 125M = 1920947 178 TTTCCAACCATTTTTTACATAAAACAACTACAATATATTATAAAAACATTTTTAACATATTTTTATACATTTTTAATTTTTAACCCAAAATAACAATTTTACAAAATCTATAACCTTTACTTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:4A120 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:40417:1070_1:N:0:CGGCATTA+TGACTGAC/1 77 * 0 0 * * 0 0 AAAATAAAATTTTAAAATAATTTTATATTATTAAAAATATTATAAATAATAAAATTTATTTTTA III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40417:1070_2:N:0:CGGCATTA+TGACTGAC/2 141 * 0 0 * * 0 0 TATTTTTAATAATATAAAATTATTTTAAAATTTTATTTTTAAAAATTTATATATAAAAATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Reading in the sequence files 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:40417:1070_1:N:0:CGGCATTA+TGACTGAC/1 83 ptg000024l_GA_converted 5550858 1 64M = 5550883 89 CAAAAATAAACTCTACTATTTACAACATCCCTAACAACATAAAATTATCTTAAAATCCCACCCC -IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:64 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40417:1070_2:N:0:CGGCATTA+TGACTGAC/2 163 ptg000024l_GA_converted 5550883 1 64M = 5550858 -89 CATCCCTAACAACATAAAATTATCTTAAAATCCCACCCCTAAAAACCTATACACAAAAACCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:64 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1306:10678:24673_1:N:0:CGGCATTA+TGACTGAC ptg000002l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1339:20057:27377_1:N:0:CGGCATTA+TGACTGAC ptg000066l 66345 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1362:17532:4908_1:N:0:CGGCATTA+TGACTGAC ptg000083l 1 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 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2139:18479:3746_1:N:0:CGGCATTA+TGACTGAC ptg000033l 2625597 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2154:13389:8634_1:N:0:CGGCATTA+TGACTGAC ptg000015l 14997093 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2223:25584:7416_1:N:0:CGGCATTA+TGACTGAC ptg000066l 66382 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 LH00526:197:22KFKVLT4:3:2285:45378:25990_1:N:0:CGGCATTA+TGACTGAC ptg000015l 14997092 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2395:22695:21549_1:N:0:CGGCATTA+TGACTGAC ptg000025l 21443081 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2371:7263:16941_1:N:0:CGGCATTA+TGACTGAC ptg000066l 66348 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2426:8971:3283_1:N:0:CGGCATTA+TGACTGAC ptg000025l 21443081 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1159:15606:19252_1:N:0:CGGCATTA+TGACTGAC ptg000066l 66349 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1298:9651:14041_1:N:0:CGGCATTA+TGACTGAC ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1298:9643:14055_1:N:0:CGGCATTA+TGACTGAC ptg000113l 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2188:46729:13817_1:N:0:CGGCATTA+TGACTGAC ptg000015l 14997092 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2152:20543:14630_1:N:0:CGGCATTA+TGACTGAC ptg000036l 6407224 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1371:2351:24827_1:N:0:CGGCATTA+TGACTGAC ptg000092l 2 Processed 8000000 sequence pairs so far Processed 7000000 sequence pairs so far 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 8147423 (99.61%) aligned concordantly 0 times 10680 (0.13%) aligned concordantly exactly 1 time 21298 (0.26%) aligned concordantly >1 times 0.39% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 3530357 (43.16%) aligned concordantly 0 times 1544198 (18.88%) aligned concordantly exactly 1 time 3104846 (37.96%) aligned concordantly >1 times 56.84% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 8149611 (99.64%) aligned concordantly 0 times 10459 (0.13%) aligned concordantly exactly 1 time 19331 (0.24%) aligned concordantly >1 times 0.36% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 3526219 (43.11%) aligned concordantly 0 times 1545162 (18.89%) aligned concordantly exactly 1 time 3108020 (38.00%) aligned concordantly >1 times 56.89% overall alignment rate Processed 8179401 sequences in total Successfully deleted the temporary files 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8179401 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198757629 Total methylated C's in CpG context: 2906125 Total methylated C's in CHG context: 195888 Total methylated C's in CHH context: 933902 Total methylated C's in Unknown context: 7345 Total unmethylated C's in CpG context: 30074889 Total unmethylated C's in CHG context: 34026473 Total unmethylated C's in CHH context: 130620352 Total unmethylated C's in Unknown context: 270012 C methylated in CpG context: 8.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.6% Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2305:16529:11268_1:N:0:CGGCATTA+TGACTGAC ntLink_4 304046 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2284:38516:20835_1:N:0:CGGCATTA+TGACTGAC ptg000015l 14997091 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2340:23173:25261_1:N:0:CGGCATTA+TGACTGAC ptg000066l 66348 Processed 8000000 sequence pairs so far 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 8147483 (99.61%) aligned concordantly 0 times 10712 (0.13%) aligned concordantly exactly 1 time 21205 (0.26%) aligned concordantly >1 times 0.39% overall alignment rate 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 3530741 (43.17%) aligned concordantly 0 times 1544915 (18.89%) aligned concordantly exactly 1 time 3103744 (37.95%) aligned concordantly >1 times 56.83% overall alignment rate 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 8149342 (99.63%) aligned concordantly 0 times 10620 (0.13%) aligned concordantly exactly 1 time 19438 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 3525153 (43.10%) aligned concordantly 0 times 1547146 (18.92%) aligned concordantly exactly 1 time 3107101 (37.99%) aligned concordantly >1 times 56.90% overall alignment rate Processed 8179400 sequences in total Successfully deleted the temporary files 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8179400 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198855785 Total methylated C's in CpG context: 2911308 Total methylated C's in CHG context: 196666 Total methylated C's in CHH context: 942768 Total methylated C's in Unknown context: 7300 Total unmethylated C's in CpG context: 30079660 Total unmethylated C's in CHG context: 34033150 Total unmethylated C's in CHH context: 130692233 Total unmethylated C's in Unknown context: 270710 C methylated in CpG context: 8.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.6% Now waiting for all child processes to complete Processed 8000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 3529044 (43.15%) aligned concordantly 0 times 1543117 (18.87%) aligned concordantly exactly 1 time 3107239 (37.99%) aligned concordantly >1 times 56.85% overall alignment rate 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 8147345 (99.61%) aligned concordantly 0 times 10784 (0.13%) aligned concordantly exactly 1 time 21271 (0.26%) aligned concordantly >1 times 0.39% overall alignment rate 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 3523712 (43.08%) aligned concordantly 0 times 1545656 (18.90%) aligned concordantly exactly 1 time 3110032 (38.02%) aligned concordantly >1 times 56.92% overall alignment rate 8179400 reads; of these: 8179400 (100.00%) were paired; of these: 8149343 (99.63%) aligned concordantly 0 times 10578 (0.13%) aligned concordantly exactly 1 time 19479 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate Processed 8179400 sequences in total Successfully deleted the temporary files 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8179400 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198855858 Total methylated C's in CpG context: 2909009 Total methylated C's in CHG context: 195839 Total methylated C's in CHH context: 945572 Total methylated C's in Unknown context: 7504 Total unmethylated C's in CpG context: 30071173 Total unmethylated C's in CHG context: 34046748 Total unmethylated C's in CHH context: 130687517 Total unmethylated C's in Unknown context: 271450 C methylated in CpG context: 8.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.7% 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 3526723 (43.12%) aligned concordantly 0 times 1543214 (18.87%) aligned concordantly exactly 1 time 3109464 (38.02%) aligned concordantly >1 times 56.88% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 8147230 (99.61%) aligned concordantly 0 times 10724 (0.13%) aligned concordantly exactly 1 time 21447 (0.26%) aligned concordantly >1 times 0.39% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 3527279 (43.12%) aligned concordantly 0 times 1545486 (18.89%) aligned concordantly exactly 1 time 3106636 (37.98%) aligned concordantly >1 times 56.88% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 8149277 (99.63%) aligned concordantly 0 times 10575 (0.13%) aligned concordantly exactly 1 time 19549 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate Processed 8179401 sequences in total Successfully deleted the temporary files 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8179401 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198826658 Total methylated C's in CpG context: 2899425 Total methylated C's in CHG context: 195383 Total methylated C's in CHH context: 946196 Total methylated C's in Unknown context: 7352 Total unmethylated C's in CpG context: 30076121 Total unmethylated C's in CHG context: 34029056 Total unmethylated C's in CHH context: 130680477 Total unmethylated C's in Unknown context: 270607 C methylated in CpG context: 8.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.6% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2305:16545:11268_1:N:0:CGGCATTA+TGACTGAC ntLink_4 304046 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2360:47514:4278_1:N:0:CGGCATTA+TGACTGAC ptg000015l 14997092 Processed 8000000 sequence pairs so far 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 3528508 (43.14%) aligned concordantly 0 times 1544724 (18.89%) aligned concordantly exactly 1 time 3106169 (37.98%) aligned concordantly >1 times 56.86% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 3524936 (43.10%) aligned concordantly 0 times 1544986 (18.89%) aligned concordantly exactly 1 time 3109479 (38.02%) aligned concordantly >1 times 56.90% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 8147215 (99.61%) aligned concordantly 0 times 10781 (0.13%) aligned concordantly exactly 1 time 21405 (0.26%) aligned concordantly >1 times 0.39% overall alignment rate 8179401 reads; of these: 8179401 (100.00%) were paired; of these: 8149237 (99.63%) aligned concordantly 0 times 10425 (0.13%) aligned concordantly exactly 1 time 19739 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate Processed 8179401 sequences in total Successfully deleted the temporary files 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1H5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8179401 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198720973 Total methylated C's in CpG context: 2906128 Total methylated C's in CHG context: 195424 Total methylated C's in CHH context: 935742 Total methylated C's in Unknown context: 7315 Total unmethylated C's in CpG context: 30054760 Total unmethylated C's in CHG context: 34016471 Total unmethylated C's in CHH context: 130612448 Total unmethylated C's in Unknown context: 271605 C methylated in CpG context: 8.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.6% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1H5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1H5_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1H5_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/1H5_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1H5_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/1H5_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1H5_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: 40897003 Final Cytosine Methylation Report ================================= Total number of C's analysed: 994016903 Total methylated C's in CpG context: 14531995 Total methylated C's in CHG context: 979200 Total methylated C's in CHH context: 4704180 Total methylated C's in Unknown context: 36816 Total unmethylated C's in CpG context: 150356603 Total unmethylated C's in CHG context: 170151898 Total unmethylated C's in CHH context: 653293027 Total unmethylated C's in Unknown context: 1354384 C methylated in CpG context: 8.8% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.6% Deleting temporary report files... Bismark completed in 0d 4h 50m 57s ==================== Bismark run complete ====================