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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_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/2D2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6008013) Using the subset file >2D2_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/2D2_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/2D2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6008013) Using the subset file >2D2_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/2D2_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/2D2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6008014) Using the subset file >2D2_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/2D2_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/2D2_R1_001.fastp-trim.fq.gz for PID: 14145 and offset 5 (sequences written out: 6008013) Using the subset file >2D2_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/2D2_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/2D2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6008014) Using the subset file >2D2_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/2D2_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/2D2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 6008013) Using the subset file >2D2_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/2D2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz to 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz to 2D2_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/2D2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 6008013) Using the subset file >2D2_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/2D2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz to 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz to 2D2_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/2D2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 6008014) Using the subset file >2D2_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/2D2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz to 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz to 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/2D2_R2_001.fastp-trim.fq.gz for PID: 14145 and offset 5 (sequences written out: 6008013) Using the subset file >2D2_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/2D2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz to 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz to 2D2_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/2D2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 6008014) Using the subset file >2D2_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/2D2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz to 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz to 2D2_R1_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 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz (6008013 sequences in total) Writing a C -> T converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz to 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz to 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz (6008014 sequences in total) Writing a C -> T converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz to 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz to 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz (6008013 sequences in total) Writing a C -> T converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz to 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz to 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz (6008014 sequences in total) Writing a C -> T converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz to 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz to 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz (6008013 sequences in total) Writing a C -> T converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz to 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz to 2D2_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 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz (6008013 sequences in total) Input files are 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz (6008013 sequences in total) Input files are 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D2_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 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz (6008013 sequences in total) Input files are 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D2_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 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz (6008014 sequences in total) Input files are 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D2_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 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz (6008014 sequences in total) Input files are 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D2_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 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:5676:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 ATAAAATTTTGTGTTGGTAAGTTTTGTTTTATTGTTAATTTAAAAGTTATTGTTGGTTATATTAAAGTATGGAATATGATATAAAATAGGATTATTTTGAAATTTTTGTGTTTGGAAAAATTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:5676:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 CTATTTTAAATACAATAAAAATACCAAAAAATCTAAATAAAACTTAAAAATAACAATAACATATTAATAAAATAACAATTTACCACTAATTAAATTAATATTTATAATTAAATAAATTCTTATAT IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII-II9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:8394:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TGTTTTTAGAAATTGATGTTTTTTTTTATATTTTTTTTTATTGTTTTGTTTTTTGATATAAATATATAAATTGAAATTTGTTTGTATTTATTTGTTAAGATGGTAAGTATTGTAATGTAGATGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:8394:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 ATTTCTTACTTCAAAAACTTAAACCTATATTTAAAATACCTCAACACCAAAACTTCCCTATATCTTATTCATTTAAAACAATAAAAAACTTACCAAACTCCAAAACCCTTCCATCTACATTACAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:13620:1084_1:N:0:GTAACCGA+GGTGTCTT/1 99 ptg000020l_CT_converted 7549956 42 125M = 7550032 201 TATTATAATTGTGAAGTATTTTAAAAGGTATTTTTTTAGTAGTGGTAAATAGGAGTTTAGATGTGAGAAGTATTATTATTATTGGTTATTTTGTTTTATTAATTAAGGAAGAATTTTTTTTGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:31A5G34G52 YS:i:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:13620:1084_2:N:0:GTAACCGA+GGTGTCTT/2 147 ptg000020l_CT_converted 7550032 42 125M = 7549956 -201 TATTATTGGTTATTTTGTTTTATTAATTAAGGAAGAATTTTTTTTGGATATTGAATTTAAAAGATTTATTTTGTTTTTGTATATTTTAGAGAAATTTTTATGAATTGATTTTTTTTTTAAGTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:65A59 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:6242:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TAGAATAATTTGAAAATTTTTTGAGTTGGAGTTTTAAATTAATTATAATATGAGTTAAAATAATTAAGTTAAATGATAATTGTTGTTATTTTAATGGAGGAAATTATTTTTTTTGTATTTTGTAT I9-III9III--I9IIII-IIIIII-9I9IIIIII9-99IIIII99I9I--II9IIIIIIIII9I9IIIIIIIII9II99I9I9-IIIIII9II9IIIIIIIIII-9II9IIII9IIIIIIII9I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6242:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 CAAAATAATTAAAAAACTACTTAAATTAAAACCCCAAATTAATTATAACATAAACCAAAATAATTAAATTAAATAACAATTATTATCATACTAATAAAAAAAACTATTTTTTCTACACTTTATAC IIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-I9IIIIII99I-IIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:5692:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 ATAAAATTTTGTGTTGGTAAGTTTTGTTTTATTGTTAATTTAAAAGTTATTGTTGGTTATATTAAAGTATGGAATATGATATAAAATAGGATTATTTTGAAATTTTTGTGTTTGGAAAAATTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII-IIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:5692:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 CTATTTTAAATACAACAAAAATACCAAAAAATCTAAATAAAACTTAAAAATAACAATAACATATTAATAAAATAACAATTTACCACTAATTAAATTAATATTTATAATTAAATAAATTCTTATAT II9IIII9IIII-II-9IIIIIIIIIIIIIIIIIIII99IIIIII-IIIII9IIIII9IIIIIIIIIIIIII9-III9II9III9II-IIIIIIIIIII9IIIIIIIIIII9I9IIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:5676:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 ATAAAATTTTATATTAATAAATTTTATTTTATTATTAATTTAAAAATTATTATTAATTATATTAAAATATAAAATATAATATAAAATAAAATTATTTTAAAATTTTTATATTTAAAAAAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:5676:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 TTATTTTAAATATAATAAAAATATTAAAAAATTTAAATAAAATTTAAAAATAATAATAATATATTAATAAAATAATAATTTATTATTAATTAAATTAATATTTATAATTAAATAAATTTTTATAT IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII-II9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:13620:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TATTATAATTACAAAATATTTTAAAAAATATTTTTTTAATAATAATAAATAAAAATTTAAATATAAAAAATATTATTATTATTAATTATTTTATTTTATTAATTAAAAAAAAATTTTTTTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13620:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 ATAATTTAAAAAAAAAATTAATTTATAAAAATTTTTTTAAAATATATAAAAATAAAATAAATTTTTTAAATTTAATATTTAAAAAAAATTTTTTTTTAATTAATAAAATAAAATAATTAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:6242:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TAAAATAATTCAAAAATTCTTTAAATTAAAATTTTAAATTAATTATAATATAAATTAAAATAATTAAATTAAATAATAATTATTATTATCTTAACAAAAAAAATTATTTTTTTTATATTTTATAT I9-III9III--I9IIII-IIIIII-9I9IIIIII9-99IIIII99I9I--II9IIIIIIIII9I9IIIIIIIII9II99I9I9-IIIIII9II9IIIIIIIIII-9II9IIII9IIIIIIII9I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6242:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 TAAAATAATTAAAAAATTATTTAAATTAAAATTTTAAATTAATTATAATATAAATTAAAATAATTAAATTAAATAATAATTATTATTATATTAATAAAAAAAATTATTTTTTTTATATTTTATAT IIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-I9IIIIII99I-IIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:8394:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TATTTTTAAAAATTAATATTTTTTTTTATATTTTTTTTTATTATTTTATTTTTTAATATAAATATATAAATTAAAATTTATTTATATTTATTTATTAAAATAATAAATATTATAATATAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:8394:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 ATTTTTTATTTTAAAAATTTAAATTTATATTTAAAATATTTTAATATTAAAATTTTTTTATATTTTATTTATTTAAAATAATAAAAAATTTATTAAATTTTAAAATTTTTTTATTTATATTATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:5692:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 ATAAAATTTTATATTAATAAATTTTATTTTATTATTAATTTAAAAATTATTATTAATTATATTAAAATATAAAATATAATATAAAATAAAATTATTTTAAAATTTTTATATTTAAAAAAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII-IIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:5692:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 TTATTTTAAATATAATAAAAATATTAAAAAATTTAAATAAAATTTAAAAATAATAATAATATATTAATAAAATAATAATTTATTATTAATTAAATTAATATTTATAATTAAATAAATTTTTATAT II9IIII9IIII-II-9IIIIIIIIIIIIIIIIIIII99IIIIII-IIIII9IIIII9IIIIIIIIIIIIII9-III9II9III9II-IIIIIIIIIII9IIIIIIIIIII9I9IIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:6242:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TAAAATAATTCAAAAATTCTTTAAATTAAAATTTTAAATTAATTATAATATAAATTAAAATAATTAAATTAAATAATAATTATTATTATCTTAACAAAAAAAATTATTTTTTTTATATTTTATAT I9-III9III--I9IIII-IIIIII-9I9IIIIII9-99IIIII99I9I--II9IIIIIIIII9I9IIIIIIIII9II99I9I9-IIIIII9II9IIIIIIIIII-9II9IIII9IIIIIIII9I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6242:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 TAAAATAATTAAAAAATTATTTAAATTAAAATTTTAAATTAATTATAATATAAATTAAAATAATTAAATTAAATAATAATTATTATTATATTAATAAAAAAAATTATTTTTTTTATATTTTATAT IIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-I9IIIIII99I-IIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:5676:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 ATAAAATTTTATATTAATAAATTTTATTTTATTATTAATTTAAAAATTATTATTAATTATATTAAAATATAAAATATAATATAAAATAAAATTATTTTAAAATTTTTATATTTAAAAAAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:5676:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 TTATTTTAAATATAATAAAAATATTAAAAAATTTAAATAAAATTTAAAAATAATAATAATATATTAATAAAATAATAATTTATTATTAATTAAATTAATATTTATAATTAAATAAATTTTTATAT IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII-II9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:5692:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 ATAAAATTTTATATTAATAAATTTTATTTTATTATTAATTTAAAAATTATTATTAATTATATTAAAATATAAAATATAATATAAAATAAAATTATTTTAAAATTTTTATATTTAAAAAAATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII-IIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:5692:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 TTATTTTAAATATAATAAAAATATTAAAAAATTTAAATAAAATTTAAAAATAATAATAATATATTAATAAAATAATAATTTATTATTAATTAAATTAATATTTATAATTAAATAAATTTTTATAT II9IIII9IIII-II-9IIIIIIIIIIIIIIIIIIII99IIIIII-IIIII9IIIII9IIIIIIIIIIIIII9-III9II9III9II-IIIIIIIIIII9IIIIIIIIIII9I9IIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:8394:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TATTTTTAAAAATTAATATTTTTTTTTATATTTTTTTTTATTATTTTATTTTTTAATATAAATATATAAATTAAAATTTATTTATATTTATTTATTAAAATAATAAATATTATAATATAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:8394:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 ATTTTTTATTTTAAAAATTTAAATTTATATTTAAAATATTTTAATATTAAAATTTTTTTATATTTTATTTATTTAAAATAATAAAAAATTTATTAAATTTTAAAATTTTTTTATTTATATTATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:13620:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TATTATAATTACAAAATATTTTAAAAAATATTTTTTTAATAATAATAAATAAAAATTTAAATATAAAAAATATTATTATTATTAATTATTTTATTTTATTAATTAAAAAAAAATTTTTTTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13620:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 ATAATTTAAAAAAAAAATTAATTTATAAAAATTTTTTTAAAATATATAAAAATAAAATAAATTTTTTAAATTTAATATTTAAAAAAAATTTTTTTTTAATTAATAAAATAAAATAATTAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D2_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: LH00652:104:22KG7JLT4:7:1101:13620:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TATTATAATTGTGAAGTATTTTAAAAGGTATTTTTTTAGTAGTGGTAAATAGGAGTTTAGATGTGAGAAGTATTATTATTATTGGTTATTTTGTTTTATTAATTAAGGAAGAATTTTTTTTGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13620:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 ATAACTTAAAAAAAAAATCAATTCATAAAAATTTCTCTAAAATATACAAAAACAAAATAAATCTTTTAAATTCAATATCCAAAAAAAATTCTTCCTTAATTAATAAAACAAAATAACCAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:5692:1084_1:N:0:GTAACCGA+GGTGTCTT/1 83 ptg000024l_GA_converted 7591048 42 125M = 7590874 -299 ATCAATTTTTCCAAACACAAAAATTTCAAAATAATCCTATTTTATATCATATTCCATACTTTAATATAACCAACAATAACTTTTAAATTAACAATAAAACAAAACTTACCAACACAAAATTTTAT IIIII-IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:47T1C75 YS:i:-12 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:5692:1084_2:N:0:GTAACCGA+GGTGTCTT/2 163 ptg000024l_GA_converted 7590874 42 125M = 7591048 299 CTATTTTAAATACAACAAAAATACCAAAAAATCTAAATAAAACTTAAAAATAACAATAACATATTAATAAAATAACAATTTACCACTAATTAAATTAATATTTATAATTAAATAAATTCTTATAT II9IIII9IIII-II-9IIIIIIIIIIIIIIIIIIII99IIIIII-IIIII9IIIII9IIIIIIIIIIIIII9-III9II9III9II-IIIIIIIIIII9IIIIIIIIIII9I9IIIIIII9III AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:15T62A46 YS:i:-12 YT:Z:CP Found first alignment: LH00652:104:22KG7JLT4:7:1101:5676:1084_1:N:0:GTAACCGA+GGTGTCTT/1 83 ptg000024l_GA_converted 7591048 42 125M = 7590874 -299 ATCAATTTTTCCAAACACAAAAATTTCAAAATAATCCTATTTTATATCATATTCCATACTTTAATATAACCAACAATAACTTTTAAATTAACAATAAAACAAAACTTACCAACACAAAATTTTAT IIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:47T1C75 YS:i:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:5676:1084_2:N:0:GTAACCGA+GGTGTCTT/2 163 ptg000024l_GA_converted 7590874 42 125M = 7591048 299 CTATTTTAAATACAATAAAAATACCAAAAAATCTAAATAAAACTTAAAAATAACAATAACATATTAATAAAATAACAATTTACCACTAATTAAATTAATATTTATAATTAAATAAATTCTTATAT IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIII-II9IIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:78A46 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:8394:1084_1:N:0:GTAACCGA+GGTGTCTT/1 83 ptg000009l_GA_converted 6009470 40 95M3D30M = 6009361 -237 TCCATCTACATTACAATACTTACCATCTTAACAAATAAATACAAACAAATTTCAATTTATATATTTATATCAAAAAACAAAACAATAAAAAAAAATATAAAAAAAAACATCAATTTCTAAAAACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-32 XN:i:0 XM:i:3 XO:i:1 XG:i:3 NM:i:6 MD:Z:63A1A29^TAT14C15 YS:i:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:8394:1084_2:N:0:GTAACCGA+GGTGTCTT/2 163 ptg000009l_GA_converted 6009361 40 125M = 6009470 237 ATTTCTTACTTCAAAAACTTAAACCTATATTTAAAATACCTCAACACCAAAACTTCCCTATATCTTATTCATTTAAAACAATAAAAAACTTACCAAACTCCAAAACCCTTCCATCTACATTACAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6A118 YS:i:-32 YT:Z:CP >>> Writing bisulfite mapping results to 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:6242:1084_1:N:0:GTAACCGA+GGTGTCTT/1 77 * 0 0 * * 0 0 TAGAATAATTTGAAAATTTTTTGAGTTGGAGTTTTAAATTAATTATAATATGAGTTAAAATAATTAAGTTAAATGATAATTGTTGTTATTTTAATGGAGGAAATTATTTTTTTTGTATTTTGTAT I9-III9III--I9IIII-IIIIII-9I9IIIIII9-99IIIII99I9I--II9IIIIIIIII9I9IIIIIIIII9II99I9I9-IIIIII9II9IIIIIIIIII-9II9IIII9IIIIIIII9I YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6242:1084_2:N:0:GTAACCGA+GGTGTCTT/2 141 * 0 0 * * 0 0 CAAAATAATTAAAAAACTACTTAAATTAAAACCCCAAATTAATTATAACATAAACCAAAATAATTAAATTAAATAACAATTATTATCATACTAATAAAAAAAACTATTTTTTCTACACTTTATAC IIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-I9IIIIII99I-IIII9 YT:Z:UP >>> Writing bisulfite mapping results to 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1248:12795:26306_1:N:0:GTAACCGA+GGTGTCTT ptg000066l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1240:51425:16568_1:N:0:GTAACCGA+GGTGTCTT ptg000083l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1310:8815:23980_1:N:0:GTAACCGA+GGTGTCTT ptg000048l 76426 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 LH00652:104:22KG7JLT4:7:1338:24857:29599_1:N:0:GTAACCGA+GGTGTCTT ptg000025l 21443092 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2167:15683:9029_1:N:0:GTAACCGA+GGTGTCTT ptg000024l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2123:37106:22677_1:N:0:GTAACCGA+GGTGTCTT ptg000056l 59099 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2275:43804:16736_1:N:0:GTAACCGA+GGTGTCTT 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 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2282:27762:27147_1:N:0:GTAACCGA+GGTGTCTT ptg000096l 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1275:5005:14354_1:N:0:GTAACCGA+GGTGTCTT ptg000025l 21443080 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1365:45511:27539_1:N:0:GTAACCGA+GGTGTCTT ptg000098l 55086 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1438:14615:19202_1:N:0:GTAACCGA+GGTGTCTT ptg000127l 2 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1378:25319:19776_1:N:0:GTAACCGA+GGTGTCTT ptg000025l 21443080 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2184:8216:25998_1:N:0:GTAACCGA+GGTGTCTT ptg000096l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1305:20246:19510_1:N:0:GTAACCGA+GGTGTCTT ptg000009l 19096018 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 5994081 (99.77%) aligned concordantly 0 times 4921 (0.08%) aligned concordantly exactly 1 time 9012 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 2730321 (45.44%) aligned concordantly 0 times 1283899 (21.37%) aligned concordantly exactly 1 time 1993794 (33.19%) aligned concordantly >1 times 54.56% overall alignment rate 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 2735641 (45.53%) aligned concordantly 0 times 1281517 (21.33%) aligned concordantly exactly 1 time 1990856 (33.14%) aligned concordantly >1 times 54.47% overall alignment rate 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 5995470 (99.79%) aligned concordantly 0 times 4862 (0.08%) aligned concordantly exactly 1 time 7682 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate Processed 6000000 sequence pairs so far Processed 6008014 sequences in total Successfully deleted the temporary files 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6008014 Final Cytosine Methylation Report ================================= Total number of C's analysed: 166215177 Total methylated C's in CpG context: 2819472 Total methylated C's in CHG context: 141360 Total methylated C's in CHH context: 634104 Total methylated C's in Unknown context: 5069 Total unmethylated C's in CpG context: 22986613 Total unmethylated C's in CHG context: 27969721 Total unmethylated C's in CHH context: 111663907 Total unmethylated C's in Unknown context: 243196 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 5994120 (99.77%) aligned concordantly 0 times 4869 (0.08%) aligned concordantly exactly 1 time 9024 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 2732239 (45.48%) aligned concordantly 0 times 1280684 (21.32%) aligned concordantly exactly 1 time 1995090 (33.21%) aligned concordantly >1 times 54.52% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 5995389 (99.79%) aligned concordantly 0 times 4901 (0.08%) aligned concordantly exactly 1 time 7723 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 2731900 (45.47%) aligned concordantly 0 times 1283105 (21.36%) aligned concordantly exactly 1 time 1993008 (33.17%) aligned concordantly >1 times 54.53% overall alignment rate Processed 6000000 sequence pairs so far Processed 6008013 sequences in total Successfully deleted the temporary files 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6008013 Final Cytosine Methylation Report ================================= Total number of C's analysed: 166201292 Total methylated C's in CpG context: 2813530 Total methylated C's in CHG context: 141097 Total methylated C's in CHH context: 626498 Total methylated C's in Unknown context: 4988 Total unmethylated C's in CpG context: 23000571 Total unmethylated C's in CHG context: 27966236 Total unmethylated C's in CHH context: 111653360 Total unmethylated C's in Unknown context: 243511 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2273:15619:28814_1:N:0:GTAACCGA+GGTGTCTT ptg000006l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2326:26581:24204_1:N:0:GTAACCGA+GGTGTCTT ptg000095l 40232 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2329:28506:3410_1:N:0:GTAACCGA+GGTGTCTT ntLink_1 163091 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2411:37623:15839_1:N:0:GTAACCGA+GGTGTCTT ptg000127l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2470:48011:19426_1:N:0:GTAACCGA+GGTGTCTT ptg000077l 42476 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 5993792 (99.76%) aligned concordantly 0 times 4992 (0.08%) aligned concordantly exactly 1 time 9229 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 5995417 (99.79%) aligned concordantly 0 times 4736 (0.08%) aligned concordantly exactly 1 time 7860 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 2732373 (45.48%) aligned concordantly 0 times 1280942 (21.32%) aligned concordantly exactly 1 time 1994698 (33.20%) aligned concordantly >1 times 54.52% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 2734462 (45.51%) aligned concordantly 0 times 1280945 (21.32%) aligned concordantly exactly 1 time 1992606 (33.17%) aligned concordantly >1 times 54.49% overall alignment rate Processed 6000000 sequence pairs so far Processed 6008013 sequences in total Successfully deleted the temporary files 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6008013 Final Cytosine Methylation Report ================================= Total number of C's analysed: 166078579 Total methylated C's in CpG context: 2819436 Total methylated C's in CHG context: 141683 Total methylated C's in CHH context: 636068 Total methylated C's in Unknown context: 5054 Total unmethylated C's in CpG context: 22970634 Total unmethylated C's in CHG context: 27930544 Total unmethylated C's in CHH context: 111580214 Total unmethylated C's in Unknown context: 243310 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Now waiting for all child processes to complete 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 5993863 (99.76%) aligned concordantly 0 times 4967 (0.08%) aligned concordantly exactly 1 time 9183 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 2733153 (45.49%) aligned concordantly 0 times 1279603 (21.30%) aligned concordantly exactly 1 time 1995257 (33.21%) aligned concordantly >1 times 54.51% overall alignment rate Processed 6000000 sequence pairs so far 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 5995307 (99.79%) aligned concordantly 0 times 4949 (0.08%) aligned concordantly exactly 1 time 7757 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 6008013 reads; of these: 6008013 (100.00%) were paired; of these: 2733372 (45.50%) aligned concordantly 0 times 1281312 (21.33%) aligned concordantly exactly 1 time 1993329 (33.18%) aligned concordantly >1 times 54.50% overall alignment rate Processed 6008013 sequences in total Successfully deleted the temporary files 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6008013 Final Cytosine Methylation Report ================================= Total number of C's analysed: 166021420 Total methylated C's in CpG context: 2811866 Total methylated C's in CHG context: 140683 Total methylated C's in CHH context: 634607 Total methylated C's in Unknown context: 5304 Total unmethylated C's in CpG context: 22967564 Total unmethylated C's in CHG context: 27934208 Total unmethylated C's in CHH context: 111532492 Total unmethylated C's in Unknown context: 244070 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2411:37615:15825_1:N:0:GTAACCGA+GGTGTCTT ptg000127l 1 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 5994000 (99.77%) aligned concordantly 0 times 4955 (0.08%) aligned concordantly exactly 1 time 9059 (0.15%) aligned concordantly >1 times 0.23% overall alignment rate 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 5995246 (99.79%) aligned concordantly 0 times 4991 (0.08%) aligned concordantly exactly 1 time 7777 (0.13%) aligned concordantly >1 times 0.21% overall alignment rate 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 2734949 (45.52%) aligned concordantly 0 times 1280884 (21.32%) aligned concordantly exactly 1 time 1992181 (33.16%) aligned concordantly >1 times 54.48% overall alignment rate 6008014 reads; of these: 6008014 (100.00%) were paired; of these: 2729072 (45.42%) aligned concordantly 0 times 1284630 (21.38%) aligned concordantly exactly 1 time 1994312 (33.19%) aligned concordantly >1 times 54.58% overall alignment rate Processed 6000000 sequence pairs so far Processed 6008014 sequences in total Successfully deleted the temporary files 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2D2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 6008014 Final Cytosine Methylation Report ================================= Total number of C's analysed: 166212103 Total methylated C's in CpG context: 2814822 Total methylated C's in CHG context: 142210 Total methylated C's in CHH context: 637181 Total methylated C's in Unknown context: 5147 Total unmethylated C's in CpG context: 22984941 Total unmethylated C's in CHG context: 27961982 Total unmethylated C's in CHH context: 111670967 Total unmethylated C's in Unknown context: 243260 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 2D2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 2D2_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 2D2_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/2D2_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 2D2_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/2D2_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 2D2_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: 30040067 Final Cytosine Methylation Report ================================= Total number of C's analysed: 830728571 Total methylated C's in CpG context: 14079126 Total methylated C's in CHG context: 707033 Total methylated C's in CHH context: 3168458 Total methylated C's in Unknown context: 25562 Total unmethylated C's in CpG context: 114910323 Total unmethylated C's in CHG context: 139762691 Total unmethylated C's in CHH context: 558100940 Total unmethylated C's in Unknown context: 1217347 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% Deleting temporary report files... Bismark completed in 0d 4h 39m 16s ==================== Bismark run complete ====================