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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_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/2C2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8503471) Using the subset file >2C2_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/2C2_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/2C2_R1_001.fastp-trim.fq.gz for PID: 82617 and offset 5 (sequences written out: 8503471) Using the subset file >2C2_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/2C2_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/2C2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8503472) Using the subset file >2C2_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/2C2_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/2C2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8503472) Using the subset file >2C2_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/2C2_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/2C2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8503472) Using the subset file >2C2_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/2C2_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/2C2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8503472) Using the subset file >2C2_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/2C2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz to 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz to 2C2_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/2C2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8503472) Using the subset file >2C2_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/2C2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz to 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz to 2C2_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/2C2_R2_001.fastp-trim.fq.gz for PID: 82617 and offset 5 (sequences written out: 8503471) Using the subset file >2C2_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/2C2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz to 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz to 2C2_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/2C2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8503472) Using the subset file >2C2_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/2C2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz to 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz to 2C2_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/2C2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8503471) Using the subset file >2C2_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/2C2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz to 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz to 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz (8503472 sequences in total) Writing a C -> T converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz to 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz to 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz (8503472 sequences in total) Writing a C -> T converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz to 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz to 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz (8503471 sequences in total) Writing a C -> T converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz to 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz to 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz (8503472 sequences in total) Writing a C -> T converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz to 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz to 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz (8503471 sequences in total) Writing a C -> T converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz to 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz to 2C2_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 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz (8503472 sequences in total) Input files are 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2C2_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 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz (8503472 sequences in total) Input files are 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz (8503471 sequences in total) Input files are 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2C2_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 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz (8503472 sequences in total) Input files are 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2C2_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 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz (8503471 sequences in total) Input files are 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2C2_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 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:4641:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 TTATTGGATTAATGTATATAAGAGTTGTATGTTGAATAGTATAGTAAGTTGTAGAGAAATTTGGTGAATTTAATGTTTTAGGTAGATGGAATTGTAATGAATGTAGGTGTAAAATGGTTGTTGGT IIIIIIIIIIIIIIIIIIII9I-II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIII-I99II9IIIIIIIIIIIII9II9-I-IIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:4641:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 AAAACAAAAATAAATTTAAAACAACATATACAACAACAACATCTAAAATATCCTTCAAAAAACCAACAACCATTTTACACCTACATTCATTACAATTCCATCTACCTAAAACATTAAATTCACCA III9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9-I-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:14187:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 ATTGGGATATATGTTAATTTATAATTTATGGTAATTTTTTGTTTTAATAGTAGATTTTTAAGTGATTTGTTAGTGTTTTTTAATTTATTTGTTTTTTTTGAGTATTATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII-IIIIIIIIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14187:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 AAATTAAAAAACACTAACAAATCACTTAAAAATCTACTATTAAAACAAAAAATTACCATAAATTATAAATTAACATATATCCCAATAAAAATCTTTAAACTTTTACACCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:14704:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 AATGAGATGGAAAATGGGTTAAATTGTGGGATATGTGGATAAATAAGATAGAATGAGGTTAATAAGGGTTAAATGAGGGTGAATGAAGTAGAATGTTAGATTAGAGTAATATATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14704:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 ATTCTACTTCATTCACCCTCATTTAACCCTTATTAACCTCATTCTATCTTATTTATCCACATATCCCACAATTTAACCCATTTTCCATCTCATTTACCCCAAATAACAAAATTAACCTC IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:18847:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 ATAAAAAAGTTAAGTAAATAGAAATATAAAATTAAAAAATATTTTTTAATTATTTGTATGTTTATAGTTTATAATGTAATAAGTAGAATTTTAGAGTATTTGTTTTAGTAGTGGATTGTTGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIII-IIIIIIII9II9IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:18847:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 TAATATTTCATTATCTTTAAACAATACTAAAATTCTTTTATTAATAAAATAACTAAACACTATAATCAAAATAATAATTTTTTAAATCATATTAAATATAATTTAACAAAATTAACAACCAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:15352:1084_1:N:0:CAAGGTAC+GAGATACG/1 99 ptg000018l_CT_converted 14960241 1 125M = 14960254 138 TGTTTATTTTGAGGAGATTGATAAGTTTTGGTGGTTTTTTAGTAAATGTTTTATTTTTTGTAATATTTTGTTAAAAATTGGGTTAAAATTTTAGTGTATGGTATTTTGTAGAAAAAGTTGTTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII 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 LH00652:104:22KG7JLT4:7:1101:15352:1084_2:N:0:CAAGGTAC+GAGATACG/2 147 ptg000018l_CT_converted 14960254 1 125M = 14960241 -138 GAGATTGATAAGTTTTGGTGGTTTTTTAGTAAATGTTTTATTTTTTGTAATATTTTGTTAAAAATTGGGTTAAAATTTTAGTGTATGGTATTTTGTAGAAAAAGTTGTTTATTTTGAGGAGATTG IIII-II9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- 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 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:15352:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 TATTTATTTTAAAAAAATTAATAAATTTTAATAATTTTTTAATAAATATTTTATTTTTTATAATATTTTATTAAAAATTAAATTAAAATTTTAATATATAATATTTTATAAAAAAAATTATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:15352:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 TAATTTTTTTAAAATAAATAATTTTTTTTATAAAATATTATATATTAAAATTTTAATTTAATTTTTAATAAAATATTATAAAAAATAAAATATTTATTAAAAAATTATTAAAATTTATTAATTTT -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:4641:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 TTATTAAATTAATATATATAAAAATTATATATTAAATAATATAATAAATTATAAAAAAATTTAATAAATTTAATATTTTAAATAAATAAAATTATAATAAATATAAATATAAAATAATTATTAAT IIIIIIIIIIIIIIIIIIII9I-II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIII-I99II9IIIIIIIIIIIII9II9-I-IIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:4641:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 AAAATAAAAATAAATTTAAAATAATATATATAATAATAATATTTAAAATGTTTTTTAAAAAATTAATAATTATTTTATATTTATATTTATTATAATTTTATTTATTTAAAATATTAAATTTATTA III9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9-I-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:14704:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 AATAAAATAAAAAATAAATTAAATTATAAAATATATAAATAAATAAAATAAAATAAAATTAATAAAAATTAAATAAAAATAAATAAAATAAAATATTAAATTAAAATAATATATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14704:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 ATTTTATTTTATTTATTTTTATTTAATTTTTATTAATTTTATTTTATTTTATTTATTTATATATTTTATAATTTAATTTATTTTTTATTTTATTTATTTTAAATAATAAAATTAATTTT IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:14187:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 ATTAAAATATATATTAATTTATAATTTATAATAATTTTTTATTTTAATAATAAATTTTTAAATAATTTATTAATATTTTTTAATTTATTTATTTTTTTCAAATATTATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII-IIIIIIIIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14187:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 AAATTAAAAAATATTAATAAATTATTTAAAAATTTATTATTAAAATAAAAAATTATTATAAATTATAAATTAATATATATTTTAATAAAAATTTTTAAATTTTTATATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:18847:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 ATAAAAAAATTAAATAAATAAAAATATAAAATTAAAAAATATTTTTTAATTATTTATACATTTATAATTTATAATATAATAAATAAAATTTTAAAATATTTATTTTAATAACAAATTATTAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIII-IIIIIIII9II9IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:18847:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 TAATATTTTATTATTTTTAAATAATATTAAAATTTTTTTATTAATAAAATAATTAAATATTATAATTAAAATAATAATTTTTTAAATTATATTAAATATAATTTAATAAAATTAATAATTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:4641:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 TTATTAAATTAATATATATAAAAATTATATATTAAATAATATAATAAATTATAAAAAAATTTAATAAATTTAATATTTTAAATAAATAAAATTATAATAAATATAAATATAAAATAATTATTAAT IIIIIIIIIIIIIIIIIIII9I-II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIII-I99II9IIIIIIIIIIIII9II9-I-IIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:4641:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 AAAATAAAAATAAATTTAAAATAATATATATAATAATAATATTTAAAATGTTTTTTAAAAAATTAATAATTATTTTATATTTATATTTATTATAATTTTATTTATTTAAAATATTAAATTTATTA III9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9-I-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:14704:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 AATAAAATAAAAAATAAATTAAATTATAAAATATATAAATAAATAAAATAAAATAAAATTAATAAAAATTAAATAAAAATAAATAAAATAAAATATTAAATTAAAATAATATATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14704:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 ATTTTATTTTATTTATTTTTATTTAATTTTTATTAATTTTATTTTATTTTATTTATTTATATATTTTATAATTTAATTTATTTTTTATTTTATTTATTTTAAATAATAAAATTAATTTT IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:18847:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 ATAAAAAAATTAAATAAATAAAAATATAAAATTAAAAAATATTTTTTAATTATTTATACATTTATAATTTATAATATAATAAATAAAATTTTAAAATATTTATTTTAATAACAAATTATTAAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIII-IIIIIIII9II9IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:18847:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 TAATATTTTATTATTTTTAAATAATATTAAAATTTTTTTATTAATAAAATAATTAAATATTATAATTAAAATAATAATTTTTTAAATTATATTAAATATAATTTAATAAAATTAATAATTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:15352:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 TATTTATTTTAAAAAAATTAATAAATTTTAATAATTTTTTAATAAATATTTTATTTTTTATAATATTTTATTAAAAATTAAATTAAAATTTTAATATATAATATTTTATAAAAAAAATTATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:15352:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 TAATTTTTTTAAAATAAATAATTTTTTTTATAAAATATTATATATTAAAATTTTAATTTAATTTTTAATAAAATATTATAAAAAATAAAATATTTATTAAAAAATTATTAAAATTTATTAATTTT -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II-IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:14187:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 ATTAAAATATATATTAATTTATAATTTATAATAATTTTTTATTTTAATAATAAATTTTTAAATAATTTATTAATATTTTTTAATTTATTTATTTTTTTCAAATATTATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII-IIIIIIIIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14187:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 AAATTAAAAAATATTAATAAATTATTTAAAAATTTATTATTAAAATAAAAAATTATTATAAATTATAAATTAATATATATTTTAATAAAAATTTTTAAATTTTTATATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2C2_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: LH00652:104:22KG7JLT4:7:1101:15352:1084_1:N:0:CAAGGTAC+GAGATACG/1 83 ptg000015l_GA_converted 14993430 1 125M = 14993417 -138 ATAAACAACTTTTTCTACAAAATACCATACACTAAAATTTTAACCCAATTTTTAACAAAATATTACAAAAAATAAAACATTTACTAAAAAACCACCAAAACTTATCAATCTCCTCAAAATAAACA IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00652:104:22KG7JLT4:7:1101:15352:1084_2:N:0:CAAGGTAC+GAGATACG/2 163 ptg000015l_GA_converted 14993417 1 125M = 14993430 138 CAATCTCCTCAAAATAAACAACTTTTTCTACAAAATACCATACACTAAAATTTTAACCCAATTTTTAACAAAATATTACAAAAAATAAAACATTTACTAAAAAACCACCAAAACTTATCAATCTC -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II-IIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:14187:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 ATTGGGATATATGTTAATTTATAATTTATGGTAATTTTTTGTTTTAATAGTAGATTTTTAAGTGATTTGTTAGTGTTTTTTAATTTATTTGTTTTTTTTGAGTATTATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIII-IIIIIIIIIII9 YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14187:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 AAATTAAAAAACACTAACAAATCACTTAAAAATCTACTATTAAAACAAAAAATTACCATAAATTATAAATTAACATATATCCCAATAAAAATCTTTAAACTTTTACACCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP Found first alignment: LH00652:104:22KG7JLT4:7:1101:4641:1084_1:N:0:CAAGGTAC+GAGATACG/1 83 ptg000008l_GA_converted 22595204 42 125M = 22595143 -186 ACCAACAACCATTTTACACCTACATTCATTACAATTCCATCTACCTAAAACATTAAATTCACCAAATTTCTCTACAACTTACTATACTATTCAACATACAACTCTTATATACATTAATCCAATAA IIIIIIIIIII-I-9II9IIIIIIIIIIIII9II99I-IIIIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II-I9IIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:4641:1084_2:N:0:CAAGGTAC+GAGATACG/2 163 ptg000008l_GA_converted 22595143 42 125M = 22595204 186 AAAACAAAAATAAATTTAAAACAACATATACAACAACAACATCTAAAATATCCTTCAAAAAACCAACAACCATTTTACACCTACATTCATTACAATTCCATCTACCTAAAACATTAAATTCACCA III9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9-I-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9IIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Found first alignment: LH00652:104:22KG7JLT4:7:1101:14704:1084_1:N:0:CAAGGTAC+GAGATACG/1 77 * 0 0 * * 0 0 AATGAGATGGAAAATGGGTTAAATTGTGGGATATGTGGATAAATAAGATAGAATGAGGTTAATAAGGGTTAAATGAGGGTGAATGAAGTAGAATGTTAGATTAGAGTAATATATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:14704:1084_2:N:0:CAAGGTAC+GAGATACG/2 141 * 0 0 * * 0 0 ATTCTACTTCATTCACCCTCATTTAACCCTTATTAACCTCATTCTATCTTATTTATCCACATATCCCACAATTTAACCCATTTTCCATCTCATTTACCCCAAATAACAAAATTAACCTC IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:18847:1084_1:N:0:CAAGGTAC+GAGATACG/1 83 ptg000012l_GA_converted 10208822 2 103M3D22M = 10208502 -448 TATCCAACAATCCACTACTAAAACAAATACTCTAAAATTCTACTTATTACATTATAAACTATAAACATACAAATAATTAAAAAATATTTTTTAATTTTATATTTCTATTTACTTAACTTTTTTAT IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII9II9IIIIIIII-IIII9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-58 XN:i:0 XM:i:7 XO:i:1 XG:i:3 NM:i:10 MD:Z:12A52A9T11A4T10^TTA1T11T8 YS:i:-26 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:18847:1084_2:N:0:CAAGGTAC+GAGATACG/2 163 ptg000012l_GA_converted 10208502 2 77M1I47M = 10208822 448 TAATATTTCATTATCTTTAAACAATACTAAAATTCTTTTATTAATAAAATAACTAAACACTATAATCAAAATAATAATTTTTTAAATCATATTAAATATAATTTAACAAAATTAACAACCAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-26 XS:i:-32 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:54T2A4A61 YS:i:-56 YT:Z:CP >>> Writing bisulfite mapping results to 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1191:6534:5568_1:N:0:CAAGGTAC+GAGATACG ptg000007l 12295855 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 LH00652:104:22KG7JLT4:7:1285:5862:2051_1:N:0:CAAGGTAC+GAGATACG ptg000033l 2625607 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1302:37187:6955_1:N:0:CAAGGTAC+GAGATACG ptg000066l 66345 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2219:10392:22173_1:N:0:CAAGGTAC+GAGATACG ptg000054l 36026 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2263:15109:4391_1:N:0:CAAGGTAC+GAGATACG ptg000066l 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2342:43028:15839_1:N:0:CAAGGTAC+GAGATACG ptg000015l 14997091 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2497:13402:3424_1:N:0:CAAGGTAC+GAGATACG ptg000015l 14997092 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2128:11509:6030_1:N:0:CAAGGTAC+GAGATACG ptg000097l 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2223:33506:12686_1:N:0:CAAGGTAC+GAGATACG ptg000048l 1 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 7000000 sequence pairs so far 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 3783004 (44.49%) aligned concordantly 0 times 1688115 (19.85%) aligned concordantly exactly 1 time 3032352 (35.66%) aligned concordantly >1 times 55.51% overall alignment rate 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 3781664 (44.47%) aligned concordantly 0 times 1686484 (19.83%) aligned concordantly exactly 1 time 3035323 (35.70%) aligned concordantly >1 times 55.53% overall alignment rate 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 8475911 (99.68%) aligned concordantly 0 times 10021 (0.12%) aligned concordantly exactly 1 time 17539 (0.21%) aligned concordantly >1 times 0.32% overall alignment rate 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 8476868 (99.69%) aligned concordantly 0 times 9821 (0.12%) aligned concordantly exactly 1 time 16782 (0.20%) aligned concordantly >1 times 0.31% overall alignment rate Processed 8503471 sequences in total Processed 8000000 sequence pairs so far Successfully deleted the temporary files 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8503471 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222047058 Total methylated C's in CpG context: 3105279 Total methylated C's in CHG context: 223420 Total methylated C's in CHH context: 969279 Total methylated C's in Unknown context: 6537 Total unmethylated C's in CpG context: 33235784 Total unmethylated C's in CHG context: 38252978 Total unmethylated C's in CHH context: 146260318 Total unmethylated C's in Unknown context: 308485 C methylated in CpG context: 8.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.1% Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2488:46433:20309_1:N:0:CAAGGTAC+GAGATACG ptg000094l 2 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 8476722 (99.69%) aligned concordantly 0 times 9786 (0.12%) aligned concordantly exactly 1 time 16964 (0.20%) aligned concordantly >1 times 0.31% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 3776304 (44.41%) aligned concordantly 0 times 1687453 (19.84%) aligned concordantly exactly 1 time 3039715 (35.75%) aligned concordantly >1 times 55.59% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 8475551 (99.67%) aligned concordantly 0 times 10211 (0.12%) aligned concordantly exactly 1 time 17710 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 3781575 (44.47%) aligned concordantly 0 times 1686599 (19.83%) aligned concordantly exactly 1 time 3035298 (35.69%) aligned concordantly >1 times 55.53% overall alignment rate Processed 8503472 sequences in total Successfully deleted the temporary files 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8503472 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222166805 Total methylated C's in CpG context: 3113399 Total methylated C's in CHG context: 224615 Total methylated C's in CHH context: 966420 Total methylated C's in Unknown context: 6523 Total unmethylated C's in CpG context: 33239260 Total unmethylated C's in CHG context: 38282700 Total unmethylated C's in CHH context: 146340411 Total unmethylated C's in Unknown context: 306810 C methylated in CpG context: 8.6% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.1% Processed 8000000 sequence pairs so far 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 3777029 (44.42%) aligned concordantly 0 times 1686481 (19.83%) aligned concordantly exactly 1 time 3039962 (35.75%) aligned concordantly >1 times 55.58% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 3781286 (44.47%) aligned concordantly 0 times 1687070 (19.84%) aligned concordantly exactly 1 time 3035116 (35.69%) aligned concordantly >1 times 55.53% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 8475546 (99.67%) aligned concordantly 0 times 10033 (0.12%) aligned concordantly exactly 1 time 17893 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 8476375 (99.68%) aligned concordantly 0 times 10131 (0.12%) aligned concordantly exactly 1 time 16966 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate Processed 8503472 sequences in total Successfully deleted the temporary files 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8503472 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222091319 Total methylated C's in CpG context: 3102688 Total methylated C's in CHG context: 224027 Total methylated C's in CHH context: 974291 Total methylated C's in Unknown context: 6738 Total unmethylated C's in CpG context: 33232483 Total unmethylated C's in CHG context: 38256610 Total unmethylated C's in CHH context: 146301220 Total unmethylated C's in Unknown context: 306708 C methylated in CpG context: 8.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.1% Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2431:43432:18669_1:N:0:CAAGGTAC+GAGATACG ntLink_1 163090 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 3775609 (44.40%) aligned concordantly 0 times 1686456 (19.83%) aligned concordantly exactly 1 time 3041407 (35.77%) aligned concordantly >1 times 55.60% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 8475462 (99.67%) aligned concordantly 0 times 10157 (0.12%) aligned concordantly exactly 1 time 17853 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 3779417 (44.45%) aligned concordantly 0 times 1686258 (19.83%) aligned concordantly exactly 1 time 3037797 (35.72%) aligned concordantly >1 times 55.55% overall alignment rate 8503472 reads; of these: 8503472 (100.00%) were paired; of these: 8476499 (99.68%) aligned concordantly 0 times 9818 (0.12%) aligned concordantly exactly 1 time 17155 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate Processed 8503472 sequences in total Successfully deleted the temporary files 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8503472 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222078452 Total methylated C's in CpG context: 3102328 Total methylated C's in CHG context: 222738 Total methylated C's in CHH context: 963006 Total methylated C's in Unknown context: 6438 Total unmethylated C's in CpG context: 33221113 Total unmethylated C's in CHG context: 38252638 Total unmethylated C's in CHH context: 146316629 Total unmethylated C's in Unknown context: 306076 C methylated in CpG context: 8.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.1% 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 8475579 (99.67%) aligned concordantly 0 times 10083 (0.12%) aligned concordantly exactly 1 time 17809 (0.21%) aligned concordantly >1 times 0.33% overall alignment rate 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 3782297 (44.48%) aligned concordantly 0 times 1685190 (19.82%) aligned concordantly exactly 1 time 3035984 (35.70%) aligned concordantly >1 times 55.52% overall alignment rate 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 8476559 (99.68%) aligned concordantly 0 times 9999 (0.12%) aligned concordantly exactly 1 time 16913 (0.20%) aligned concordantly >1 times 0.32% overall alignment rate 8503471 reads; of these: 8503471 (100.00%) were paired; of these: 3775791 (44.40%) aligned concordantly 0 times 1687685 (19.85%) aligned concordantly exactly 1 time 3039995 (35.75%) aligned concordantly >1 times 55.60% overall alignment rate Processed 8503471 sequences in total Successfully deleted the temporary files 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 2C2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8503471 Final Cytosine Methylation Report ================================= Total number of C's analysed: 222155453 Total methylated C's in CpG context: 3105432 Total methylated C's in CHG context: 224680 Total methylated C's in CHH context: 972573 Total methylated C's in Unknown context: 6569 Total unmethylated C's in CpG context: 33237266 Total unmethylated C's in CHG context: 38272963 Total unmethylated C's in CHH context: 146342539 Total unmethylated C's in Unknown context: 307607 C methylated in CpG context: 8.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.1% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 2C2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 2C2_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 2C2_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/2C2_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 2C2_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/2C2_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 2C2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 2C2_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: 42517358 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1110539087 Total methylated C's in CpG context: 15529126 Total methylated C's in CHG context: 1119480 Total methylated C's in CHH context: 4845569 Total methylated C's in Unknown context: 32805 Total unmethylated C's in CpG context: 166165906 Total unmethylated C's in CHG context: 191317889 Total unmethylated C's in CHH context: 731561117 Total unmethylated C's in Unknown context: 1535686 C methylated in CpG context: 8.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.1% Deleting temporary report files... Bismark completed in 0d 5h 39m 25s ==================== Bismark run complete ====================