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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_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/1B5_R1_001.fastp-trim.fq.gz for PID: 71942 and offset 5 (sequences written out: 8193745) Using the subset file >1B5_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/1B5_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/1B5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8193746) Using the subset file >1B5_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/1B5_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/1B5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8193746) Using the subset file >1B5_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/1B5_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/1B5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8193745) Using the subset file >1B5_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/1B5_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/1B5_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8193745) Using the subset file >1B5_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/1B5_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/1B5_R2_001.fastp-trim.fq.gz for PID: 71942 and offset 5 (sequences written out: 8193745) Using the subset file >1B5_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/1B5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz to 1B5_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/1B5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8193746) Using the subset file >1B5_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/1B5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz to 1B5_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/1B5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8193745) Using the subset file >1B5_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/1B5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz to 1B5_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/1B5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8193745) Using the subset file >1B5_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/1B5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz to 1B5_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/1B5_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8193746) Using the subset file >1B5_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/1B5_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz to 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz (8193745 sequences in total) Writing a C -> T converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz to 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz (8193745 sequences in total) Writing a C -> T converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz to 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz (8193746 sequences in total) Writing a C -> T converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz to 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz (8193745 sequences in total) Writing a C -> T converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz to 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz (8193746 sequences in total) Writing a C -> T converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz to 1B5_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 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz (8193745 sequences in total) Input files are 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B5_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 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz (8193746 sequences in total) Input files are 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B5_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 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz (8193745 sequences in total) Input files are 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B5_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 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz (8193746 sequences in total) Input files are 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B5_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 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz (8193745 sequences in total) Input files are 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B5_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 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49974:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AGTTATTGTTTGGAATTAAGTATGATAGTTGATAATGTGAAAGAAAATTTGGAAAATTTTTTTATTATTTTTTTAAAATTATTTTTTTTTTTTATTGTATATAAAATAAATTATAGTTGTTTTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49974:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 AATTTAACCACTCAAACACTTCAAAAATCCTTAATTAAAAAAACTTATTTTTTTACTATAACAAATCAACAAATAAAATTTACAAAATTATTAAAAAATACTCTACACCATCTTCTTACCAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49521:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AAGGGGTTTGGTTTTTTTTTTTTTTGTGTTGATTTTTTTTAATAGAGTTGTAATAATTTTTTTAATTTGGGGAAAAAATATTAGTAATAAGTTTTATAATTTTTTTTAAATGAAAATATTGGTTT IIIIIIIIIIIIIIIIIIIIIIIII--9-I9I-9-9IIIII----9-9----9-----9-9I9-I999999999--99-9-99-9-9--99--9-9-9--999-99II99--99999-9999-99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49521:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 ATTTAATTTAATTTATATAAAATTATTATCTCCAATTAACTCCATAAAAAACTAAAATACCTATTATTATTAATAAACTTATAACCCTCAAACTAACATACATCAATATTTTCAAAATAAAAACC IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIII9II9I-III9IIIII9II9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:44512:1070_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AATGATTTATTTGTGAATAAAATTATTAATAGAGATAATTAGTGTATTAAATATTTTTAATTTTGTAAAAAATGAGTAATTTGGAGGGTAAGAGATAGGGAATTATGAAGAGTATTTATATTGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIIII9II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44512:1070_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 AAAATTACAAAATTACAACTACACATAACTATCTAAATAATACTCTAAATAAACAACATACTCCTATAATTATAACATAAAAAAAATTCAAACATTTCAATACAATAATCTAAACTCCATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:40757:1070_1:N:0:TCGGATTC+TAGTTGCG/1 99 ntLink_8_CT_converted 36472225 6 125M = 36472322 222 AATATTTTGTAATAATGTATTTATAGTAATTTTTAAAAGAGTTATGTGTATTTTAAGTAAGGTGGGAATAAAATGAGAAGATGAGGTTGTTTTTTGGGTAAGTTGTTGTTTGGGGTTATTAGTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40757:1070_2:N:0:TCGGATTC+TAGTTGCG/2 147 ntLink_8_CT_converted 36472322 6 125M = 36472225 -222 GTAAGTTGTTGTTTGGGGTTATTAGTTTAAAGGTTTGAGGAGGGAGTTGGAAATTAAGTTGTTTATAGAGAATAATTAGGTTTATTGAATTATGTAAAATATAAGTAAGGATATTAAGTATAGAT III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50233:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 ATTATATTATATAAATTTTTATAATTTGATTTTTGTTTATTATAGAGTTTTTAGTAGTTTAGTGGTTATAGTATTTGATTAGATTATGGAGGGTTGTGGGTTTTAATTTTTTTTTGGGTTTGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-IIIIII9IIIIIIIIII9III9II9-9-IIIII-I9I99-I---9- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50233:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 TAAATTTTAAATATCATATTAAATAAATTCTTAAAAAAATATAAACTCAAAAAAATCCAAACCCCAAATAAAATTTAAACCCACAACCCTCCATAATCTAATCAAATACTATAACCACTAAACTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:44512:1070_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AATAATTTATTTATAAATAAAATTATTAATAAAAATAATTAATATATTAAATATTTTTAATTTTATAAAAAACAAATAATTCAAAAAATAAAAAATAAAAAATTATAAAAAATATTTATATTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIIII9II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44512:1070_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 AAAATTATAAAATTATAATTATATATAATTATTTAAATAATATTTTAAATAAATGATATATTTTTATAATTATAATATAAAAAAAATTTAAATATTTTAATATAATAATTTAAATTTTATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50233:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 ATTATATTATATAAATTTTTATAATTTAATTTTTATTTATTATAAAATTTTTAATAATTTAATAATTATAATATTTAATTAAATTATAAAAAATCATAAATTTCAATTTTCTTTTAAATTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-IIIIII9IIIIIIIIII9III9II9-9-IIIII-I9I99-I---9- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50233:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 TAAATTTTAAATATTATATTAAATAAATTTTTAAAAAAATATAAATTTAAAAAAATTTGAATTTTAAATAAAATTTAAATTTATGATTTTTTATAATTTAATTAAATATTATAATTATTAAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49521:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AAAAAATTCAATTTTTTTTTTTTTTATATTAATCCCTTTTAATAAAATTATAACAATTTTTTTAATTTAAAAAAAAAACATTAATAACAAATCCCACAATTTTTTTCAAATAAAAACATTAATTT IIIIIIIIIIIIIIIIIIIIIIIII--9-I9I-9-9IIIII----9-9----9-----9-9I9-I999999999--99-9-99-9-9--99--9-9-9--999-99II99--99999-9999-99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49521:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 ATTTAATTTAATTTATATAAAATTATTATTTTTAATTAATTTTATAAAAAATTAAAATATTTATTATTATTAATAAATTTATAATTTTTAAATTAATATATGTTAATATTTTTAAAATAAAAATT IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIII9II9I-III9IIIII9II9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49974:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AATTATTATTTAAAATTAAATATAATAATCAATAATATAAAAAAAAATTTAAAAAATTTTTTTATTATTTTTTTAAAATTATTTTTTTTTTTTATTATATATAAAATAAATTATAATTATTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49974:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 AATTTAATTATTTAAATATTTTAAAAATTTTTAATTAAAAAAATTTATTTTTTTATTATAATAAATTAATAAATAAAATTTATGAAATTATTAAAAAATATTTTATATTATTTTTTTATTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:40757:1070_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AATATTTTATAATAATATATTTATAATAATTTTTAAAAAAATTATATATATTTTAAATAAAATAAAAATAAAATAAAAAAATAAAATTATTTTTTAAATAAATTATTATTTAAAATTATTAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40757:1070_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 ATTTATATTTAATATTTTTATTTATATTTTATATAATTTAATAAATTTAATTATTTTTTATAAATAATTTAATTTTTAATTTTTTTTTTAAATTTTTAAATTAATAATTTTAAATAATAATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49521:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AAAAAATTCAATTTTTTTTTTTTTTATATTAATCCCTTTTAATAAAATTATAACAATTTTTTTAATTTAAAAAAAAAACATTAATAACAAATCCCACAATTTTTTTCAAATAAAAACATTAATTT IIIIIIIIIIIIIIIIIIIIIIIII--9-I9I-9-9IIIII----9-9----9-----9-9I9-I999999999--99-9-99-9-9--99--9-9-9--999-99II99--99999-9999-99 YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49521:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 ATTTAATTTAATTTATATAAAATTATTATTTTTAATTAATTTTATAAAAAATTAAAATATTTATTATTATTAATAAATTTATAATTTTTAAATTAATATATGTTAATATTTTTAAAATAAAAATT IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIII9II9I-III9IIIII9II9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:40757:1070_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AATATTTTATAATAATATATTTATAATAATTTTTAAAAAAATTATATATATTTTAAATAAAATAAAAATAAAATAAAAAAATAAAATTATTTTTTAAATAAATTATTATTTAAAATTATTAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:40757:1070_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 ATTTATATTTAATATTTTTATTTATATTTTATATAATTTAATAAATTTAATTATTTTTTATAAATAATTTAATTTTTAATTTTTTTTTTAAATTTTTAAATTAATAATTTTAAATAATAATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50233:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 ATTATATTATATAAATTTTTATAATTTAATTTTTATTTATTATAAAATTTTTAATAATTTAATAATTATAATATTTAATTAAATTATAAAAAATCATAAATTTCAATTTTCTTTTAAATTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-IIIIII9IIIIIIIIII9III9II9-9-IIIII-I9I99-I---9- YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50233:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 TAAATTTTAAATATTATATTAAATAAATTTTTAAAAAAATATAAATTTAAAAAAATTTGAATTTTAAATAAAATTTAAATTTATGATTTTTTATAATTTAATTAAATATTATAATTATTAAATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:44512:1070_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AATAATTTATTTATAAATAAAATTATTAATAAAAATAATTAATATATTAAATATTTTTAATTTTATAAAAAACAAATAATTCAAAAAATAAAAAATAAAAAATTATAAAAAATATTTATATTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIIII9II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:44512:1070_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 AAAATTATAAAATTATAATTATATATAATTATTTAAATAATATTTTAAATAAATGATATATTTTTATAATTATAATATAAAAAAAATTTAAATATTTTAATATAATAATTTAAATTTTATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49974:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AATTATTATTTAAAATTAAATATAATAATCAATAATATAAAAAAAAATTTAAAAAATTTTTTTATTATTTTTTTAAAATTATTTTTTTTTTTTATTATATATAAAATAAATTATAATTATTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49974:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 AATTTAATTATTTAAATATTTTAAAAATTTTTAATTAAAAAAATTTATTTTTTTATTATAATAAATTAATAAATAAAATTTATGAAATTATTAAAAAATATTTTATATTATTTTTTTATTAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50233:1056_1:N:0:TCGGATTC+TAGTTGCG/1 83 ptg000008l_GA_converted 3357396 42 125M = 3357342 -179 ATCCAAACCCAAAAAAAAATTAAAACCCACAACCCTCCATAATCTAATCAAATACTATAACCACTAAACTACTAAAAACTCTATAATAAACAAAAATCAAATTATAAAAATTTATATAATATAAT -9---I-99I9I-IIIII-9-9II9III9IIIIIIIIII9IIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:10C3T6T103 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50233:1056_2:N:0:TCGGATTC+TAGTTGCG/2 163 ptg000008l_GA_converted 3357342 42 125M = 3357396 179 TAAATTTTAAATATCATATTAAATAAATTCTTAAAAAAATATAAACTCAAAAAAATCCAAACCCCAAATAAAATTTAAACCCACAACCCTCCATAATCTAATCAAATACTATAACCACTAAACTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-18 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:49521:1056_1:N:0:TCGGATTC+TAGTTGCG/1 83 ptg000027l_GA_converted 3715831 23 100M1I24M = 3715503 -452 AAACCAATATTTTCATTTAAAAAAAATTATAAAACTTATTACTAATATTTTTTCCCCAAATTAAAAAAATTATTACAACTCTATTAAAAAAAATCAACACAAAAAAAAAAAAAACCAAACCCCTT 99-9999-99999--99II99-999--9-9-9--99--9-9-99-9-99--999999999I-9I9-9-----9----9-9----IIIII9-9-I9I-9--IIIIIIIIIIIIIIIIIIIIIIIII AS:i:-62 XN:i:0 XM:i:9 XO:i:1 XG:i:1 NM:i:10 MD:Z:7C10T7C3T1T32C3C19T1T32 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49521:1056_2:N:0:TCGGATTC+TAGTTGCG/2 163 ptg000027l_GA_converted 3715503 23 125M = 3715831 452 ATTTAATTTAATTTATATAAAATTATTATCTCCAATTAACTCCATAAAAAACTAAAATACCTATTATTATTAATAAACTTATAACCCTCAAACTAACATACATCAATATTTTCAAAATAAAAACC IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIII9II9I-III9IIIII9II9I AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-62 YT:Z:CP >>> Writing bisulfite mapping results to 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:49974:1056_1:N:0:TCGGATTC+TAGTTGCG/1 77 * 0 0 * * 0 0 AGTTATTGTTTGGAATTAAGTATGATAGTTGATAATGTGAAAGAAAATTTGGAAAATTTTTTTATTATTTTTTTAAAATTATTTTTTTTTTTTATTGTATATAAAATAAATTATAGTTGTTTTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49974:1056_2:N:0:TCGGATTC+TAGTTGCG/2 141 * 0 0 * * 0 0 AATTTAACCACTCAAACACTTCAAAAATCCTTAATTAAAAAAACTTATTTTTTTACTATAACAAATCAACAAATAAAATTTACAAAATTATTAAAAAATACTCTACACCATCTTCTTACCAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:40757:1070_1:N:0:TCGGATTC+TAGTTGCG/1 83 ptg000008l_GA_converted 17759282 1 125M = 17759185 -222 AAACTAATAACCCCAAACAACAACTTACCCAAAAAACAACCTCATCTTCTCATTTTATTCCCACCTTACTTAAAATACACATAACTCTTTTAAAAATTACTATAAATACATTATTACAAAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:12T44A2T64 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:40757:1070_2:N:0:TCGGATTC+TAGTTGCG/2 163 ptg000008l_GA_converted 17759185 1 125M = 17759282 222 ATCTATACTTAATATCCTTACTTATATTTTACATAATTCAATAAACCTAATTATTCTCTATAAACAACTTAATTTCCAACTCCCTCCTCAAACCTTTAAACTAATAACCCCAAACAACAACTTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III AS:i:-24 XS:i:-12 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:38A11C6T51T15 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:44512:1070_1:N:0:TCGGATTC+TAGTTGCG/1 83 ptg000011l_GA_converted 12573989 42 125M = 12573860 -254 AACAATATAAATACTCTTCATAATTCCCTATCTCTTACCCTCCAAATTACTCATTTTTTACAAAATTAAAAATATTTAATACACTAATTATCTCTATTAATAATTTTATTCACAAATAAATCATT II9IIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:44512:1070_2:N:0:TCGGATTC+TAGTTGCG/2 163 ptg000011l_GA_converted 12573860 42 125M = 12573989 254 AAAATTACAAAATTACAACTACACATAACTATCTAAATAATACTCTAAATAAACAACATACTCCTATAATTATAACATAAAAAAAATTCAAACATTTCAATACAATAATCTAAACTCCATTTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1313:44043:3928_1:N:0:TCGGATTC+TAGTTGCG ptg000045l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1313:44051:3942_1:N:0:TCGGATTC+TAGTTGCG ptg000045l 1 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1393:18649:21633_1:N:0:TCGGATTC+TAGTTGCG ptg000025l 21443080 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1468:42238:11534_1:N:0:TCGGATTC+TAGTTGCG ptg000025l 21443080 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2277:40798:2345_1:N:0:TCGGATTC+TAGTTGCG ptg000033l 2625622 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2468:17209:16002_1:N:0:TCGGATTC+TAGTTGCG ptg000159l 21840 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1120:40102:14279_1:N:0:TCGGATTC+TAGTTGCG ptg000025l 21443080 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1333:6333:23314_1:N:0:TCGGATTC+TAGTTGCG ptg000007l 12295855 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2283:2877:8956_1:N:0:TCGGATTC+TAGTTGCG ptg000027l 16268248 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2242:42893:6169_1:N:0:TCGGATTC+TAGTTGCG ptg000007l 12295855 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2132:21878:8676_1:N:0:TCGGATTC+TAGTTGCG ptg000083l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2155:47919:26074_1:N:0:TCGGATTC+TAGTTGCG ptg000033l 2625597 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 7000000 sequence pairs so far 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 8173088 (99.75%) aligned concordantly 0 times 8513 (0.10%) aligned concordantly exactly 1 time 12145 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 3766419 (45.97%) aligned concordantly 0 times 1777228 (21.69%) aligned concordantly exactly 1 time 2650099 (32.34%) aligned concordantly >1 times 54.03% overall alignment rate 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 8171533 (99.73%) aligned concordantly 0 times 8530 (0.10%) aligned concordantly exactly 1 time 13683 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 3769301 (46.00%) aligned concordantly 0 times 1777939 (21.70%) aligned concordantly exactly 1 time 2646506 (32.30%) aligned concordantly >1 times 54.00% overall alignment rate Processed 8193746 sequences in total Successfully deleted the temporary files 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8193746 Final Cytosine Methylation Report ================================= Total number of C's analysed: 230599675 Total methylated C's in CpG context: 4590947 Total methylated C's in CHG context: 256867 Total methylated C's in CHH context: 1097013 Total methylated C's in Unknown context: 7464 Total unmethylated C's in CpG context: 30737977 Total unmethylated C's in CHG context: 38795990 Total unmethylated C's in CHH context: 155120881 Total unmethylated C's in Unknown context: 336787 C methylated in CpG context: 13.0% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2484:48509:17067_1:N:0:TCGGATTC+TAGTTGCG ptg000025l 21443080 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 3769579 (46.01%) aligned concordantly 0 times 1777888 (21.70%) aligned concordantly exactly 1 time 2646279 (32.30%) aligned concordantly >1 times 53.99% overall alignment rate 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 8171318 (99.73%) aligned concordantly 0 times 8471 (0.10%) aligned concordantly exactly 1 time 13957 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 3765056 (45.95%) aligned concordantly 0 times 1777267 (21.69%) aligned concordantly exactly 1 time 2651423 (32.36%) aligned concordantly >1 times 54.05% overall alignment rate 8193746 reads; of these: 8193746 (100.00%) were paired; of these: 8172657 (99.74%) aligned concordantly 0 times 8611 (0.11%) aligned concordantly exactly 1 time 12478 (0.15%) aligned concordantly >1 times 0.26% overall alignment rate Processed 8193746 sequences in total Successfully deleted the temporary files 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8193746 Final Cytosine Methylation Report ================================= Total number of C's analysed: 230597105 Total methylated C's in CpG context: 4592227 Total methylated C's in CHG context: 255839 Total methylated C's in CHH context: 1102618 Total methylated C's in Unknown context: 7819 Total unmethylated C's in CpG context: 30732598 Total unmethylated C's in CHG context: 38782034 Total unmethylated C's in CHH context: 155131789 Total unmethylated C's in Unknown context: 336750 C methylated in CpG context: 13.0% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.3% Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 3763572 (45.93%) aligned concordantly 0 times 1778374 (21.70%) aligned concordantly exactly 1 time 2651799 (32.36%) aligned concordantly >1 times 54.07% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 8171365 (99.73%) aligned concordantly 0 times 8504 (0.10%) aligned concordantly exactly 1 time 13876 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 8172777 (99.74%) aligned concordantly 0 times 8555 (0.10%) aligned concordantly exactly 1 time 12413 (0.15%) aligned concordantly >1 times 0.26% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 3769974 (46.01%) aligned concordantly 0 times 1775323 (21.67%) aligned concordantly exactly 1 time 2648448 (32.32%) aligned concordantly >1 times 53.99% overall alignment rate Processed 8193745 sequences in total Successfully deleted the temporary files 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8193745 Final Cytosine Methylation Report ================================= Total number of C's analysed: 230652073 Total methylated C's in CpG context: 4593506 Total methylated C's in CHG context: 255339 Total methylated C's in CHH context: 1100523 Total methylated C's in Unknown context: 7692 Total unmethylated C's in CpG context: 30765507 Total unmethylated C's in CHG context: 38809621 Total unmethylated C's in CHH context: 155127577 Total unmethylated C's in Unknown context: 337209 C methylated in CpG context: 13.0% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 8171370 (99.73%) aligned concordantly 0 times 8554 (0.10%) aligned concordantly exactly 1 time 13821 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 8172710 (99.74%) aligned concordantly 0 times 8704 (0.11%) aligned concordantly exactly 1 time 12331 (0.15%) aligned concordantly >1 times 0.26% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 3770370 (46.02%) aligned concordantly 0 times 1777286 (21.69%) aligned concordantly exactly 1 time 2646089 (32.29%) aligned concordantly >1 times 53.98% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 3767211 (45.98%) aligned concordantly 0 times 1776681 (21.68%) aligned concordantly exactly 1 time 2649853 (32.34%) aligned concordantly >1 times 54.02% overall alignment rate Processed 8193745 sequences in total Successfully deleted the temporary files 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8193745 Final Cytosine Methylation Report ================================= Total number of C's analysed: 230570114 Total methylated C's in CpG context: 4589551 Total methylated C's in CHG context: 257476 Total methylated C's in CHH context: 1098776 Total methylated C's in Unknown context: 7573 Total unmethylated C's in CpG context: 30733626 Total unmethylated C's in CHG context: 38796915 Total unmethylated C's in CHH context: 155093770 Total unmethylated C's in Unknown context: 336532 C methylated in CpG context: 13.0% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Processed 8000000 sequence pairs so far 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 8172762 (99.74%) aligned concordantly 0 times 8587 (0.10%) aligned concordantly exactly 1 time 12396 (0.15%) aligned concordantly >1 times 0.26% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 3764937 (45.95%) aligned concordantly 0 times 1778333 (21.70%) aligned concordantly exactly 1 time 2650475 (32.35%) aligned concordantly >1 times 54.05% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 8171578 (99.73%) aligned concordantly 0 times 8411 (0.10%) aligned concordantly exactly 1 time 13756 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8193745 reads; of these: 8193745 (100.00%) were paired; of these: 3771298 (46.03%) aligned concordantly 0 times 1776723 (21.68%) aligned concordantly exactly 1 time 2645724 (32.29%) aligned concordantly >1 times 53.97% overall alignment rate Processed 8193745 sequences in total Successfully deleted the temporary files 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1B5_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8193745 Final Cytosine Methylation Report ================================= Total number of C's analysed: 230613384 Total methylated C's in CpG context: 4588939 Total methylated C's in CHG context: 255546 Total methylated C's in CHH context: 1095622 Total methylated C's in Unknown context: 7457 Total unmethylated C's in CpG context: 30751000 Total unmethylated C's in CHG context: 38801327 Total unmethylated C's in CHH context: 155120950 Total unmethylated C's in Unknown context: 335594 C methylated in CpG context: 13.0% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1B5_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1B5_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1B5_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/1B5_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1B5_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/1B5_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B5_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1B5_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: 40968727 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1153032351 Total methylated C's in CpG context: 22955170 Total methylated C's in CHG context: 1281067 Total methylated C's in CHH context: 5494552 Total methylated C's in Unknown context: 38005 Total unmethylated C's in CpG context: 153720708 Total unmethylated C's in CHG context: 193985887 Total unmethylated C's in CHH context: 775594967 Total unmethylated C's in Unknown context: 1682872 C methylated in CpG context: 13.0% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Deleting temporary report files... Bismark completed in 0d 6h 56m 59s ==================== Bismark run complete ====================