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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_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/1D7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_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/1D7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_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/1D7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_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/1D7_R1_001.fastp-trim.fq.gz for PID: 70131 and offset 5 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_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/1D7_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_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/1D7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz to 1D7_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/1D7_R2_001.fastp-trim.fq.gz for PID: 70131 and offset 5 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz to 1D7_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/1D7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz to 1D7_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/1D7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz to 1D7_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/1D7_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7345043) Using the subset file >1D7_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/1D7_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz to 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz (7345043 sequences in total) Writing a C -> T converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz to 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz (7345043 sequences in total) Writing a C -> T converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz to 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz (7345043 sequences in total) Writing a C -> T converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz to 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz (7345043 sequences in total) Writing a C -> T converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz to 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz (7345043 sequences in total) Writing a C -> T converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz to 1D7_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 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz (7345043 sequences in total) Input files are 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D7_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 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz (7345043 sequences in total) Input files are 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D7_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 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz (7345043 sequences in total) Input files are 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D7_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 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz (7345043 sequences in total) Input files are 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D7_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 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz (7345043 sequences in total) Input files are 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D7_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 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:30164:1084_1:N:0:AGGAACAC+GACATTCC/1 99 ptg000022l_CT_converted 3298015 1 125M = 3298140 250 TTAAAATTGAGTTTAGAGTTTATGTTAATTTTTAAAAGATTAATATTATTGTATTTTTGTATTTGTTGTTTATTGATATTGAAAGAAAAGTTTTGTTTAGTATTATTTAATATTAATGTTTGAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:116A8 YS:i:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:30164:1084_2:N:0:AGGAACAC+GACATTCC/2 147 ptg000022l_CT_converted 3298140 1 125M = 3298015 -250 TTTGTTGGGATTAGTTATTAGGTTATTTATTTTGAATTATTGTGATATTTTTTTTAATTTGTGGTTTAATTTTGTTTATAGGGTTTTATGATTATTATTTGTGTTATATAATTGTTGATTATTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:6T39G28A49 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:34826:1084_1:N:0:AGGAACAC+GACATTCC/1 99 ptg000035l_CT_converted 1366795 1 125M = 1366981 311 TAAGGTTGGGTGGGTTTTTGTTTGTTTGAAAGTAATAGAGTGTTTTTGTGTGATGTTATGGTGGTTATTTTGGTGTTTTTAAATAAAGGAATGGTGGTTATGTTGGTGTTTTTAATTAATTTTTT IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII9IIIIIIIIIIIII99I99III9IIIIIIIIII99IIIII-IIIIII-IIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:34826:1084_2:N:0:AGGAACAC+GACATTCC/2 147 ptg000035l_CT_converted 1366981 1 125M = 1366795 -311 AAATATTTTATTTGTAGGTTATTTTGTTTTAATGGATTTATATTAAGTTTTATTATTGTGTTTTTAATATAGATAAAGTTTATTTTTAAAATTAATAGATTAGAATGATTATTATTTATTGATTT IIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIII 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 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:29436:1084_1:N:0:AGGAACAC+GACATTCC/1 99 ntLink_6_CT_converted 21874519 1 125M = 21874556 162 AAAAATATAATTAAAAGTTTTGTTGTTTTTTTATTTTTTTAAAAATTAGAAATGTTAAATTTATGGTTATATGTTTGTTTTAGTTTTTTGGGAAAATGGGAAAATTATGTATTTTTATTGAGTTT 9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:32G19A72 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:29436:1084_2:N:0:AGGAACAC+GACATTCC/2 147 ntLink_6_CT_converted 21874556 1 125M = 21874519 -162 TTTAAAAATTAGAAATGTTAAATTTATGGTTATATGTTTGTTTTAGTTTTTTGGGAAAATGGGAAAATTATGTATTTTTATTGAGTTTGTATTTTGTAATGGAAATTATTTTTGTTATTTTATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15A109 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:51075:1056_1:N:0:AGGAACAC+GACATTCC/1 99 ptg000031l_CT_converted 14283047 12 125M = 14283144 222 AGTAATGTTTTAAAAAATTAAAAATTAATTAATTAAAGTTTGAAATTTGATTGGAAAGTATGTAATTTATTTAAAATTGATTGAAATTAATAATAATAATTAAATTGTAAATATAGGAATAGTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIII9II9IIIIIIIIIII9III99IIIIIIIIIIIIII-IIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51075:1056_2:N:0:AGGAACAC+GACATTCC/2 147 ptg000031l_CT_converted 14283144 12 125M = 14283047 -222 AATTAAATTGTGAATATAGGAATAGTAAATTAAAGAAATATATTTTTGTTGTATTAAGGTATAAGAATGGTAGTAGTTGAGGAATTTTGTTGGTTGTTATGAATTTTTTTAATATTTGAATATTA IIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIII-9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-24 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:11A113 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:51139:1056_1:N:0:AGGAACAC+GACATTCC/1 99 ptg000001l_CT_converted 7183604 40 53M2D72M = 7183717 238 TTTTTTTTTTTTTTAATAGGATTATAAAAAGAAAATTGAATTTTATTTGGGATAAATTTAGGAGTTATAATATATATTGATTTTTTTAATAGGAAGAGAAAGAAAATGAAATTTTATTTGTGGAT IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII9IIIIII9-IIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIII-III9IIII9IIIIII9II AS:i:-29 XN:i:0 XM:i:3 XO:i:1 XG:i:2 NM:i:5 MD:Z:0A35G16^AG10A61 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51139:1056_2:N:0:AGGAACAC+GACATTCC/2 147 ptg000001l_CT_converted 7183717 40 125M = 7183604 -238 TTTTATTTGTGGATAGAAATTTAGGGTAGTTGTATAGTTATAAGTGAATAATTATTAATAATGAATATTGGGGTGTTTTATAGAGTAGTGTAGTTGTGTTATAATTTTATTGAAGGATGATATTT IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:59T65 YS:i:-29 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:29436:1084_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 AAAAATATAATTAAAAATTTTATTATTTTTTTATTTTTTTAAAAATTAAAAATATTAAATTTATAATTATATATTTATTTTAATTTTTTAAAAAAATAAAAAAATTATATATTTTTATTAAATTT 9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29436:1084_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 TAATAAAATAATAAAAATAATTTTTATTATAAAATATAAATTTAATAAAAATATATAATTTTTTTATTTTTTTAAAAAATTAAAATAAATATATAATTATAAATTTAATATTTTTAATTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:30164:1084_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 TTAAAATTAAATTTAAAATTTATATTAATTTTTAAAAAATTAATATTATTATATTTTTATATTTATTATTTATTAATATTAAAAAAAAAATTTTATTTAATATTATTTAATATTAATATTTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30164:1084_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 TTAATAATTAATAATTATATAATATAAATAATAATTATAAAATTTTATAAATAAAATTAAATTATAAATTAAAAAAAATATTATAATAATTTAAAATAAATAATTTAATAATTAATTTTAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:51075:1056_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 AATAATATTTTAAAAAATTAAAAATTAATTAATTAAAATTTAAAATTCAATTAAAAAATATATAATTTATTTAAAATCAATTAAAATCAATAATAATAATCAAATTATAAATATAAAAATAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIII9II9IIIIIIIIIII9III99IIIIIIIIIIIIII-IIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51075:1056_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 TAATATTTAAATATTAAAAAAATTTATAATAATTAATAAAATTTTTTAATTATTATTATTTTTATATTTTAATATAATAAAAATATATTTTTTTAATTTATTATTTTTATATTTATAATTTAATT IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:34826:1084_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 TAAAATTAAATAAATTTTTATTTATTTAAAAATAATAAAATATTTTTATATAATATTATAATAATTATTTTAATATTTTTAAATAAAAAAATAATAATTATATTAATATTTTTAATTAATTTTTT IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII9IIIIIIIIIIIII99I99III9IIIIIIIIII99IIIII-IIIIII-IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:34826:1084_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 AAATTAATAAATAATAATTATTTTAATTTATTAATTTTAAAAATAAATTTTATTTATATTAAAAATATAATAATAAAATTTAATATAAATTTATTAAAATAAAATAATTTATAAATAAAATATTT IIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:30164:1084_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 TTAAAATTAAATTTAAAATTTATATTAATTTTTAAAAAATTAATATTATTATATTTTTATATTTATTATTTATTAATATTAAAAAAAAAATTTTATTTAATATTATTTAATATTAATATTTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:30164:1084_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 TTAATAATTAATAATTATATAATATAAATAATAATTATAAAATTTTATAAATAAAATTAAATTATAAATTAAAAAAAATATTATAATAATTTAAAATAAATAATTTAATAATTAATTTTAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:34826:1084_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 TAAAATTAAATAAATTTTTATTTATTTAAAAATAATAAAATATTTTTATATAATATTATAATAATTATTTTAATATTTTTAAATAAAAAAATAATAATTATATTAATATTTTTAATTAATTTTTT IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII9IIIIIIIIIIIII99I99III9IIIIIIIIII99IIIII-IIIIII-IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:34826:1084_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 AAATTAATAAATAATAATTATTTTAATTTATTAATTTTAAAAATAAATTTTATTTATATTAAAAATATAATAATAAAATTTAATATAAATTTATTAAAATAAAATAATTTATAAATAAAATATTT IIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:51075:1056_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 AATAATATTTTAAAAAATTAAAAATTAATTAATTAAAATTTAAAATTCAATTAAAAAATATATAATTTATTTAAAATCAATTAAAATCAATAATAATAATCAAATTATAAATATAAAAATAATAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIII9II9IIIIIIIIIII9III99IIIIIIIIIIIIII-IIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51075:1056_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 TAATATTTAAATATTAAAAAAATTTATAATAATTAATAAAATTTTTTAATTATTATTATTTTTATATTTTAATATAATAAAAATATATTTTTTTAATTTATTATTTTTATATTTATAATTTAATT IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:51139:1056_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 TTTTTTTTTTTTTTAATAAAATTATAAAAAAAAAATTAAATTTTATTTAAAATAAATTTAAAAATTATAATATATATTAATTTTTTTAATAAAAAAAAAAAAAAAATAAAATTTTATTTATAAAT IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII9IIIIII9-IIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIII-III9IIII9IIIIII9II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51139:1056_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 AAATATTATTTTTTAATAAAATTATAATATAATTATATTATTTTATAAAATATTTTAATATTTATTATTAATAATTATTTATTTATAATTATATAATTATTTTAAATTTTTATTTATAAATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:29436:1084_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 AAAAATATAATTAAAAATTTTATTATTTTTTTATTTTTTTAAAAATTAAAAATATTAAATTTATAATTATATATTTATTTTAATTTTTTAAAAAAATAAAAAAATTATATATTTTTATTAAATTT 9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:29436:1084_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 TAATAAAATAATAAAAATAATTTTTATTATAAAATATAAATTTAATAAAAATATATAATTTTTTTATTTTTTTAAAAAATTAAAATAAATATATAATTATAAATTTAATATTTTTAATTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:30164:1084_1:N:0:AGGAACAC+GACATTCC/1 83 ntLink_6_GA_converted 11844435 11 125M = 11844310 -250 TTTCAAACATTAATATTAAATAATACTAAACAAAACTTTTCTTTCAATATCAATAAACAACAAATACAAAAATACAATAATATTAATCTTTTAAAAATTAACATAAACTCTAAACTCAATTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-29 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:30164:1084_2:N:0:AGGAACAC+GACATTCC/2 163 ntLink_6_GA_converted 11844310 11 125M = 11844435 250 CCAATAATCAACAATTATATAACACAAATAATAATCATAAAACCCTATAAACAAAATTAAACCACAAATTAAAAAAAATATCACAATAATTCAAAATAAATAACCTAATAACTAATCCCAACAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-30 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:1T39T7T28C46 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:51139:1056_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 TTTTTTTTTTTTTTAATAAAATTATAAAAAAAAAATTAAATTTTATTTAAAATAAATTTAAAAATTATAATATATATTAATTTTTTTAATAAAAAAAAAAAAAAAATAAAATTTTATTTATAAAT IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII9IIIIII9-IIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIII-III9IIII9IIIIII9II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51139:1056_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 AAATATTATTTTTTAATAAAATTATAATATAATTATATTATTTTATAAAATATTTTAATATTTATTATTAATAATTATTTATTTATAATTATATAATTATTTTAAATTTTTATTTATAAATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D7_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: LH00526:197:22KFKVLT4:3:1101:34826:1084_1:N:0:AGGAACAC+GACATTCC/1 83 ptg000011l_GA_converted 632467 0 125M = 632288 -304 AAAAAATTAATTAAAAACACCAACATAACCACCATTCCTTTATTTAAAAACACCAAAATAACCACCATAACATCACACAAAAACACTCTATTACTTTCAAACAAACAAAAACCCACCCAACCTTA IIIIIIIIIII-IIIIII-IIIII99IIIIIIIIII9III99I99IIIIIIIIIIIII9IIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII AS:i:-42 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:4C51C5T33C0A22A0T3 YS:i:-68 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:34826:1084_2:N:0:AGGAACAC+GACATTCC/2 163 ptg000011l_GA_converted 632288 0 55M7I63M = 632467 304 AAATCAATAAATAATAATCATTCTAATCTATTAATTTTAAAAATAAACTTTATCTATATTAAAAACACAATAATAAAACTTAATATAAATCCATTAAAACAAAATAACCTACAAATAAAATATTT IIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIII AS:i:-68 XN:i:0 XM:i:7 XO:i:1 XG:i:7 NM:i:14 MD:Z:18A4A36A3T0C13C3A34 YS:i:-42 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:51075:1056_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 AGTAATGTTTTAAAAAATTAAAAATTAATTAATTAAAGTTTGAAATTTGATTGGAAAGTATGTAATTTATTTAAAATTGATTGAAATTAATAATAATAATTAAATTGTAAATATAGGAATAGTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIII9II9IIIIIIIIIII9III99IIIIIIIIIIIIII-IIII9IIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51075:1056_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 TAATATTCAAATATTAAAAAAATTCATAACAACCAACAAAATTCCTCAACTACTACCATTCTTATACCTTAATACAACAAAAATATATTTCTTTAATTTACTATTCCTATATTCACAATTTAATT IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9-IIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:29436:1084_1:N:0:AGGAACAC+GACATTCC/1 83 ptg000036l_GA_converted 4211843 6 125M = 4211806 -162 AAACTCAATAAAAATACATAATTTTCCCATTTTCCCAAAAAACTAAAACAAACATATAACCATAAATTTAACATTTCTAATTTTTAAAAAAATAAAAAAACAACAAAACTTTTAATTATATTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9 AS:i:-12 XS:i:-18 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:72T19C32 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:29436:1084_2:N:0:AGGAACAC+GACATTCC/2 163 ptg000036l_GA_converted 4211806 6 125M = 4211843 162 CAATAAAATAACAAAAATAATTTCCATTACAAAATACAAACTCAATAAAAATACATAATTTTCCCATTTTCCCAAAAAACTAAAACAAACATATAACCATAAATTTAACATTTCTAATTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:109T15 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:51139:1056_1:N:0:AGGAACAC+GACATTCC/1 77 * 0 0 * * 0 0 TTTTTTTTTTTTTTAATAGGATTATAAAAAGAAAATTGAATTTTATTTGGGATAAATTTAGGAGTTATAATATATATTGATTTTTTTAATAGGAAGAGAAAGAAAATGAAATTTTATTTGTGGAT IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9IIIIII9IIIIII9-IIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIII-III9IIII9IIIIII9II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51139:1056_2:N:0:AGGAACAC+GACATTCC/2 141 * 0 0 * * 0 0 AAATATCATCCTTCAATAAAATTATAACACAACTACACTACTCTATAAAACACCCCAATATTCATTATTAATAATTATTCACTTATAACTATACAACTACCCTAAATTTCTATCCACAAATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1230:50185:8340_1:N:0:AGGAACAC+GACATTCC ptg000007l 12295855 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 LH00526:197:22KFKVLT4:3:1305:26482:9643_1:N:0:AGGAACAC+GACATTCC ptg000065l 49673 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2125:47360:1854_1:N:0:AGGAACAC+GACATTCC ptg000047l 1 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 LH00526:197:22KFKVLT4:3:2358:28327:28833_1:N:0:AGGAACAC+GACATTCC ptg000133l 37098 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2358:28344:28833_1:N:0:AGGAACAC+GACATTCC ptg000133l 37098 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2411:41283:3241_1:N:0:AGGAACAC+GACATTCC ptg000098l 55082 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2425:42392:11240_1:N:0:AGGAACAC+GACATTCC ptg000133l 37126 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2444:40328:17193_1:N:0:AGGAACAC+GACATTCC ptg000057l 39948 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1141:8105:3017_1:N:0:AGGAACAC+GACATTCC ptg000025l 21443080 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 LH00526:197:22KFKVLT4:4:1202:15299:21774_1:N:0:AGGAACAC+GACATTCC ptg000094l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1198:41906:17011_1:N:0:AGGAACAC+GACATTCC ptg000033l 2625625 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1309:30812:24029_1:N:0:AGGAACAC+GACATTCC ptg000128l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2367:28506:15162_1:N:0:AGGAACAC+GACATTCC ptg000006l 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3139011 (42.74%) aligned concordantly 0 times 1598484 (21.76%) aligned concordantly exactly 1 time 2607548 (35.50%) aligned concordantly >1 times 57.26% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7325368 (99.73%) aligned concordantly 0 times 7071 (0.10%) aligned concordantly exactly 1 time 12604 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7327087 (99.76%) aligned concordantly 0 times 6818 (0.09%) aligned concordantly exactly 1 time 11138 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3136213 (42.70%) aligned concordantly 0 times 1597175 (21.74%) aligned concordantly exactly 1 time 2611655 (35.56%) aligned concordantly >1 times 57.30% overall alignment rate Processed 7345043 sequences in total Successfully deleted the temporary files 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7345043 Final Cytosine Methylation Report ================================= Total number of C's analysed: 207350518 Total methylated C's in CpG context: 3264543 Total methylated C's in CHG context: 199487 Total methylated C's in CHH context: 879236 Total methylated C's in Unknown context: 5895 Total unmethylated C's in CpG context: 29190957 Total unmethylated C's in CHG context: 35137701 Total unmethylated C's in CHH context: 138678594 Total unmethylated C's in Unknown context: 281388 C methylated in CpG context: 10.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3136776 (42.71%) aligned concordantly 0 times 1597686 (21.75%) aligned concordantly exactly 1 time 2610581 (35.54%) aligned concordantly >1 times 57.29% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3140131 (42.75%) aligned concordantly 0 times 1598574 (21.76%) aligned concordantly exactly 1 time 2606338 (35.48%) aligned concordantly >1 times 57.25% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7325565 (99.73%) aligned concordantly 0 times 6854 (0.09%) aligned concordantly exactly 1 time 12624 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7326997 (99.75%) aligned concordantly 0 times 6828 (0.09%) aligned concordantly exactly 1 time 11218 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate Processed 7345043 sequences in total Successfully deleted the temporary files 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7345043 Final Cytosine Methylation Report ================================= Total number of C's analysed: 207410362 Total methylated C's in CpG context: 3262728 Total methylated C's in CHG context: 199669 Total methylated C's in CHH context: 876419 Total methylated C's in Unknown context: 5760 Total unmethylated C's in CpG context: 29195382 Total unmethylated C's in CHG context: 35146319 Total unmethylated C's in CHH context: 138729845 Total unmethylated C's in Unknown context: 282801 C methylated in CpG context: 10.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3136424 (42.70%) aligned concordantly 0 times 1598256 (21.76%) aligned concordantly exactly 1 time 2610363 (35.54%) aligned concordantly >1 times 57.30% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7325763 (99.74%) aligned concordantly 0 times 6863 (0.09%) aligned concordantly exactly 1 time 12417 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7327040 (99.75%) aligned concordantly 0 times 6885 (0.09%) aligned concordantly exactly 1 time 11118 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3140563 (42.76%) aligned concordantly 0 times 1598830 (21.77%) aligned concordantly exactly 1 time 2605650 (35.47%) aligned concordantly >1 times 57.24% overall alignment rate Processed 7345043 sequences in total Successfully deleted the temporary files 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7345043 Final Cytosine Methylation Report ================================= Total number of C's analysed: 207328350 Total methylated C's in CpG context: 3266598 Total methylated C's in CHG context: 200636 Total methylated C's in CHH context: 877268 Total methylated C's in Unknown context: 5918 Total unmethylated C's in CpG context: 29179990 Total unmethylated C's in CHG context: 35127826 Total unmethylated C's in CHH context: 138676032 Total unmethylated C's in Unknown context: 282702 C methylated in CpG context: 10.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.1% 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7325771 (99.74%) aligned concordantly 0 times 6875 (0.09%) aligned concordantly exactly 1 time 12397 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3135752 (42.69%) aligned concordantly 0 times 1599227 (21.77%) aligned concordantly exactly 1 time 2610064 (35.54%) aligned concordantly >1 times 57.31% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7327255 (99.76%) aligned concordantly 0 times 6821 (0.09%) aligned concordantly exactly 1 time 10967 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3140010 (42.75%) aligned concordantly 0 times 1598734 (21.77%) aligned concordantly exactly 1 time 2606299 (35.48%) aligned concordantly >1 times 57.25% overall alignment rate Processed 7345043 sequences in total Successfully deleted the temporary files 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7345043 Final Cytosine Methylation Report ================================= Total number of C's analysed: 207370153 Total methylated C's in CpG context: 3257284 Total methylated C's in CHG context: 200742 Total methylated C's in CHH context: 874267 Total methylated C's in Unknown context: 5907 Total unmethylated C's in CpG context: 29203866 Total unmethylated C's in CHG context: 35146043 Total unmethylated C's in CHH context: 138687951 Total unmethylated C's in Unknown context: 283661 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Processed 7000000 sequence pairs so far 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7325590 (99.74%) aligned concordantly 0 times 7083 (0.10%) aligned concordantly exactly 1 time 12370 (0.17%) aligned concordantly >1 times 0.26% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 7327180 (99.76%) aligned concordantly 0 times 6904 (0.09%) aligned concordantly exactly 1 time 10959 (0.15%) aligned concordantly >1 times 0.24% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3142305 (42.78%) aligned concordantly 0 times 1597385 (21.75%) aligned concordantly exactly 1 time 2605353 (35.47%) aligned concordantly >1 times 57.22% overall alignment rate 7345043 reads; of these: 7345043 (100.00%) were paired; of these: 3135580 (42.69%) aligned concordantly 0 times 1601148 (21.80%) aligned concordantly exactly 1 time 2608315 (35.51%) aligned concordantly >1 times 57.31% overall alignment rate Processed 7345043 sequences in total Successfully deleted the temporary files 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1D7_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7345043 Final Cytosine Methylation Report ================================= Total number of C's analysed: 207379317 Total methylated C's in CpG context: 3260560 Total methylated C's in CHG context: 200881 Total methylated C's in CHH context: 880532 Total methylated C's in Unknown context: 6044 Total unmethylated C's in CpG context: 29194190 Total unmethylated C's in CHG context: 35137685 Total unmethylated C's in CHH context: 138705469 Total unmethylated C's in Unknown context: 281876 C methylated in CpG context: 10.0% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% 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 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1D7_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1D7_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1D7_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/1D7_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1D7_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/1D7_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D7_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1D7_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: 36725215 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1036838700 Total methylated C's in CpG context: 16311713 Total methylated C's in CHG context: 1001415 Total methylated C's in CHH context: 4387722 Total methylated C's in Unknown context: 29524 Total unmethylated C's in CpG context: 145964385 Total unmethylated C's in CHG context: 175695574 Total unmethylated C's in CHH context: 693477891 Total unmethylated C's in Unknown context: 1412428 C methylated in CpG context: 10.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Deleting temporary report files... Bismark completed in 0d 4h 36m 44s ==================== Bismark run complete ====================