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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_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/1A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_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/1A3_R1_001.fastp-trim.fq.gz for PID: 80746 and offset 5 (sequences written out: 9409013) Using the subset file >1A3_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/1A3_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/1A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_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/1A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_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/1A3_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_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/1A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz to 1A3_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/1A3_R2_001.fastp-trim.fq.gz for PID: 80746 and offset 5 (sequences written out: 9409013) Using the subset file >1A3_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/1A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz to 1A3_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/1A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz to 1A3_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/1A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz to 1A3_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/1A3_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 9409014) Using the subset file >1A3_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/1A3_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz to 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz (9409013 sequences in total) Writing a C -> T converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz to 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz (9409014 sequences in total) Created C -> T as well as G -> A converted versions of the FastQ file 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz (9409014 sequences in total) Writing a C -> T converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a C -> T converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz to 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a G -> A converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz to 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz (9409014 sequences in total) Writing a C -> T converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz to 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz (9409014 sequences in total) Writing a C -> T converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz to 1A3_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 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz (9409014 sequences in total) Input files are 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A3_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 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz (9409014 sequences in total) Input files are 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A3_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 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz (9409014 sequences in total) Input files are 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A3_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 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz (9409013 sequences in total) Input files are 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:47393:1070_1:N:0:TTCCAGGT+AAGCACTG/1 99 ptg000008l_CT_converted 27392673 1 125M = 27392767 219 TTTTGAAGAGTTTTTTTAGTTTTTGATAATATAGAGGGTTTTGGATAGAAGAAGATTGGGGGAAGTATTTTTGTTGTTTGGTTGTTTAATGTTGTTATGAAAAAGTATAATTTTAGTTTTTTTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:47393:1070_2:N:0:TTCCAGGT+AAGCACTG/2 147 ptg000008l_CT_converted 27392767 1 125M = 27392673 -219 TTATGAAAAAGTATAATTTTAGTTTTTTTGATATTTTATGTAATGGATGATAGTAATGAATTGGTATAAGTTATTGTAGGAAATTTTATGATGTTTTTGTGTAAATATGGGGAGGTGAGTGTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII 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 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:48768:1070_1:N:0:TTCCAGGT+AAGCACTG/1 99 ptg000033l_CT_converted 2491706 2 125M = 2491899 318 AAAAAGGTGGGATTTGTTTTATTTTTAATGTGTAAATTTTTTGGGTGAGGATAGTATTTGTATGGTTAATTTGTTGGAAATATTTTAAAAGATAGTGTTTTTTTTATTATATGATTGATTTGTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIII AS:i:-66 XS:i:-62 XN:i:0 XM:i:11 XO:i:0 XG:i:0 NM:i:11 MD:Z:3T15G19G32A1A9G1G1G0T0A5T28 YS:i:-36 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:48768:1070_2:N:0:TTCCAGGT+AAGCACTG/2 147 ptg000033l_CT_converted 2491899 2 125M = 2491706 -318 TATATTTTTAGATTAATTTATGTTTAGTTGTAAATAAGAATGTTTTGTTTGATTTTTAAAGTGTTTGTTATGTATTTGATAGAGATAAGATGAGATGTTTAGGGAATATAATGTTTTAAAAAGTT IIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-36 XS:i:-48 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:6G17A26T6T20A15A29 YS:i:-66 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:39025:1070_1:N:0:TTCCAGGT+AAGCACTG/1 99 ptg000047l_CT_converted 9625691 24 37M1D88M = 9625749 179 AATTTGGTATATAGTAATAGTTTTATAATAGATTTAATTTTTTTTTTGTTTGTTTTTGTTTGTTTTTAGGGATAGTAATTAGGTTAGTAATTAGGTTAAGGTAAATTTATTTTAAGTGGTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII AS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:6A8T21^T78A9 YS:i:-29 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39025:1070_2:N:0:TTCCAGGT+AAGCACTG/2 147 ptg000047l_CT_converted 9625749 24 100M4I21M = 9625691 -179 GTTTGTTTTTAGGGATAGTAATTAGGTTAGTAATTAGGTTAAGGTAAATTTATTTTAAGTGGTTAAATTGTTGAATAGTTAAAGATGGATTTAGTAATAAAATTAATGTTTTGTTTTTTGAAGTA 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-29 XN:i:0 XM:i:2 XO:i:1 XG:i:4 NM:i:6 MD:Z:58A56A5 YS:i:-26 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:28675:1084_1:N:0:TTCCAGGT+AAGCACTG/1 99 ptg000023l_CT_converted 7072886 1 125M = 7073006 245 GAAGTTGTGATTGGTGGAATTATGTTGATGTTATTTTTTAGTGATGTAGTTTTTTTATTAATGTGTTATTAAGTAATGAAGAATTTTGTGAGTTAAATGAATATTTTAGTAATTTTTGTATTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIII9III9III9IIIIIII9I 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:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:28675:1084_2:N:0:TTCCAGGT+AAGCACTG/2 147 ptg000023l_CT_converted 7073006 1 125M = 7072886 -245 TTGATAATTTATATATAGAGTTATTAAATGTTGTTATTGATGATGATGAAGAAATATTGGAGTTTATAGAAGTGTAAGTATGGAATTGTATAATTTGTTTAAAGAATATTTTTATGGGTTTAGAT IIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIII9IIIIIIII9IIIIII-9IIII9II9-I9II9II9IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:53G42A13G14 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:47393:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 TTTTAAAAAATTTTTTTAATTTTTAACAATATAAAAAATTTTAAATAAAAAAAAATTAAAAAAAATATTTTTATTATTTAATTATTTAATATTATTATAAAAAAATATAATTTTAATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:47393:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 AATATATTTATTTTTTTATATTTATATAAAAATATTATAAAATTTTTTATAATAATTTATATTAATTTATTATTATTATTTATTATATAAAATATTAAAAAAATTAAAATTATATTTTTTTATAA IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1A3_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz (9409014 sequences in total) Found first alignment: LH00526:197:22KFKVLT4:3:1101:48768:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AAAAAAATAAAATTTATTTTATTTTTAATATATAAATTTTTTAAATAAAAATAATATTTATATAATTAATTTATTAAAAATATTTTAAAAAATAATATTTTTTTTATTATATAATTAATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48768:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 AATTTTTTAAAATATTATATTTTTTAAATATTTTATTTTATTTTTATTAAATATATAATAAATATTTTAAAAATTAAATAAAATATTTTTATTTATAATTAAATATAAATTAATTTAAAAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1A3_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)) Input files are 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A3_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 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:28675:1084_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AAAATTATAATTAATAAAATTATATTAATATTATTTTTTAATAATATAATTTTTTTATTAATATATTATTAAATAATAAAAAATTTTATAAATTAAATAAATATTTTAATAATTTTTATATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIII9III9III9IIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28675:1084_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 ATTTAAATTTATAAAAATATTTTTTAAATAAATTATATAATTTTATATTTATATTTTTATAAATTTTAATATTTTTTTATTATTATTAATAATAATATTTAATAATTTTATATATAAATTATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9II9II9I-9II9IIII9-IIIIII9IIIIIIII9IIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:39025:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AATTTAATATATAATAATAATTTTATAATAAATTTAATTTTTTTTTTATTTATTTTTATTTATTTTTAAAAATAATAATTAAATTAATAATTAAATTAAAATAAATTTATTTTAAATAATTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39025:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 TATTTTGAAAAATAAAATATTAATTTTATTATTAAATTTATTTTTAATTATTTAATGATTTAATTATTTAAAATAAATTTATTTTAATTTAATTATTAATTTAATTATTATTTTTAAAAATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:28675:1084_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AAAATTATAATTAATAAAATTATATTAATATTATTTTTTAATAATATAATTTTTTTATTAATATATTATTAAATAATAAAAAATTTTATAAATTAAATAAATATTTTAATAATTTTTATATTAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIII9III9III9IIIIIII9I YT:Z:UP LH00526:197:22KFKVLT4:3:1101:28675:1084_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 ATTTAAATTTATAAAAATATTTTTTAAATAAATTATATAATTTTATATTTATATTTTTATAAATTTTAATATTTTTTTATTATTATTAATAATAATATTTAATAATTTTATATATAAATTATTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9II9II9I-9II9IIII9-IIIIII9IIIIIIII9IIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:48768:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AAAAAAATAAAATTTATTTTATTTTTAATATATAAATTTTTTAAATAAAAATAATATTTATATAATTAATTTATTAAAAATATTTTAAAAAATAATATTTTTTTTATTATATAATTAATTTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:48768:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 AATTTTTTAAAATATTATATTTTTTAAATATTTTATTTTATTTTTATTAAATATATAATAAATATTTTAAAAATTAAATAAAATATTTTTATTTATAATTAAATATAAATTAATTTAAAAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:39025:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AATTTAATATATAATAATAATTTTATAATAAATTTAATTTTTTTTTTATTTATTTTTATTTATTTTTAAAAATAATAATTAAATTAATAATTAAATTAAAATAAATTTATTTTAAATAATTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39025:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 TATTTTGAAAAATAAAATATTAATTTTATTATTAAATTTATTTTTAATTATTTAATGATTTAATTATTTAAAATAAATTTATTTTAATTTAATTATTAATTTAATTATTATTTTTAAAAATAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:47393:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 TTTTAAAAAATTTTTTTAATTTTTAACAATATAAAAAATTTTAAATAAAAAAAAATTAAAAAAAATATTTTTATTATTTAATTATTTAATATTATTATAAAAAAATATAATTTTAATTTTTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:47393:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 AATATATTTATTTTTTTATATTTATATAAAAATATTATAAAATTTTTTATAATAATTTATATTAATTTATTATTATTATTTATTATATAAAATATTAAAAAAATTAAAATTATATTTTTTTATAA IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:41728:1070_1:N:0:TTCCAGGT+AAGCACTG/1 99 ptg000004l_CT_converted 4412105 6 62M5I58M = 4412230 250 GATAATGGATATTATGTGTTATTGTAATTTTGTATGAGATATGTTTTAATTATTGTTGTTTTTAATGTAATTGTTTTTATTTATTATAAAAGAATTAAATAGATATTTTGAGTTTTGTTAATTTT I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII AS:i:-44 XS:i:-44 XN:i:0 XM:i:4 XO:i:1 XG:i:5 NM:i:9 MD:Z:33T8A5T24T46 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41728:1070_2:N:0:TTCCAGGT+AAGCACTG/2 147 ptg000004l_CT_converted 4412230 6 125M = 4412105 -250 TATGTTTAAAAATAAATTTTGTAAAGGGTTATTTTTTTTGATTTGTTGATTTTTTTTTGTTAGATATGGTGGTTGTTTGTGTTTTTTTAATGGTTGTTGATATTGTAAAAGAGTAGATGTTAAAA I99I-IIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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:-44 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:28675:1084_1:N:0:TTCCAGGT+AAGCACTG/1 83 ptg000009l_GA_converted 11713401 0 125M = 11713281 -245 ATCAATACAAAAATTACTAAAATATTCATTTAACTCACAAAATTCTTCATTACTTAATAACACATTAATAAAAAAACTACATCACTAAAAAATAACATCAACATAATTCCACCAATCACAACTTC I9IIIIIII9III9III9IIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-6 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:53A8T21T40 YS:i:-42 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:28675:1084_2:N:0:TTCCAGGT+AAGCACTG/2 163 ptg000009l_GA_converted 11713281 0 125M = 11713401 245 ATCTAAACCCATAAAAATATTCTTTAAACAAATTATACAATTCCATACTTACACTTCTATAAACTCCAATATTTCTTCATCATCATCAATAACAACATTTAATAACTCTATATATAAATTATCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9II9II9I-9II9IIII9-IIIIII9IIIIIIII9IIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-42 XS:i:-54 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:8T5C11T1T24A0C16C53 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:39025:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AATTTGGTATATAGTAATAGTTTTATAATAGATTTAATTTTTTTTTTGTTTGTTTTTGTTTGTTTTTAGGGATAGTAATTAGGTTAGTAATTAGGTTAAGGTAAATTTATTTTAAGTGGTTAAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39025:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 TACTTCAAAAAACAAAACATTAATTTTATTACTAAATCCATCTTTAACTATTCAACAATTTAACCACTTAAAATAAATTTACCTTAACCTAATTACTAACCTAATTACTATCCCTAAAAACAAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP Found first alignment: LH00526:197:22KFKVLT4:3:1101:47393:1070_1:N:0:TTCCAGGT+AAGCACTG/1 83 ptg000036l_GA_converted 5873305 1 125M = 5873211 -219 TCAAAAAAACTAAAATTATACTTTTTCATAACAACATTAAACAACCAAACAACAAAAATACTTCCCCCAATCTTCTTCTATCCAAAACCCTCTATATTATCAAAAACTAAAAAAACTCTTCAAAA IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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 LH00526:197:22KFKVLT4:3:1101:47393:1070_2:N:0:TTCCAGGT+AAGCACTG/2 163 ptg000036l_GA_converted 5873211 1 125M = 5873305 219 AATACACTCACCTCCCCATATTTACACAAAAACATCATAAAATTTCCTACAATAACTTATACCAATTCATTACTATCATCCATTACATAAAATATCAAAAAAACTAAAATTATACTTTTTCATAA IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:48768:1070_1:N:0:TTCCAGGT+AAGCACTG/1 83 ptg000034l_GA_converted 2550420 6 125M = 2550227 -318 AAACAAATCAATCATATAATAAAAAAAACACTATCTTTTAAAATATTTCCAACAAATTAACCATACAAATACTATCCTCACCCAAAAAATTTACACATTAAAAATAAAACAAATCCCACCTTTTT IIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 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:-18 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:48768:1070_2:N:0:TTCCAGGT+AAGCACTG/2 163 ptg000034l_GA_converted 2550227 6 125M = 2550420 318 AACTTTTTAAAACATTATATTCCCTAAACATCTCATCTTATCTCTATCAAATACATAACAAACACTTTAAAAATCAAACAAAACATTCTTATTTACAACTAAACATAAATTAATCTAAAAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIII AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:16T56A26T24 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:41728:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AATAATAAATATTATATATTATTATAATTTTATATAAAATATATTTTAATTATTATTATTTTTAATATAATTATTTTTATTTATTATAAAAAAATTAAATAAATATTTTAAATTTTATTAATTTT I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41728:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 TTTTAATATTTATTTTTTTATAATATTAATAATTATTAAAAAAATATAAATAATTATTATATTTAATAAAAAAAAATTAATAAATTAAAAAAAATAATTTTTTATAAAATTTATTTTTAAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIII-I99I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1A3_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)) Reading in the sequence files 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:41728:1070_1:N:0:TTCCAGGT+AAGCACTG/1 77 * 0 0 * * 0 0 AATAATAAATATTATATATTATTATAATTTTATATAAAATATATTTTAATTATTATTATTTTTAATATAATTATTTTTATTTATTATAAAAAAATTAAATAAATATTTTAAATTTTATTAATTTT I-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:41728:1070_2:N:0:TTCCAGGT+AAGCACTG/2 141 * 0 0 * * 0 0 TTTTAATATTTATTTTTTTATAATATTAATAATTATTAAAAAAATATAAATAATTATTATATTTAATAAAAAAAAATTAATAAATTAAAAAAAATAATTTTTTATAAAATTTATTTTTAAATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIII-I99I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A3_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: LH00526:197:22KFKVLT4:3:1101:41728:1070_1:N:0:TTCCAGGT+AAGCACTG/1 83 ptg000009l_GA_converted 17047605 1 54M5I66M = 17047475 -250 AAAATTAACAAAACTCAAAATATCTATTTAATTCTTTTATAATAAATAAAAACAATTACATTAAAAACAACAATAATTAAAACATATCTCATACAAAATTACAATAACACATAATATCCATTATC IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-I AS:i:-32 XS:i:-32 XN:i:0 XM:i:2 XO:i:1 XG:i:5 NM:i:7 MD:Z:71C5T42 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:41728:1070_2:N:0:TTCCAGGT+AAGCACTG/2 163 ptg000009l_GA_converted 17047475 1 125M = 17047605 250 TTTTAACATCTACTCTTTTACAATATCAACAACCATTAAAAAAACACAAACAACCACCATATCTAACAAAAAAAAATCAACAAATCAAAAAAAATAACCCTTTACAAAATTTATTTTTAAACATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIII-I99I 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:-32 YT:Z:CP >>> Writing bisulfite mapping results to 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1179:11512:27293_1:N:0:TTCCAGGT+AAGCACTG ptg000090l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1205:2246:14475_1:N:0:TTCCAGGT+AAGCACTG ptg000048l 1 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 LH00526:197:22KFKVLT4:3:1315:2756:22054_1:N:0:TTCCAGGT+AAGCACTG ptg000155l 36785 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 LH00526:197:22KFKVLT4:3:2105:47668:28105_1:N:0:TTCCAGGT+AAGCACTG ptg000114l 51134 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 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 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 LH00526:197:22KFKVLT4:4:1228:44528:16563_1:N:0:TTCCAGGT+AAGCACTG ptg000007l 12295855 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1232:22833:10049_1:N:0:TTCCAGGT+AAGCACTG ptg000006l 3 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 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2340:19046:22348_1:N:0:TTCCAGGT+AAGCACTG ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2307:15517:2681_1:N:0:TTCCAGGT+AAGCACTG ptg000077l 42461 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2424:4884:5903_1:N:0:TTCCAGGT+AAGCACTG ptg000018l 2 Processed 9000000 sequence pairs so far 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9383395 (99.73%) aligned concordantly 0 times 9820 (0.10%) aligned concordantly exactly 1 time 15799 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9384391 (99.74%) aligned concordantly 0 times 9486 (0.10%) aligned concordantly exactly 1 time 15137 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4215694 (44.80%) aligned concordantly 0 times 1860849 (19.78%) aligned concordantly exactly 1 time 3332471 (35.42%) aligned concordantly >1 times 55.20% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4219634 (44.85%) aligned concordantly 0 times 1861834 (19.79%) aligned concordantly exactly 1 time 3327546 (35.37%) aligned concordantly >1 times 55.15% overall alignment rate Processed 9409014 sequences in total Successfully deleted the temporary files 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9409014 Final Cytosine Methylation Report ================================= Total number of C's analysed: 246024848 Total methylated C's in CpG context: 3454572 Total methylated C's in CHG context: 228022 Total methylated C's in CHH context: 971310 Total methylated C's in Unknown context: 6383 Total unmethylated C's in CpG context: 36301420 Total unmethylated C's in CHG context: 42030155 Total unmethylated C's in CHH context: 163039369 Total unmethylated C's in Unknown context: 339345 C methylated in CpG context: 8.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9383704 (99.73%) aligned concordantly 0 times 9451 (0.10%) aligned concordantly exactly 1 time 15859 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9384436 (99.74%) aligned concordantly 0 times 9585 (0.10%) aligned concordantly exactly 1 time 14993 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4221967 (44.87%) aligned concordantly 0 times 1860155 (19.77%) aligned concordantly exactly 1 time 3326892 (35.36%) aligned concordantly >1 times 55.13% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4215963 (44.81%) aligned concordantly 0 times 1859741 (19.77%) aligned concordantly exactly 1 time 3333310 (35.43%) aligned concordantly >1 times 55.19% overall alignment rate Processed 9409014 sequences in total Successfully deleted the temporary files 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9409014 Final Cytosine Methylation Report ================================= Total number of C's analysed: 245810177 Total methylated C's in CpG context: 3447972 Total methylated C's in CHG context: 229939 Total methylated C's in CHH context: 969574 Total methylated C's in Unknown context: 6710 Total unmethylated C's in CpG context: 36260683 Total unmethylated C's in CHG context: 42016990 Total unmethylated C's in CHH context: 162885019 Total unmethylated C's in Unknown context: 340707 C methylated in CpG context: 8.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Processed 9000000 sequence pairs so far 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9383259 (99.73%) aligned concordantly 0 times 9798 (0.10%) aligned concordantly exactly 1 time 15957 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9384450 (99.74%) aligned concordantly 0 times 9477 (0.10%) aligned concordantly exactly 1 time 15087 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4216768 (44.82%) aligned concordantly 0 times 1861510 (19.78%) aligned concordantly exactly 1 time 3330736 (35.40%) aligned concordantly >1 times 55.18% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4221528 (44.87%) aligned concordantly 0 times 1861732 (19.79%) aligned concordantly exactly 1 time 3325754 (35.35%) aligned concordantly >1 times 55.13% overall alignment rate Processed 9409014 sequences in total Successfully deleted the temporary files 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9409014 Final Cytosine Methylation Report ================================= Total number of C's analysed: 245954817 Total methylated C's in CpG context: 3446306 Total methylated C's in CHG context: 230073 Total methylated C's in CHH context: 972396 Total methylated C's in Unknown context: 6583 Total unmethylated C's in CpG context: 36298642 Total unmethylated C's in CHG context: 42041892 Total unmethylated C's in CHH context: 162965508 Total unmethylated C's in Unknown context: 339861 C methylated in CpG context: 8.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 9409013 reads; of these: 9409013 (100.00%) were paired; of these: 4215518 (44.80%) aligned concordantly 0 times 1861259 (19.78%) aligned concordantly exactly 1 time 3332236 (35.42%) aligned concordantly >1 times 55.20% overall alignment rate 9409013 reads; of these: 9409013 (100.00%) were paired; of these: 4220441 (44.86%) aligned concordantly 0 times 1862289 (19.79%) aligned concordantly exactly 1 time 3326283 (35.35%) aligned concordantly >1 times 55.14% overall alignment rate 9409013 reads; of these: 9409013 (100.00%) were paired; of these: 9383186 (99.73%) aligned concordantly 0 times 9655 (0.10%) aligned concordantly exactly 1 time 16172 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 9409013 reads; of these: 9409013 (100.00%) were paired; of these: 9384314 (99.74%) aligned concordantly 0 times 9496 (0.10%) aligned concordantly exactly 1 time 15203 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate Processed 9409013 sequences in total Successfully deleted the temporary files 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9409013 Final Cytosine Methylation Report ================================= Total number of C's analysed: 246069430 Total methylated C's in CpG context: 3451278 Total methylated C's in CHG context: 228788 Total methylated C's in CHH context: 974111 Total methylated C's in Unknown context: 6464 Total unmethylated C's in CpG context: 36318456 Total unmethylated C's in CHG context: 42052298 Total unmethylated C's in CHH context: 163044499 Total unmethylated C's in Unknown context: 339075 C methylated in CpG context: 8.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Now waiting for all child processes to complete 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9384666 (99.74%) aligned concordantly 0 times 9509 (0.10%) aligned concordantly exactly 1 time 14839 (0.16%) aligned concordantly >1 times 0.26% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4219199 (44.84%) aligned concordantly 0 times 1861262 (19.78%) aligned concordantly exactly 1 time 3328553 (35.38%) aligned concordantly >1 times 55.16% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 9383403 (99.73%) aligned concordantly 0 times 9634 (0.10%) aligned concordantly exactly 1 time 15977 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 9409014 reads; of these: 9409014 (100.00%) were paired; of these: 4222826 (44.88%) aligned concordantly 0 times 1860562 (19.77%) aligned concordantly exactly 1 time 3325626 (35.35%) aligned concordantly >1 times 55.12% overall alignment rate Processed 9409014 sequences in total Successfully deleted the temporary files 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1A3_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 9409014 Final Cytosine Methylation Report ================================= Total number of C's analysed: 245896608 Total methylated C's in CpG context: 3455948 Total methylated C's in CHG context: 231358 Total methylated C's in CHH context: 972316 Total methylated C's in Unknown context: 6321 Total unmethylated C's in CpG context: 36267732 Total unmethylated C's in CHG context: 42034369 Total unmethylated C's in CHH context: 162934885 Total unmethylated C's in Unknown context: 340331 C methylated in CpG context: 8.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.8% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1A3_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1A3_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1A3_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/1A3_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1A3_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/1A3_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A3_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1A3_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: 47045069 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1229755880 Total methylated C's in CpG context: 17256076 Total methylated C's in CHG context: 1148180 Total methylated C's in CHH context: 4859707 Total methylated C's in Unknown context: 32461 Total unmethylated C's in CpG context: 181446933 Total unmethylated C's in CHG context: 210175704 Total unmethylated C's in CHH context: 814869280 Total unmethylated C's in Unknown context: 1699319 C methylated in CpG context: 8.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% Deleting temporary report files... Bismark completed in 0d 6h 5m 27s ==================== Bismark run complete ====================