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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_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/39--2E2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7762629) Using the subset file >39--2E2_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/39--2E2_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/39--2E2_R1_001.fastp-trim.fq.gz for PID: 24335 and offset 5 (sequences written out: 7762628) Using the subset file >39--2E2_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/39--2E2_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/39--2E2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7762629) Using the subset file >39--2E2_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/39--2E2_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/39--2E2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7762628) Using the subset file >39--2E2_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/39--2E2_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/39--2E2_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7762629) Using the subset file >39--2E2_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/39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz for PID: 24335 and offset 5 (sequences written out: 7762628) Using the subset file >39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz to 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz to 39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 7762628) Using the subset file >39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz to 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz to 39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 7762629) Using the subset file >39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz to 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz to 39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 7762629) Using the subset file >39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz to 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz to 39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 7762629) Using the subset file >39--2E2_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/39--2E2_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz to 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz to 39--2E2_R1_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz (7762629 sequences in total) Writing a C -> T converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz to 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz to 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz (7762629 sequences in total) Writing a C -> T converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz to 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz to 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz (7762628 sequences in total) Writing a C -> T converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz to 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz to 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz (7762629 sequences in total) Writing a C -> T converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz to 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz to 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz (7762628 sequences in total) Writing a C -> T converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz to 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz to 39--2E2_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 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz (7762629 sequences in total) Input files are 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 39--2E2_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 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz (7762629 sequences in total) Input files are 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz (7762628 sequences in total) Input files are 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:4560:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TGTTGAAAAGTGTTTATTTTTGTTGAGATGTATAAATGGGTTTTAGATGAAGGAGGATGATGGTGATTTTTTTTAGAGTTTTTTGGGGTATTTTGGGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:4560:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TAAAAAAAATCACCATCATCCTCCTTCATCTAAAACCCATTTATACATCTCAACAAAAATAAACACTTTTCAACATAATCTAACCACAAATTTACTTAAC IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:6323:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TTTGAAAAAATATTAAATTTTTGAGAAATTAGAGGATTTTGAAAATGGGTTATTTGAGGTTAAGGTTATAGTTTATGTAAAGGTTATAGTTTTTGTTAAATGGTTTGTTTGTGTTAAAAATTAAA IIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9III9IIIIIII-I9-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6323:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAATATTTTTTCAAACTAATTTTTTCACAAAACAACTCTAATATACTTACAAAATTATTTATCACATATTTTTAACACTTTTAATTTTTAACCCAAACTAACAATTTAACAAAAACTATAACCT IIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIII9IIIIII-IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIIIIIIII9IIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:13637:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 99 ptg000002l_CT_converted 11291633 42 125M = 11291800 292 TAGAGAGAAAATTTTGAGGAAAGAGTTGAATAGAATAATTTAGAATTATTGAAAATGATATATATTTATTAGAGTTGTATGATGTATTAGTTAATTATAGTTGATGAAAATTTGTAGATTTGTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:13637:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 147 ptg000002l_CT_converted 11291800 42 125M = 11291633 -292 TATTATTATAATTAGTTGGATTGGTATTATTAATGATAATAATAGTAGTTGTTGTAGTATTATGAATGTAATTGTTATGATGAGGAGAAATTTAAGATTTTTATGTATGTTTTTAATAAATGTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 39--2E2_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)) Created C -> T as well as G -> A converted versions of the FastQ file 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz (7762629 sequences in total) Input files are 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:13637:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TAAAAAAAAAATTTTAAAAAAAAAATTAAATAAAATAATTTAAAATTATTAAAAATAATATATATTTATTAAAATTATATAATATATTAATTAATTATAATTAATAAAAATTTATAAATTTATCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13637:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTATATTTATTAAAAATGTATGTAAAAATTTTAAATTTTTTTTTATTATAATAATTATATTTATAATATTATAATGATTATTATTATTATTATTAATAATATTAATTTAATTAATTATAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:6323:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TTTAAAAAAATATTAAATTTTTAAAAAATTAAAAAATTTTAAAAATAAATTATTTAAAATCAAAATTATAATTTATATAAAAATTATAATTTTTATTAAATAATTTATTTATATTAAAAATTAAA IIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9III9IIIIIII-I9-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6323:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAATATTTTTTTAAATTAATTTTTTTATAAAATAATTTTAATATATTTATAAAATTATTTATTATATATTTTTAATATTTTTAATTTTTAATTTAAATTAATAATTTAATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIII9IIIIII-IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIIIIIIII9IIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:4560:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TATTAAAAAATATTTATTTTTATTAAAATATATAAATAAATTTTAAATAAAAAAAAATAATAATAATTTTTTTTAAAATTTTTTAAAATATTTTAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:4560:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TAAAAAAAATTATTATTATTTTTTTTTATTTAAAATTTATTTATATATTTTAATAAAAATAAATATTTTTTAATATAATTTAATTATAAATTTATTTAAT IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:13637:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TAAAAAAAAAATTTTAAAAAAAAAATTAAATAAAATAATTTAAAATTATTAAAAATAATATATATTTATTAAAATTATATAATATATTAATTAATTATAATTAATAAAAATTTATAAATTTATCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13637:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTATATTTATTAAAAATGTATGTAAAAATTTTAAATTTTTTTTTATTATAATAATTATATTTATAATATTATAATGATTATTATTATTATTATTAATAATATTAATTTAATTAATTATAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:6339:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 99 ntLink_6_CT_converted 10439274 0 53M1D2M3I67M = 10439165 -232 TTTGAAAAAATATTAAATTTTTGAGAAATTAGAGGATTTTGAAAATGGGTTATTTGAGGTAAAGGTTATAGTTTATGTAAAGGTTATAGTTTTTGTTAAATGGTTTGTTTGTGTTAAAAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-70 XS:i:-70 XN:i:0 XM:i:8 XO:i:2 XG:i:4 NM:i:12 MD:Z:18A10G3T12T6^G24G15A8A5G13 YS:i:-64 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:6339:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 147 ntLink_6_CT_converted 10439165 0 99M1D8M1I17M = 10439274 232 AGGTTATAGTTTTTGTTAAATTGTTAGTTTGGGTTAAAAATTAAAAGTGTTAAAAATATGTGATAAATAATTTTGTAAGTATATTAGAGTTGTTTTGTGAAAAAATTAGTTTGAAAAAATATTAA IIIIIII9-IIIIIIIIIIIIIIIIIII9-IIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIII99II9IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-64 XS:i:-64 XN:i:0 XM:i:8 XO:i:2 XG:i:2 NM:i:10 MD:Z:3A12A4G41A1T2T5A4A19^T25 YS:i:-70 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:6323:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TTTAAAAAAATATTAAATTTTTAAAAAATTAAAAAATTTTAAAAATAAATTATTTAAAATCAAAATTATAATTTATATAAAAATTATAATTTTTATTAAATAATTTATTTATATTAAAAATTAAA IIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII9III9IIIIIII-I9-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6323:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAATATTTTTTTAAATTAATTTTTTTATAAAATAATTTTAATATATTTATAAAATTATTTATTATATATTTTTAATATTTTTAATTTTTAATTTAAATTAATAATTTAATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIII9IIIIII-IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIIIIIIII9IIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:4560:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TATTAAAAAATATTTATTTTTATTAAAATATATAAATAAATTTTAAATAAAAAAAAATAATAATAATTTTTTTTAAAATTTTTTAAAATATTTTAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:4560:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TAAAAAAAATTATTATTATTTTTTTTTATTTAAAATTTATTTATATATTTTAATAAAAATAAATATTTTTTAATATAATTTAATTATAAATTTATTTAAT IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:6339:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TTTAAAAAAATATTAAATTTTTAAAAAATTAAAAAATTTTAAAAATAAATTATTTAAAATAAAAATTATAATTTATATAAAAATTATAATTTTTATTAAATAATTTATTTATATTAAAAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6339:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAATATTTTTTTAAATTAATTTTTTTATAAAATAATTTTAATATATTTATAAAATTATTTATTATATATTTTTAATATTTTTAATTTTTAATTTAAATTAATAATTTAATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII9II99IIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIII-9IIIIIIIIIIIIIIIIIII-9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:13637:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TAGAGAGAAAATTTTGAGGAAAGAGTTGAATAGAATAATTTAGAATTATTGAAAATGATATATATTTATTAGAGTTGTATGATGTATTAGTTAATTATAGTTGATGAAAATTTGTAGATTTGTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:13637:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 CCACATTTATTAAAAACATACATAAAAATCTTAAATTTCTCCTCATCATAACAATTACATTCATAATACTACAACAACTACTATTATTATCATTAATAATACCAATCCAACTAATTATAATAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:6323:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 83 ntLink_6_GA_converted 424584 2 125M = 424329 -380 TTTAATTTTTAACACAAACAAACCATTTAACAAAAACTATAACCTTTACATAAACTATAACCTTAACCTCAAATAACCCATTTTCAAAATCCTCTAATTTCTCAAAAATTTAATATTTTTTCAAA IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-9I-IIIIIII9III9IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIIII AS:i:-60 XS:i:-72 XN:i:0 XM:i:10 XO:i:0 XG:i:0 NM:i:10 MD:Z:13C5T19A19C4T11T1A16C15C10T2 YS:i:-72 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:6323:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 163 ntLink_6_GA_converted 424329 2 125M = 424584 380 TTAATATTTTTTCAAACTAATTTTTTCACAAAACAACTCTAATATACTTACAAAATTATTTATCACATATTTTTAACACTTTTAATTTTTAACCCAAACTAACAATTTAACAAAAACTATAACCT IIIIIIIIIIIIIIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIII9IIIIII-IIIIII-IIIIIIIIIIIIIIIIIIIIIIIIII-III9IIIIIIIIII9IIIIIIIIIIIIIIIIII AS:i:-72 XS:i:-66 XN:i:0 XM:i:12 XO:i:0 XG:i:0 NM:i:12 MD:Z:6A5A5T0C23C1T4T5C1A2T16T11C34 YS:i:-60 YT:Z:CP >>> Writing bisulfite mapping results to 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:6339:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 TTTAAAAAAATATTAAATTTTTAAAAAATTAAAAAATTTTAAAAATAAATTATTTAAAATAAAAATTATAATTTATATAAAAATTATAATTTTTATTAAATAATTTATTTATATTAAAAATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:6339:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAATATTTTTTTAAATTAATTTTTTTATAAAATAATTTTAATATATTTATAAAATTATTTATTATATATTTTTAATATTTTTAATTTTTAATTTAAATTAATAATTTAATAAAAATTATAATTT IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII9II99IIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIII-9IIIIIIIIIIIIIIIIIII-9IIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 39--2E2_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)) Reading in the sequence files 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: LH00652:104:22KG7JLT4:7:1101:6339:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 83 ntLink_6_GA_converted 423465 2 125M = 423385 -205 TTTAATTTTTAACACAAACAAACCATTTAACAAAAACTATAACCTTTACATAAACTATAACCTTTACCTCAAATAACCCATTTTCAAAATCCTCTAATTTCTCAAAAATTTAATATTTTTTCAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-48 XS:i:-54 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:13C5T39C5C12A9C6C10T18 YS:i:-66 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:6339:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 163 ntLink_6_GA_converted 423385 2 125M = 423465 205 TTAATATTTTTTCAAACTAATTTTTTCACAAAACAACTCTAATATACTTACAAAATTATTTATCACATATTTTTAACACTTTTAATTTTTAACCCAAACTAACAATTTAACAAAAACTATAACCT IIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIII9II99IIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIII-9IIIIIIIIIIIIIIIIIII-9IIIIIII AS:i:-66 XS:i:-66 XN:i:0 XM:i:11 XO:i:0 XG:i:0 NM:i:11 MD:Z:18T0C4C20T4T5C4T10C0A4T24C21 YS:i:-48 YT:Z:CP >>> Writing bisulfite mapping results to 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00652:104:22KG7JLT4:7:1101:4560:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 83 ptg000018l_GA_converted 8565526 42 100M = 8565551 125 ATACCCAAAATACCCCAAAAAACTCTAAAAAAAATCACCATCATCCTCCTTCATCTAAAACCCATTTATACATCTCAACAAAAATAAACACTTTTCAACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:-6 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:4560:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 163 ptg000018l_GA_converted 8565551 42 100M = 8565526 -125 TAAAAAAAATCACCATCATCCTCCTTCATCTAAAACCCATTTATACATCTCAACAAAAATAAACACTTTTCAACATAATCTAACCACAAATTTACTTAAC IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:75C24 YS:i:0 YT:Z:CP Reading in the sequence files 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz >>> Writing bisulfite mapping results to 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz (7762628 sequences in total) Input files are 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 39--2E2_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 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 39--2E2_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: LH00652:104:22KG7JLT4:7:1101:15141:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 AAATATTTGATAGATTATAATAATTGTTATTATGATTGTTTATTTGATTATGGTTTTTATGATAGAATGATTGAATGTTTTGGGTTTGTTTTTAATATTAGTATTAATATATGTAAAAGAGTTTT I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:15141:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAAAAAAAAAAATATTAAAACCATTACACAATTTTATTTTTATCTAAAAAAAAACCAAAATTCAAATATCAACTTTCAATTTCTTCAAAATAATATCCAATCTCAACCAACTTATTAAAAACTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:15141:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 AAATATTTAATAAATTATAATAATTATTATTATAATTATTTATTTAATTATAATTTTTATAATAAAATAATTAAATATTTTAAATTTATTTTTAATATTAATATTAATATATATAAAAAAATTTT I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:15141:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAAAAAAAAAAATATTAAAATTATTATATAATTTTATTTTTATTTAAAAAAAAATTAAAATTTAAATATTAATTTTTAATTTTTTTAAAATAATATTTAATTTTAATTAATTTATTAAAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:15141:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 77 * 0 0 * * 0 0 AAATATTTAATAAATTATAATAATTATTATTATAATTATTTATTTAATTATAATTTTTATAATAAAATAATTAAATATTTTAAATTTATTTTTAATATTAATATTAATATATATAAAAAAATTTT I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00652:104:22KG7JLT4:7:1101:15141:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 141 * 0 0 * * 0 0 TTAAAAAAAAAAATATTAAAATTATTATATAATTTTATTTTTATTTAAAAAAAAATTAAAATTTAAATATTAATTTTTAATTTTTTTAAAATAATATTTAATTTTAATTAATTTATTAAAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00652:104:22KG7JLT4:7:1101:15141:1084_1:N:0:CTTAGGAC+CAGTGAAG/1 83 ntLink_8_GA_converted 22400947 42 125M = 22400829 -243 AAAACTCTTTTACATATATTAATACTAATATTAAAAACAAACCCAAAACATTCAATCATTCTATCATAAAAACCATAATCAAATAAACAATCATAATAACAATTATTATAATCTATCAAATATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:68C56 YS:i:0 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:15141:1084_2:N:0:CTTAGGAC+CAGTGAAG/2 163 ntLink_8_GA_converted 22400829 42 125M = 22400947 243 TTAAAAAAAAAAATATTAAAACCATTACACAATTTTATTTTTATCTAAAAAAAAACCAAAATTCAAATATCAACTTTCAATTTCTTCAAAATAATATCCAATCTCAACCAACTTATTAAAAACTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2396:50478:10444_1:N:0:CTTAGGAC+CAGTGAAG ptg000059l 1573514 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 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1484:21613:14984_1:N:0:CTTAGGAC+CAGTGAAG ptg000024l 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2269:8152:24737_1:N:0:CTTAGGAC+CAGTGAAG ptg000098l 55082 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2269:8135:24737_1:N:0:CTTAGGAC+CAGTGAAG ptg000098l 55082 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2329:47396:21276_1:N:0:CTTAGGAC+CAGTGAAG ptg000033l 2625623 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2191:12973:21990_1:N:0:CTTAGGAC+CAGTGAAG ptg000092l 28970 Processed 7000000 sequence pairs so far 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 7733627 (99.63%) aligned concordantly 0 times 10145 (0.13%) aligned concordantly exactly 1 time 18857 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 3194164 (41.15%) aligned concordantly 0 times 1621761 (20.89%) aligned concordantly exactly 1 time 2946704 (37.96%) aligned concordantly >1 times 58.85% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 3198600 (41.21%) aligned concordantly 0 times 1621983 (20.89%) aligned concordantly exactly 1 time 2942046 (37.90%) aligned concordantly >1 times 58.79% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 7734791 (99.64%) aligned concordantly 0 times 10181 (0.13%) aligned concordantly exactly 1 time 17657 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate Processed 7762629 sequences in total Successfully deleted the temporary files 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7762629 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215496751 Total methylated C's in CpG context: 2841322 Total methylated C's in CHG context: 222549 Total methylated C's in CHH context: 984424 Total methylated C's in Unknown context: 6363 Total unmethylated C's in CpG context: 32275537 Total unmethylated C's in CHG context: 37317450 Total unmethylated C's in CHH context: 141855469 Total unmethylated C's in Unknown context: 294191 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.1% 7762628 reads; of these: 7762628 (100.00%) were paired; of these: 7733689 (99.63%) aligned concordantly 0 times 9963 (0.13%) aligned concordantly exactly 1 time 18976 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate 7762628 reads; of these: 7762628 (100.00%) were paired; of these: 3193925 (41.14%) aligned concordantly 0 times 1621691 (20.89%) aligned concordantly exactly 1 time 2947012 (37.96%) aligned concordantly >1 times 58.86% overall alignment rate 77626287762628 reads; of these: reads; of these: 77626287762628 ( (100.00%100.00) were paired; of these:% ) were paired; of these: 3196896 (773509941.18 (%99.65) aligned concordantly 0 times% ) aligned concordantly 0 times 1624430 (991520.93 (%0.13) aligned concordantly exactly 1 time% ) aligned concordantly exactly 1 time 2941302 (1761437.89 (%0.23) aligned concordantly >1 times% ) aligned concordantly >1 times 0.35% overall alignment rate 58.82% overall alignment rate Processed 7762628 sequences in total Successfully deleted the temporary files 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7762628 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215472094 Total methylated C's in CpG context: 2833095 Total methylated C's in CHG context: 218393 Total methylated C's in CHH context: 972071 Total methylated C's in Unknown context: 6550 Total unmethylated C's in CpG context: 32258510 Total unmethylated C's in CHG context: 37299521 Total unmethylated C's in CHH context: 141890504 Total unmethylated C's in Unknown context: 293505 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Now waiting for all child processes to complete 7762628 reads; of these: 7762628 (100.00%) were paired; of these: 7733668 (99.63%) aligned concordantly 0 times 10091 (0.13%) aligned concordantly exactly 1 time 18869 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate 7762628 reads; of these: 7762628 (100.00%) were paired; of these: 3199217 (41.21%) aligned concordantly 0 times 1620869 (20.88%) aligned concordantly exactly 1 time 2942542 (37.91%) aligned concordantly >1 times 58.79% overall alignment rate 7762628 reads; of these: 7762628 (100.00%) were paired; of these: 3192918 (41.13%) aligned concordantly 0 times 1621277 (20.89%) aligned concordantly exactly 1 time 2948433 (37.98%) aligned concordantly >1 times 58.87% overall alignment rate 7762628 reads; of these: 7762628 (100.00%) were paired; of these: 7734967 (99.64%) aligned concordantly 0 times 10093 (0.13%) aligned concordantly exactly 1 time 17568 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate Processed 7762628 sequences in total Successfully deleted the temporary files 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7762628 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215407087 Total methylated C's in CpG context: 2836490 Total methylated C's in CHG context: 220219 Total methylated C's in CHH context: 989403 Total methylated C's in Unknown context: 6683 Total unmethylated C's in CpG context: 32247170 Total unmethylated C's in CHG context: 37306738 Total unmethylated C's in CHH context: 141807067 Total unmethylated C's in Unknown context: 293157 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Processed 7000000 sequence pairs so far 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 7734795 (99.64%) aligned concordantly 0 times 10247 (0.13%) aligned concordantly exactly 1 time 17587 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 3195636 (41.17%) aligned concordantly 0 times 1620661 (20.88%) aligned concordantly exactly 1 time 2946332 (37.96%) aligned concordantly >1 times 58.83% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 3198365 (41.20%) aligned concordantly 0 times 1622747 (20.90%) aligned concordantly exactly 1 time 2941517 (37.89%) aligned concordantly >1 times 58.80% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 7733381 (99.62%) aligned concordantly 0 times 10285 (0.13%) aligned concordantly exactly 1 time 18963 (0.24%) aligned concordantly >1 times 0.38% overall alignment rate Processed 7762629 sequences in total Successfully deleted the temporary files 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7762629 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215437855 Total methylated C's in CpG context: 2844026 Total methylated C's in CHG context: 222305 Total methylated C's in CHH context: 994225 Total methylated C's in Unknown context: 6491 Total unmethylated C's in CpG context: 32253131 Total unmethylated C's in CHG context: 37303819 Total unmethylated C's in CHH context: 141820349 Total unmethylated C's in Unknown context: 292682 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 3192706 (41.13%) aligned concordantly 0 times 1623864 (20.92%) aligned concordantly exactly 1 time 2946059 (37.95%) aligned concordantly >1 times 58.87% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 7733780 (99.63%) aligned concordantly 0 times 10012 (0.13%) aligned concordantly exactly 1 time 18837 (0.24%) aligned concordantly >1 times 0.37% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 3200034 (41.22%) aligned concordantly 0 times 1621324 (20.89%) aligned concordantly exactly 1 time 2941271 (37.89%) aligned concordantly >1 times 58.78% overall alignment rate 7762629 reads; of these: 7762629 (100.00%) were paired; of these: 7734987 (99.64%) aligned concordantly 0 times 10027 (0.13%) aligned concordantly exactly 1 time 17615 (0.23%) aligned concordantly >1 times 0.36% overall alignment rate Processed 7762629 sequences in total Successfully deleted the temporary files 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 39--2E2_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 7762629 Final Cytosine Methylation Report ================================= Total number of C's analysed: 215496425 Total methylated C's in CpG context: 2838810 Total methylated C's in CHG context: 218652 Total methylated C's in CHH context: 977314 Total methylated C's in Unknown context: 6537 Total unmethylated C's in CpG context: 32276227 Total unmethylated C's in CHG context: 37315186 Total unmethylated C's in CHH context: 141870236 Total unmethylated C's in Unknown context: 293817 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 39--2E2_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 39--2E2_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 39--2E2_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/39--2E2_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 39--2E2_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/39--2E2_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 39--2E2_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 39--2E2_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: 38813143 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1077310212 Total methylated C's in CpG context: 14193743 Total methylated C's in CHG context: 1102118 Total methylated C's in CHH context: 4917437 Total methylated C's in Unknown context: 32624 Total unmethylated C's in CpG context: 161310575 Total unmethylated C's in CHG context: 186542714 Total unmethylated C's in CHH context: 709243625 Total unmethylated C's in Unknown context: 1467352 C methylated in CpG context: 8.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.7% C methylated in Unknown context (CN or CHN): 2.2% Deleting temporary report files... Bismark completed in 0d 5h 35m 11s ==================== Bismark run complete ====================