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/1C8_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/1C8_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/1C8_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/1C8_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/1C8_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/1C8_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/1C8_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/1C8_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= 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/1C8_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/1C8_R2_001.fastp-trim.fq.gz 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/1C8_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/1C8_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/1C8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8819377) Using the subset file >1C8_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/1C8_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/1C8_R1_001.fastp-trim.fq.gz for PID: 94282 and offset 5 (sequences written out: 8819377) Using the subset file >1C8_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/1C8_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/1C8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8819378) Using the subset file >1C8_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/1C8_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/1C8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8819378) Using the subset file >1C8_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/1C8_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/1C8_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8819378) Using the subset file >1C8_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/1C8_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/1C8_R2_001.fastp-trim.fq.gz for PID: 94282 and offset 5 (sequences written out: 8819377) Using the subset file >1C8_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/1C8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz to 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz to 1C8_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/1C8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 8819378) Using the subset file >1C8_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/1C8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz to 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz to 1C8_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/1C8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 4 (sequences written out: 8819377) Using the subset file >1C8_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/1C8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz to 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz to 1C8_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/1C8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 8819378) Using the subset file >1C8_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/1C8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz to 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz to 1C8_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/1C8_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 8819378) Using the subset file >1C8_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/1C8_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz to 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz to 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz (8819378 sequences in total) Writing a C -> T converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz to 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz to 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz (8819378 sequences in total) Writing a C -> T converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz to 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz to 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz (8819378 sequences in total) Writing a C -> T converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz to 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz to 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz (8819377 sequences in total) Writing a C -> T converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz to 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz to 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz (8819377 sequences in total) Writing a C -> T converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz to 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz to 1C8_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 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz (8819378 sequences in total) Input files are 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C8_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 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz (8819377 sequences in total) Input files are 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:33984:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 AGAGAGTGTTTGTGTATATTAATGGTAAAAAATAATTAAGTATTTTTGATATTTTAGTTGTTAAAGGTAGTGTTGATAATAATAAAGTTTTTGAGTTTGGTATTTTTTATGGTTGGGATGTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9III99IIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33984:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 AAAAAATATTCATATACATCAATAACAAAAAACAATCAAACACCCTCAACATCCCAACCATAAAAAATACCAAACTCAAAAACTTTATTATTATCAACACTACCTTTAACAACTAAAATATCAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:43436:1084_1:N:0:ATCTGACC+AAGTCGAG/1 99 ptg000018l_CT_converted 9657447 2 15M8D101M = 9657512 192 AGTTAATAAATTATATTATTGTTAAGGAAAATGAAGATTTTATTTGGAGTTTTTAATTTTTGTAATTTGTTAAAGTATGGGTTTGTTTAGTGTGATGGAGTGTGATGGTTTTTAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII AS:i:-41 XS:i:-41 XN:i:0 XM:i:2 XO:i:1 XG:i:8 NM:i:10 MD:Z:15^ATATATTG16G65A18 YS:i:-28 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43436:1084_2:N:0:ATCTGACC+AAGTCGAG/2 147 ptg000018l_CT_converted 9657512 2 105M1D2M1D18M = 9657447 -192 TTTTGTAATTTGTTAAAGTATGGGTTTGTTTAGTGTGATGGAGTGTGATGGTTTTTAAGTTTATTTTTTTTTGTTAAGATATATGATTTTATTATTATTATTATTTTTTTTTTTGGAGAAAGTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-28 XS:i:-29 XN:i:0 XM:i:2 XO:i:2 XG:i:2 NM:i:4 MD:Z:40A41T22^A2^A18 YS:i:-41 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C8_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz (8819378 sequences in total) Input files are 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C8_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)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:33984:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 AAAAAATATTTATATATATTAATAATAAAAAATAATTAAATATTTTTAATATTTTAATTATTAAAAATAATATTAATAATAATAAAATTTTTAAATTTAATATTTTTTATAATTAAAATATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9III99IIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33984:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 AAAAAATATTTATATATATTAATAATAAAAAATAATTAAATATTTTTAATATTTTAATTATAAAAAATATTAAATTTAAAAATTTTATTATTATTAATATTATTTTTAATAATTAAAATATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:43436:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 AATTAATAAATTATATTATTATTAAAAAAAATAAAAATTTTATTTAAAATTTTTAATTTTTATAATTTATTAAAATATAAATTTATTTAATATAATAAAATATAATAATTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43436:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TAATTTTTTTTAAAAAAAAAAATAATAATAATAATAAAATTATATATTTTAATAAAAAAAAATAAATTTAAAAATTATTATATTTTATTATATTAAATAAATTTATATTTTAATAAATTATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz and 1C8_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz (8819378 sequences in total) Input files are 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:43436:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 AATTAATAAATTATATTATTATTAAAAAAAATAAAAATTTTATTTAAAATTTTTAATTTTTATAATTTATTAAAATATAAATTTATTTAATATAATAAAATATAATAATTTTTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:43436:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TAATTTTTTTTAAAAAAAAAAATAATAATAATAATAAAATTATATATTTTAATAAAAAAAAATAAATTTAAAAATTATTATATTTTATTATATTAAATAAATTTATATTTTAATAAATTATAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:33984:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 AAAAAATATTTATATATATTAATAATAAAAAATAATTAAATATTTTTAATATTTTAATTATTAAAAATAATATTAATAATAATAAAATTTTTAAATTTAATATTTTTTATAATTAAAATATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9III99IIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33984:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 AAAAAATATTTATATATATTAATAATAAAAAATAATTAAATATTTTTAATATTTTAATTATAAAAAATATTAAATTTAAAAATTTTATTATTATTAATATTATTTTTAATAATTAAAATATTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:50185:1056_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TGTTTGGTTGGTGTGAATAGGGGGGTTATATATTTATGGTTGTTATATAGATAATATATTGGTTTTTATATTTTGTTGATAAAAGTTTTTTAAGTTTGTTTTTGAATTAGTTTTTTTAAAATTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50185:1056_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 CCACTTCTAAAATTAAAAAAAAATCAAAATAACATATATATTTTTAAAAATTCAAAAATAAATATATAATAAACACACTAACCTTTAAATTATTATTAAAAAATTTCTTTTTATAAATTTTTTCA IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:43436:1084_1:N:0:ATCTGACC+AAGTCGAG/1 83 ptg000009l_GA_converted 19024162 2 101M5D15M = 19024096 -187 CTTAAAAACCATCACACTCCATCACACTAAACAAACCCATACTTTAACAAATTACAAAAATTAAAAACTCCAAATAAAATCTTCATTTTCCTTAACAATAATATAATTTATTAACT IIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-38 XS:i:-41 XN:i:0 XM:i:3 XO:i:1 XG:i:5 NM:i:8 MD:Z:14T3T65C16^TATAT15 YS:i:-24 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:43436:1084_2:N:0:ATCTGACC+AAGTCGAG/2 163 ptg000009l_GA_converted 19024096 2 125M = 19024162 187 CAACTTTCTCCAAAAAAAAAAATAATAATAATAATAAAATCATATATCTTAACAAAAAAAAATAAACTTAAAAACCATCACACTCCATCACACTAAACAAACCCATACTTTAACAAATTACAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-29 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:22C19A37T3T40 YS:i:-38 YT:Z:CP Found first alignment: LH00526:197:22KFKVLT4:3:1101:33984:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 AGAGAGTGTTTGTGTATATTAATGGTAAAAAATAATTAAGTATTTTTGATATTTTAGTTGTTAAAGGTAGTGTTGATAATAATAAAGTTTTTGAGTTTGGTATTTTTTATGGTTGGGATGTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9III99IIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:33984:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 AAAAAATATTCATATACATCAATAACAAAAAACAATCAAACACCCTCAACATCCCAACCATAAAAAATACCAAACTCAAAAACTTTATTATTATCAACACTACCTTTAACAACTAAAATATCAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:50193:1070_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TGTTTGGTTGGTGTGAATAGGGGGGTTATATATTTATGGTTGTTATATAGATAATATATTGGTTTTTATATTTTGTTGATAAAAGTTTTTTAAGTTTGTTTTTGAATTAGTTTTTTTAAAATTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50193:1070_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 CCACTTCTAAAATTAAAAAAAAATCAAAATAACATATATATTTTTAAAAATTCAAAAATAAATATATAATAAACACACTAACCTTTAAATTATTATTAAAAAATTTCTTTTTATAAATTTTTTCA IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:50185:1056_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TATTCAATTAATACAAATAAAAAAATTATATATTTATAATTATTATATAAATAATATATCAATTTTTATATTTTATTAATAAAAATTTTTTAAATTTATTTTTAAATTAATTTTTTTAAAATCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50185:1056_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TTGTTTTTAAAATTAAAAAAAAATTGAAATAATATATATATTTTTAAAAATTTGAAAATAAATATATAATAAATATGTTAATTTTTAAATTATTATTAAAAAATTTTTTTTTATAAATTTTTTTA IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:50193:1070_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TATTCAATTAATACAAATAAAAAAATTATATATTTATAATTATTATATAAATAATATATCAATTTTTATATTTTATTAATAAAAATTTTTTAAATTTATTTTTAAATTAATTTTTTTAAAATCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50193:1070_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TTGTTTTTAAAATTAAAAAAAAATTGAAATAATATATATATTTTTAAAAATTTGAAAATAAATATATAATAAATATGTTAATTTTTAAATTATTATTAAAAAATTTTTTTTTATAAATTTTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 5 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:50185:1056_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TATTCAATTAATACAAATAAAAAAATTATATATTTATAATTATTATATAAATAATATATCAATTTTTATATTTTATTAATAAAAATTTTTTAAATTTATTTTTAAATTAATTTTTTTAAAATCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50185:1056_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TTGTTTTTAAAATTAAAAAAAAATTGAAATAATATATATATTTTTAAAAATTTGAAAATAAATATATAATAAATATGTTAATTTTTAAATTATTATTAAAAAATTTTTTTTTATAAATTTTTTTA IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C8_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)) Reading in the sequence files 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz Reading in the sequence files 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:50185:1056_1:N:0:ATCTGACC+AAGTCGAG/1 83 ptg000025l_GA_converted 18483548 42 125M = 18483325 -348 CCAATTTTAAAAAAACTAATTCAAAAACAAACTTAAAAAACTTTTATCAACAAAATATAAAAACCAATATATTATCTATATAACAACCATAAATATATAACCCCCCTATTCACACCAACCAAACA IIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50185:1056_2:N:0:ATCTGACC+AAGTCGAG/2 163 ptg000025l_GA_converted 18483325 42 125M = 18483548 348 CCACTTCTAAAATTAAAAAAAAATCAAAATAACATATATATTTTTAAAAATTCAAAAATAAATATATAATAAACACACTAACCTTTAAATTATTATTAAAAAATTTCTTTTTATAAATTTTTTCA IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:50193:1070_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TATTCAATTAATACAAATAAAAAAATTATATATTTATAATTATTATATAAATAATATATCAATTTTTATATTTTATTAATAAAAATTTTTTAAATTTATTTTTAAATTAATTTTTTTAAAATCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50193:1070_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TTGTTTTTAAAATTAAAAAAAAATTGAAATAATATATATATTTTTAAAAATTTGAAAATAAATATATAATAAATATGTTAATTTTTAAATTATTATTAAAAAATTTTTTTTTATAAATTTTTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C8_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)) Created C -> T as well as G -> A converted versions of the FastQ file 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz (8819377 sequences in total) Input files are 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C8_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 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:50193:1070_1:N:0:ATCTGACC+AAGTCGAG/1 83 ptg000025l_GA_converted 18483548 42 125M = 18483325 -348 CCAATTTTAAAAAAACTAATTCAAAAACAAACTTAAAAAACTTTTATCAACAAAATATAAAAACCAATATATTATCTATATAACAACCATAAATATATAACCCCCCTATTCACACCAACCAAACA IIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50193:1070_2:N:0:ATCTGACC+AAGTCGAG/2 163 ptg000025l_GA_converted 18483325 42 125M = 18483548 348 CCACTTCTAAAATTAAAAAAAAATCAAAATAACATATATATTTTTAAAAATTCAAAAATAAATATATAATAAACACACTAACCTTTAAATTATTATTAAAAAATTTCTTTTTATAAATTTTTTCA IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: LH00526:197:22KFKVLT4:3:1101:36023:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TAATATTTTAAGTTTAAAATTATATTTAATAGTAGTTAATAATGAAAAAAATTTTTTAATAAAATTATAGTTTAAAGGAATTTTTATGTTATTTAATGATAAAATTATTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:36023:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TAACTCTTACAATACCTATTTTTATTTATATAATAATAATTTTATCATTAAATAACATAAAAATTCCTTTAAACTATAATTTTATTAAAAAATTTTTTTCATTATTAACTACTATTAAATATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C8_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)) Reading in the sequence files 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:36023:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TAATATTTTAAATTTAAAATTATATTTAATAATAATTAATAATAAAAAAAATTTTTTAATAAAATTATAATTTAAAAAAATTTTTATATTATTTAATAATAAAATTATTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:36023:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TAATTTTTATAATATTTATTTTTATTTATATAATAATAATTTTATTATTAAATAATATAAAAATTTTTTTAAATTATAATTTTATTAAAAAATTTTTTTTATTATTAATTATTATTAAATATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and 1C8_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)) Reading in the sequence files 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: LH00526:197:22KFKVLT4:3:1101:36023:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TAATATTTTAAATTTAAAATTATATTTAATAATAATTAATAATAAAAAAAATTTTTTAATAAAATTATAATTTAAAAAAATTTTTATATTATTTAATAATAAAATTATTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:36023:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TAATTTTTATAATATTTATTTTTATTTATATAATAATAATTTTATTATTAAATAATATAAAAATTTTTTTAAATTATAATTTTATTAAAAAATTTTTTTTATTATTAATTATTATTAAATATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C8_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: LH00526:197:22KFKVLT4:3:1101:36023:1084_1:N:0:ATCTGACC+AAGTCGAG/1 77 * 0 0 * * 0 0 TAATATTTTAAGTTTAAAATTATATTTAATAGTAGTTAATAATGAAAAAAATTTTTTAATAAAATTATAGTTTAAAGGAATTTTTATGTTATTTAATGATAAAATTATTATTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:36023:1084_2:N:0:ATCTGACC+AAGTCGAG/2 141 * 0 0 * * 0 0 TAACTCTTACAATACCTATTTTTATTTATATAATAATAATTTTATCATTAAATAACATAAAAATTCCTTTAAACTATAATTTTATTAAAAAATTTTTTTCATTATTAACTACTATTAAATATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1242:17702:8200_1:N:0:ATCTGACC+AAGTCGAG ptg000007l 12295855 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1324:35012:2443_1:N:0:ATCTGACC+AAGTCGAG ptg000015l 14997091 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1435:6171:17851_1:N:0:ATCTGACC+AAGTCGAG ptg000155l 36785 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1459:38653:27040_1:N:0:ATCTGACC+AAGTCGAG ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2163:39090:3788_1:N:0:ATCTGACC+AAGTCGAG ptg000125l 18882 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1412:15526:23679_1:N:0:ATCTGACC+AAGTCGAG ptg000048l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2111:38208:26438_1:N:0:ATCTGACC+AAGTCGAG ptg000117l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2153:2845:4334_1:N:0:ATCTGACC+AAGTCGAG ptg000015l 14997092 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2111:38216:26424_1:N:0:ATCTGACC+AAGTCGAG ptg000117l 1 Processed 3000000 sequence pairs so far Processed 4000000 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 LH00526:197:22KFKVLT4:4:1174:5103:28609_1:N:0:ATCTGACC+AAGTCGAG ptg000020l 17861296 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2336:39454:1560_1:N:0:ATCTGACC+AAGTCGAG ptg000015l 14997092 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1190:42351:22040_1:N:0:ATCTGACC+AAGTCGAG ptg000039l 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1180:19604:2639_1:N:0:ATCTGACC+AAGTCGAG ptg000101l 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1287:28336:14644_1:N:0:ATCTGACC+AAGTCGAG ptg000174l 27225 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1303:22542:4978_1:N:0:ATCTGACC+AAGTCGAG ptg000133l 37107 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2151:3282:25738_1:N:0:ATCTGACC+AAGTCGAG ntLink_4 304031 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1334:41663:4740_1:N:0:ATCTGACC+AAGTCGAG ptg000130l 35797 Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2386:2885:13145_1:N:0:ATCTGACC+AAGTCGAG ptg000083l 1 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 3850498 (43.66%) aligned concordantly 0 times 1886733 (21.39%) aligned concordantly exactly 1 time 3082146 (34.95%) aligned concordantly >1 times 56.34% overall alignment rate 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 8795725 (99.73%) aligned concordantly 0 times 8816 (0.10%) aligned concordantly exactly 1 time 14836 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 8797200 (99.75%) aligned concordantly 0 times 8809 (0.10%) aligned concordantly exactly 1 time 13368 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 3844033 (43.59%) aligned concordantly 0 times 1889689 (21.43%) aligned concordantly exactly 1 time 3085655 (34.99%) aligned concordantly >1 times 56.41% overall alignment rate Processed 8819377 sequences in total Successfully deleted the temporary files 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz, 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz, 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz_C_to_T.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.5.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8819377 Final Cytosine Methylation Report ================================= Total number of C's analysed: 244714005 Total methylated C's in CpG context: 3906637 Total methylated C's in CHG context: 228884 Total methylated C's in CHH context: 991653 Total methylated C's in Unknown context: 6876 Total unmethylated C's in CpG context: 34604169 Total unmethylated C's in CHG context: 41334821 Total unmethylated C's in CHH context: 163647841 Total unmethylated C's in Unknown context: 344533 C methylated in CpG context: 10.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Now waiting for all child processes to complete Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 8797144 (99.75%) aligned concordantly 0 times 8922 (0.10%) aligned concordantly exactly 1 time 13312 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 3851780 (43.67%) aligned concordantly 0 times 1887458 (21.40%) aligned concordantly exactly 1 time 3080140 (34.92%) aligned concordantly >1 times 56.33% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 8795735 (99.73%) aligned concordantly 0 times 8822 (0.10%) aligned concordantly exactly 1 time 14821 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 3845139 (43.60%) aligned concordantly 0 times 1887552 (21.40%) aligned concordantly exactly 1 time 3086687 (35.00%) aligned concordantly >1 times 56.40% overall alignment rate Processed 8819378 sequences in total Successfully deleted the temporary files 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8819378 Final Cytosine Methylation Report ================================= Total number of C's analysed: 244677153 Total methylated C's in CpG context: 3899209 Total methylated C's in CHG context: 226706 Total methylated C's in CHH context: 985474 Total methylated C's in Unknown context: 6845 Total unmethylated C's in CpG context: 34606364 Total unmethylated C's in CHG context: 41345995 Total unmethylated C's in CHH context: 163613405 Total unmethylated C's in Unknown context: 343656 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2259:32479:10329_1:N:0:ATCTGACC+AAGTCGAG ptg000057l 39944 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 8795872 (99.73%) aligned concordantly 0 times 8686 (0.10%) aligned concordantly exactly 1 time 14819 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 8797281 (99.75%) aligned concordantly 0 times 8705 (0.10%) aligned concordantly exactly 1 time 13391 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 3849349 (43.65%) aligned concordantly 0 times 1888833 (21.42%) aligned concordantly exactly 1 time 3081195 (34.94%) aligned concordantly >1 times 56.35% overall alignment rate 8819377 reads; of these: 8819377 (100.00%) were paired; of these: 3843129 (43.58%) aligned concordantly 0 times 1889528 (21.42%) aligned concordantly exactly 1 time 3086720 (35.00%) aligned concordantly >1 times 56.42% overall alignment rate Processed 8819377 sequences in total Successfully deleted the temporary files 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8819377 Final Cytosine Methylation Report ================================= Total number of C's analysed: 244765534 Total methylated C's in CpG context: 3912794 Total methylated C's in CHG context: 227268 Total methylated C's in CHH context: 981968 Total methylated C's in Unknown context: 6989 Total unmethylated C's in CpG context: 34610083 Total unmethylated C's in CHG context: 41355076 Total unmethylated C's in CHH context: 163678345 Total unmethylated C's in Unknown context: 345079 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 3846102 (43.61%) aligned concordantly 0 times 1886523 (21.39%) aligned concordantly exactly 1 time 3086753 (35.00%) aligned concordantly >1 times 56.39% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 8795618 (99.73%) aligned concordantly 0 times 8899 (0.10%) aligned concordantly exactly 1 time 14861 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 8797233 (99.75%) aligned concordantly 0 times 8768 (0.10%) aligned concordantly exactly 1 time 13377 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 3850448 (43.66%) aligned concordantly 0 times 1887443 (21.40%) aligned concordantly exactly 1 time 3081487 (34.94%) aligned concordantly >1 times 56.34% overall alignment rate Processed 8819378 sequences in total Successfully deleted the temporary files 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8819378 Final Cytosine Methylation Report ================================= Total number of C's analysed: 244571188 Total methylated C's in CpG context: 3896815 Total methylated C's in CHG context: 226397 Total methylated C's in CHH context: 981049 Total methylated C's in Unknown context: 6737 Total unmethylated C's in CpG context: 34587206 Total unmethylated C's in CHG context: 41325659 Total unmethylated C's in CHH context: 163554062 Total unmethylated C's in Unknown context: 345234 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 1.9% 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 8795965 (99.73%) aligned concordantly 0 times 8808 (0.10%) aligned concordantly exactly 1 time 14605 (0.17%) aligned concordantly >1 times 0.27% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 8797501 (99.75%) aligned concordantly 0 times 8645 (0.10%) aligned concordantly exactly 1 time 13232 (0.15%) aligned concordantly >1 times 0.25% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 3849231 (43.65%) aligned concordantly 0 times 1887928 (21.41%) aligned concordantly exactly 1 time 3082219 (34.95%) aligned concordantly >1 times 56.35% overall alignment rate 8819378 reads; of these: 8819378 (100.00%) were paired; of these: 3844670 (43.59%) aligned concordantly 0 times 1889344 (21.42%) aligned concordantly exactly 1 time 3085364 (34.98%) aligned concordantly >1 times 56.41% overall alignment rate Processed 8819378 sequences in total Successfully deleted the temporary files 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and 1C8_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 8819378 Final Cytosine Methylation Report ================================= Total number of C's analysed: 244686667 Total methylated C's in CpG context: 3898311 Total methylated C's in CHG context: 228778 Total methylated C's in CHH context: 983979 Total methylated C's in Unknown context: 6980 Total unmethylated C's in CpG context: 34628727 Total unmethylated C's in CHG context: 41339491 Total unmethylated C's in CHH context: 163607381 Total unmethylated C's in Unknown context: 345618 C methylated in CpG context: 10.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam 1C8_R1_001.fastp-trim.fq.gz.temp.5.gz_bismark_bt2_pe.bam into >>> 1C8_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Merging from file >> 1C8_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/1C8_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt 1C8_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/1C8_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C8_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Merging from file >> 1C8_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: 44096888 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1223414547 Total methylated C's in CpG context: 19513766 Total methylated C's in CHG context: 1138033 Total methylated C's in CHH context: 4924123 Total methylated C's in Unknown context: 34427 Total unmethylated C's in CpG context: 173036549 Total unmethylated C's in CHG context: 206701042 Total unmethylated C's in CHH context: 818101034 Total unmethylated C's in Unknown context: 1724120 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 2.0% Deleting temporary report files... Bismark completed in 0d 5h 24m 0s ==================== Bismark run complete ====================