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/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ (absolute path is '/gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array'): /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_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/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/ Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Running Bismark Parallel version. Number of parallel instances to be spawned: 4 Current working directory is: /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_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/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 51511462) Using the subset file >CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 79773 and offset 4 (sequences written out: 51511462) Using the subset file >CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 51511463) Using the subset file >CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 51511462) Using the subset file >CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 51511462) Using the subset file >CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 79773 and offset 4 (sequences written out: 51511462) Using the subset file >CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 51511462) Using the subset file >CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 51511463) Using the subset file >CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF02-CM02-Zygote_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 CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (51511462 sequences in total) Writing a C -> T converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF02-CM02-Zygote_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 CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (51511462 sequences in total) Writing a C -> T converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF02-CM02-Zygote_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 CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (51511462 sequences in total) Writing a C -> T converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF02-CM02-Zygote_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 CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (51511463 sequences in total) Writing a C -> T converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF02-CM02-Zygote_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 CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (51511462 sequences in total) Input files are CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --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 CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (51511462 sequences in total) Input files are CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26937:1047_1:N:0:TTGGACTC+CTGCTTCC/1 99 NC_035788.1_CT_converted 71737341 6 116M = 71737326 -131 TATTGTATTTAATTAATTTAATTGAAAATTAATTTGTAAAATGTGTAAAATTAAAAAGAAAAAAATTTAAAATTAAATATGATTGGTAGTAGATTTTTAAATAGTATAGTATTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-12 XS:i:-18 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:82A20A12 YS:i:-6 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26937:1047_2:N:0:TTGGACTC+CTGCTTCC/2 147 NC_035788.1_CT_converted 71737326 6 116M = 71737341 131 GTTTTTTTATTGGTATATTGTATTTAATTAATTTAATTGAAAATTAATTTGTAAAATGTGTAAAATTAAAAAGAAAAAAATTTAAAATTAAATATGATTGGTAGTAGATTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:97A18 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28546:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTTTTGAAGTAATTTTATTAATTTTTTTTTTTAAAATGATAAAAAATATGTTATTATTATGGAAGAGAAAAATGAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28546:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 CATAATAATAACATATTTTTTATCATTTTAAAAAAAAAAATTAATAAAATTACTTCAAAAAATTACATAATAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26937:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TATTATATTTAATTAATTTAATCAAAAATTAATTTATAAAACATATAAAATTAAAAAAAAAAAAATTTAAAATTAAATATAATTAATAATAAATTTTTAAATAATATAATATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26937:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 TTTAAAAATTTATTATTAATTATATTTAATTTTAAATTTTTTTTTTTTTAATTTTATATGTTTTATAAATTAATTTTTGATTAAATTAATTAAATATAATATATTGATAAAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28546:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTTTTAAAATAATTTTATTAATTTTTTTTTTTAAAACAATAAAAAATATATTATTATTATAAAAAAAAAAAATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28546:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 TATAATAATAATATATTTTTTATTGTTTTAAAAAAAAAAATTAATAAAATTATTTTAAAAAATTATGTAATAAAGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28546:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTTTTAAAATAATTTTATTAATTTTTTTTTTTAAAACAATAAAAAATATATTATTATTATAAAAAAAAAAAATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28546:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 TATAATAATAATATATTTTTTATTGTTTTAAAAAAAAAAATTAATAAAATTATTTTAAAAAATTATGTAATAAAGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26937:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TATTATATTTAATTAATTTAATCAAAAATTAATTTATAAAACATATAAAATTAAAAAAAAAAAAATTTAAAATTAAATATAATTAATAATAAATTTTTAAATAATATAATATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26937:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 TTTAAAAATTTATTATTAATTATATTTAATTTTAAATTTTTTTTTTTTTAATTTTATATGTTTTATAAATTAATTTTTGATTAAATTAATTAAATATAATATATTGATAAAAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26937:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TATTGTATTTAATTAATTTAATTGAAAATTAATTTGTAAAATGTGTAAAATTAAAAAGAAAAAAATTTAAAATTAAATATGATTGGTAGTAGATTTTTAAATAGTATAGTATTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26937:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 TTTAAAAATCTACTACCAATCATATTTAATTTTAAATTTTTTTCTTTTTAATTTTACACATTTTACAAATTAATTTTCAATTAAATTAATTAAATACAATATACCAATAAAAAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28546:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTTTTGAAGTAATTTTATTAATTTTTTTTTTTAAAATGATAAAAAATATGTTATTATTATGGAAGAGAAAAATGAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28546:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 CATAATAATAACATATTTTTTATCATTTTAAAAAAAAAAATTAATAAAATTACTTCAAAAAATTACATAATAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Created C -> T as well as G -> A converted versions of the FastQ file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (51511463 sequences in total) Input files are CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ATGTTAGTTATTATTATATTTGGTGAGTAGTTAGGTGTGGTGATGTGGTGTTTTTGATGATTTTGAAAATATTAGTTATGTTGGATAGGGTGTGTGTGTTGAAGGTTTTAGTTTGTTTTTGTTTGTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AACTAAAACCTTCAACACACACACCCTATCCAACATAACTAATATTTTCAAAATCATCAAAAACACCACATCACCACACCTAACTACTCACCAAATATAATAATAACTAACATTCCCATATACCAACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ATATTAATTATTATTATATTTAATAAATAATTAAATATAATAATATAATATTTTTAATAATTTTAAAAATATTAATTATATCAAATAAAATATATATATTAAAAACTTTAATTTATTTTTATTTATTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AATTAAAGTTTTTAATATATATATTTTATTTGATATAATTAATATTTTTAAAATTATTAAAAATATTATATTATTATATTTAATTATTTATTAAATATAATAATAATTAATATTTTTATATATTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ATATTAATTATTATTATATTTAATAAATAATTAAATATAATAATATAATATTTTTAATAATTTTAAAAATATTAATTATATCAAATAAAATATATATATTAAAAACTTTAATTTATTTTTATTTATTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AATTAAAGTTTTTAATATATATATTTTATTTGATATAATTAATATTTTTAAAATTATTAAAAATATTATATTATTATATTTAATTATTTATTAAATATAATAATAATTAATATTTTTATATATTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ATGTTAGTTATTATTATATTTGGTGAGTAGTTAGGTGTGGTGATGTGGTGTTTTTGATGATTTTGAAAATATTAGTTATGTTGGATAGGGTGTGTGTGTTGAAGGTTTTAGTTTGTTTTTGTTTGTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AACTAAAACCTTCAACACACACACCCTATCCAACATAACTAATATTTTCAAAATCATCAAAAACACCACATCACCACACCTAACTACTCACCAAATATAATAATAACTAACATTCCCATATACCAACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (51511462 sequences in total) Input files are CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27751:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTGTGATTAGAATGAAGTGAATGAAATTTGTTGTTAGTGGGTTTTGGTTTTTTGGGAAAATGGGATTATTATGATGGAATAGGTTAATGTAGGAATGTGTGTTTGTTGGTAGAATTATTATTTTTGTTATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27751:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 CAATCAACTCACTAACATTTAACAATCCAACAATAACAAATACTTCTTCCCAACACCATACAACAAACTACCCAAATAATAACAAAAATAATAATTCTACCAACAAACACACATTCCTACATTAACCTATTCCAT FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27751:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTATAATTAAAATAAAATAAATAAAATTCATTATTAATAAATTTTAATTTTTTAAAAAAATAAAATTATTATAATAAAATAAATTAATATAAAAATATATATTTATTAATAAAATTATTATTTTTATTATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27751:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 TAATTAATTTGTTAATATTTAATAATTTAATAATAATAAATGTTTTTTTTTAATATTATATAATAAATTATTTAAATAATAATAAAAATAATAATTTTATTAATAAATATATATTTTTATATTAATTTATTTTAT FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27751:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTATAATTAAAATAAAATAAATAAAATTCATTATTAATAAATTTTAATTTTTTAAAAAAATAAAATTATTATAATAAAATAAATTAATATAAAAATATATATTTATTAATAAAATTATTATTTTTATTATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27751:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 TAATTAATTTGTTAATATTTAATAATTTAATAATAATAAATGTTTTTTTTTAATATTATATAATAAATTATTTAAATAATAATAAAAATAATAATTTTATTAATAAATATATATTTTTATATTAATTTATTTTAT FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_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 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27751:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TTGTGATTAGAATGAAGTGAATGAAATTTGTTGTTAGTGGGTTTTGGTTTTTTGGGAAAATGGGATTATTATGATGGAATAGGTTAATGTAGGAATGTGTGTTTGTTGGTAGAATTATTATTTTTGTTATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27751:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 CAATCAACTCACTAACATTTAACAATCCAACAATAACAAATACTTCTTCCCAACACCATACAACAAACTACCCAAATAATAACAAAAATAATAATTCTACCAACAAACACACATTCCTACATTAACCTATTCCAT FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.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 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1339:23357:2738_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 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 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1527:11180:11960_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1548:20735:5525_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1550:4472:35383_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1548:25563:5243_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1548:32009:18474_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17176 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1677:20103:13260_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17188 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2203:22191:20071_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17141 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2365:6949:4726_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2367:17589:10974_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17194 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2664:30544:6918_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17163 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1147:23375:30514_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17193 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1147:23330:30530_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17193 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1229:13557:36338_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1248:27208:31234_1:N:0:TTGGACTC+CTGATTCC NC_007175.2 17178 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1276:9986:36542_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17194 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1432:32045:1908_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17176 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1515:25654:11224_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:19569:11303_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:19506:14857_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1612:18819:17206_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1627:3188:2879_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1648:28483:31657_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1672:8585:31579_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1672:8567:31548_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 1 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1673:8386:35399_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 1 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2115:9588:20979_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2118:6090:21652_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2115:9625:20917_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2171:14389:20400_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17178 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2218:2220:24659_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 2 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2218:2889:23343_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2217:5656:23907_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 2 Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2243:30400:33004_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2251:8793:5071_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 2 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2337:16378:5901_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17189 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2465:2980:15734_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2464:29188:15687_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2433:4345:6136_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 65668305 Processed 46000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2528:2148:21809_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17188 Processed 49000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2561:26847:2143_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2578:14534:33426_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17176 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 47319832 (91.86%) aligned concordantly 0 times 1951665 (3.79%) aligned concordantly exactly 1 time 2239965 (4.35%) aligned concordantly >1 times 8.14% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 48618230 (94.38%) aligned concordantly 0 times 1325104 (2.57%) aligned concordantly exactly 1 time 1568128 (3.04%) aligned concordantly >1 times 5.62% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 47324289 (91.87%) aligned concordantly 0 times 1947778 (3.78%) aligned concordantly exactly 1 time 2239395 (4.35%) aligned concordantly >1 times 8.13% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 48618727 (94.38%) aligned concordantly 0 times 1325013 (2.57%) aligned concordantly exactly 1 time 1567722 (3.04%) aligned concordantly >1 times 5.62% overall alignment rate Processed 51511462 sequences in total Successfully deleted the temporary files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 51511462 Final Cytosine Methylation Report ================================= Total number of C's analysed: 140146912 Total methylated C's in CpG context: 3314654 Total methylated C's in CHG context: 1100841 Total methylated C's in CHH context: 7204110 Total methylated C's in Unknown context: 145852 Total unmethylated C's in CpG context: 12743551 Total unmethylated C's in CHG context: 23147395 Total unmethylated C's in CHH context: 92636361 Total unmethylated C's in Unknown context: 773308 C methylated in CpG context: 20.6% C methylated in CHG context: 4.5% C methylated in CHH context: 7.2% C methylated in Unknown context (CN or CHN): 15.9% Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 49000000 sequence pairs so far 51511463 reads; of these: 51511463 (100.00%) were paired; of these: 48621603 (94.39%) aligned concordantly 0 times 1325962 (2.57%) aligned concordantly exactly 1 time 1563898 (3.04%) aligned concordantly >1 times 5.61% overall alignment rate 51511463 reads; of these: 51511463 (100.00%) were paired; of these: 47323864 (91.87%) aligned concordantly 0 times 1948897 (3.78%) aligned concordantly exactly 1 time 2238702 (4.35%) aligned concordantly >1 times 8.13% overall alignment rate 51511463 reads; of these: 51511463 (100.00%) were paired; of these: 47317422 (91.86%) aligned concordantly 0 times 1951666 (3.79%) aligned concordantly exactly 1 time 2242375 (4.35%) aligned concordantly >1 times 8.14% overall alignment rate 51511463 reads; of these: 51511463 (100.00%) were paired; of these: 48623611 (94.39%) aligned concordantly 0 times 1323284 (2.57%) aligned concordantly exactly 1 time 1564568 (3.04%) aligned concordantly >1 times 5.61% overall alignment rate Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2660:26883:1423_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 3 Processed 51511463 sequences in total Successfully deleted the temporary files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 51511463 Final Cytosine Methylation Report ================================= Total number of C's analysed: 140194439 Total methylated C's in CpG context: 3308473 Total methylated C's in CHG context: 1100676 Total methylated C's in CHH context: 7196919 Total methylated C's in Unknown context: 145910 Total unmethylated C's in CpG context: 12754235 Total unmethylated C's in CHG context: 23160856 Total unmethylated C's in CHH context: 92673280 Total unmethylated C's in Unknown context: 771471 C methylated in CpG context: 20.6% C methylated in CHG context: 4.5% C methylated in CHH context: 7.2% C methylated in Unknown context (CN or CHN): 15.9% Processed 51000000 sequence pairs so far 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 47320872 (91.86%) aligned concordantly 0 times 1948746 (3.78%) aligned concordantly exactly 1 time 2241844 (4.35%) aligned concordantly >1 times 8.14% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 48623441 (94.39%) aligned concordantly 0 times 1321150 (2.56%) aligned concordantly exactly 1 time 1566871 (3.04%) aligned concordantly >1 times 5.61% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 48620809 (94.39%) aligned concordantly 0 times 1324361 (2.57%) aligned concordantly exactly 1 time 1566292 (3.04%) aligned concordantly >1 times 5.61% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 47322603 (91.87%) aligned concordantly 0 times 1947355 (3.78%) aligned concordantly exactly 1 time 2241504 (4.35%) aligned concordantly >1 times 8.13% overall alignment rate Processed 51511462 sequences in total Successfully deleted the temporary files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 51511462 Final Cytosine Methylation Report ================================= Total number of C's analysed: 140154429 Total methylated C's in CpG context: 3312369 Total methylated C's in CHG context: 1102180 Total methylated C's in CHH context: 7221542 Total methylated C's in Unknown context: 145773 Total unmethylated C's in CpG context: 12741357 Total unmethylated C's in CHG context: 23134074 Total unmethylated C's in CHH context: 92642907 Total unmethylated C's in Unknown context: 771513 C methylated in CpG context: 20.6% C methylated in CHG context: 4.5% C methylated in CHH context: 7.2% C methylated in Unknown context (CN or CHN): 15.9% Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 48624117 (94.39%) aligned concordantly 0 times 1319653 (2.56%) aligned concordantly exactly 1 time 1567692 (3.04%) aligned concordantly >1 times 5.61% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 47318464 (91.86%) aligned concordantly 0 times 1950001 (3.79%) aligned concordantly exactly 1 time 2242997 (4.35%) aligned concordantly >1 times 8.14% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 48620064 (94.39%) aligned concordantly 0 times 1323486 (2.57%) aligned concordantly exactly 1 time 1567912 (3.04%) aligned concordantly >1 times 5.61% overall alignment rate 51511462 reads; of these: 51511462 (100.00%) were paired; of these: 47318431 (91.86%) aligned concordantly 0 times 1950117 (3.79%) aligned concordantly exactly 1 time 2242914 (4.35%) aligned concordantly >1 times 8.14% overall alignment rate Processed 51511462 sequences in total Successfully deleted the temporary files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 51511462 Final Cytosine Methylation Report ================================= Total number of C's analysed: 140167208 Total methylated C's in CpG context: 3310099 Total methylated C's in CHG context: 1098460 Total methylated C's in CHH context: 7229250 Total methylated C's in Unknown context: 145626 Total unmethylated C's in CpG context: 12749595 Total unmethylated C's in CHG context: 23127447 Total unmethylated C's in CHH context: 92652357 Total unmethylated C's in Unknown context: 773109 C methylated in CpG context: 20.6% C methylated in CHG context: 4.5% C methylated in CHH context: 7.2% C methylated in Unknown context (CN or CHN): 15.9% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt into >>> /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.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: 206045849 Final Cytosine Methylation Report ================================= Total number of C's analysed: 560662988 Total methylated C's in CpG context: 13245595 Total methylated C's in CHG context: 4402157 Total methylated C's in CHH context: 28851821 Total methylated C's in Unknown context: 583161 Total unmethylated C's in CpG context: 50988738 Total unmethylated C's in CHG context: 92569772 Total unmethylated C's in CHH context: 370604905 Total unmethylated C's in Unknown context: 3089401 C methylated in CpG context: 20.6% C methylated in CHG context: 4.5% C methylated in CHH context: 7.2% C methylated in Unknown context (CN or CHN): 15.9% Deleting temporary report files... Bismark completed in 0d 10h 47m 23s ==================== Bismark run complete ====================