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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 50460 and offset 4 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF01-CM02-Larvae_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/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 50460 and offset 4 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF01-CM02-Larvae_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/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 33350810) Using the subset file >CF01-CM02-Larvae_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/CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz (33350810 sequences in total) Writing a C -> T converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF01-CM02-Larvae_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 CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz (33350810 sequences in total) Writing a C -> T converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF01-CM02-Larvae_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 CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz (33350810 sequences in total) Writing a C -> T converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF01-CM02-Larvae_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 CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz (33350810 sequences in total) Writing a C -> T converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF01-CM02-Larvae_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 CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz (33350810 sequences in total) Input files are CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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 CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31494:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 TATTAAAAATATTATAATTTAAATAAATATATTTTTAAAAAATTATATAATATTTTTAAATAAAATAAAAATTAAAAATAAAATTTATATATTTATAATATTTATGAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFF:FFFFFFFFFFFFFFFFFF:FFFF:F:F:FFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31494:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 AAATATATAAATTTTATTTTTAATTTTTATTTTATTTAAAAATATTATATAATTTTTTAAAAATATATTTATTTAAATTATAATATTTTTAATAATATTAAAAATATAT FFFF:FFFFFFFFFF:FFF:FFFFFF::FFF:FFFFFFF:FFF,:FFFFF:FFFFFFFFFFFFFFFFF,FFFFFFF:FFFF:FF,FFFFFFFFF:FFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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)) Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz (33350810 sequences in total) Input files are CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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 CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:31494:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 CACCAAAAATATTATAATTTAAATAAACATATCTCCAAAAAACTATATAATATTTCTAAATAAAATAAAAACCAAAAATAAAACCTATATATCCATAACACTCATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFF:FFFFFFFFFFFFFFFFFF:FFFF:F:F:FFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31494:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 GGATATATAGGTTTTATTTTTGGTTTTTATTTTATTTAGAAATATTATATAGTTTTTTGGAGATATGTTTATTTAAATTATAATATTTTTGGTGGTATTAAGGGTGTGT FFFF:FFFFFFFFFF:FFF:FFFFFF::FFF:FFFFFFF:FFF,:FFFFF:FFFFFFFFFFFFFFFFF,FFFFFFF:FFFF:FF,FFFFFFFFF:FFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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)) Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz (33350810 sequences in total) Input files are CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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 CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ATTAATAAATTTTTTTATTATAAAAATATTATTTTTAATAAATAATTTAAAATAATTTATTAAAATATAATAATTTTTATTATAAAAAAAATTATATTTTTAATAATTTAAAATTTATTAATATAATATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 ATTATTAAATTATTTTATTTTATAATTTATAATATTATATTAATAAATTTTAAATTATTAAAAATATAATTTTTTTTATAATAAAAATTATTATATTTTAATAAATTATTTTAAAATATTTATTAAAAATAATAT FFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:31494:1047_1:N:0:GCACGGAC+TGCGAGAC/1 83 NC_035784.1_CT_converted 75328634 40 109M = 75328649 124 ATTTATGAGTGTTATGGATATATAGGTTTTATTTTTGGTTTTTATTTTATTTAGAAATATTATATAGTTTTTTGGAGATATGTTTATTTAAATTATAATATTTTTGGTG FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FFF:F:F:FFFF:FFFFFFFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1G1G52G52 YS:i:-12 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:31494:1047_2:N:0:GCACGGAC+TGCGAGAC/2 163 NC_035784.1_CT_converted 75328649 40 109M = 75328634 -124 GGATATATAGGTTTTATTTTTGGTTTTTATTTTATTTAGAAATATTATATAGTTTTTTGGAGATATGTTTATTTAAATTATAATATTTTTGGTGGTATTAAGGGTGTGT FFFF:FFFFFFFFFF:FFF:FFFFFF::FFF:FFFFFFF:FFF,:FFFFF:FFFFFFFFFFFFFFFFF,FFFFFFF:FFFF:FF,FFFFFFFFF:FFFF:FFFFFFFFF AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:41G62G4 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:28908:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 TATATTTTGTTGATTTAGAGATTTATAGTGTATGTATATAGTTATTTTTGTTTTTTATGAAATTTAGTTAGAATAAAATTAAAGGTGGATTTAGTGTTGGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28908:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 CCACCTTTAATTTTATTCTAACTAAATTTCATAAAAAACAAAAATAACTATATACATACACTATAAATCTCTAAATCAACAAAATATACCAACCTACTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ATTAATAAATTTCCTCACTATAAAAATACTATCTCCAACAAACAATCCAAAACAATTTACCAAAATACAATAATTCCTATTATAAAAAAAATTATACTCTCAATAATCCAAAATTTATCAACATAACACCACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 ATTGTTGAATTGTTTTGTTTTATAGTTTGTGGTGTTATGTTGATAAATTTTGGATTATTGAGAGTATAATTTTTTTTATAATAGGAATTATTGTATTTTGGTAAATTGTTTTGGAGTGTTTGTTGGAGATAGTAT FFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:31494:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 TATTAAAAATATTATAATTTAAATAAATATATTTTTAAAAAATTATATAATATTTTTAAATAAAATAAAAATTAAAAATAAAATTTATATATTTATAATATTTATGAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFF:FFFFFFFFFFFFFFFFFF:FFFF:F:F:FFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31494:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 AAATATATAAATTTTATTTTTAATTTTTATTTTATTTAAAAATATTATATAATTTTTTAAAAATATATTTATTTAAATTATAATATTTTTAATAATATTAAAAATATAT FFFF:FFFFFFFFFF:FFF:FFFFFF::FFF:FFFFFFF:FFF,:FFFFF:FFFFFFFFFFFFFFFFF,FFFFFFF:FFFF:FF,FFFFFFFFF:FFFF:FFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28908:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 TATATTTTATTAATTTAAAAATTTATAATATATATATATAATTATTTTTATTTTTTATAAAATTTAATTAAAATAAAATTAAAAATAAATTTAATATTAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28908:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTATTTTTAATTTTATTTTAATTAAATTTTATAAAAAATAAAAATAATTATATATATATATTATAAATTTTTAAATTAATAAAATATATTGATTTATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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)) Reading in the sequence files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ATTAATAAATTTCCTCACTATAAAAATACTATCTCCAACAAACAATCCAAAACAATTTACCAAAATACAATAATTCCTATTATAAAAAAAATTATACTCTCAATAATCCAAAATTTATCAACATAACACCACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 ATTGTTGAATTGTTTTGTTTTATAGTTTGTGGTGTTATGTTGATAAATTTTGGATTATTGAGAGTATAATTTTTTTTATAATAGGAATTATTGTATTTTGGTAAATTGTTTTGGAGTGTTTGTTGGAGATAGTAT FFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:28908:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 TATATTTTATTAATTTAAAAATTTATAATATATATATATAATTATTTTTATTTTTTATAAAATTTAATTAAAATAAAATTAAAAATAAATTTAATATTAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28908:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTATTTTTAATTTTATTTTAATTAAATTTTATAAAAAATAAAAATAATTATATATATATATTATAAATTTTTAAATTAATAAAATATATTGATTTATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ATTAATAAATTTTTTTATTATAAAAATATTATTTTTAATAAATAATTTAAAATAATTTATTAAAATATAATAATTTTTATTATAAAAAAAATTATATTTTTAATAATTTAAAATTTATTAATATAATATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 ATTATTAAATTATTTTATTTTATAATTTATAATATTATATTAATAAATTTTAAATTATTAAAAATATAATTTTTTTTATAATAAAAATTATTATATTTTAATAAATTATTTTAAAATATTTATTAAAAATAATAT FFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28908:1047_1:N:0:GCACGGAC+TGCGAGAC/1 83 NC_035782.1_GA_converted 55990157 0 47M1D44M2D12M = 55990172 108 ACACCAACACTAAATCCACCTTTAATTTTATTCTAACTAAATTTCATAAAAAACAAAAATAACTATATACATACACTATAAATCTCTAAATCAACAAAATATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-43 XN:i:0 XM:i:4 XO:i:2 XG:i:3 NM:i:7 MD:Z:33A13^A41T2^AC5T1C4 YS:i:-58 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:28908:1047_2:N:0:GCACGGAC+TGCGAGAC/2 163 NC_035782.1_GA_converted 55990172 0 32M1D40M11I20M = 55990157 -108 CCACCTTTAATTTTATTCTAACTAAATTTCATAAAAAACAAAAATAACTATATACATACACTATAAATCTCTAAATCAACAAAATATACCAACCTACTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F AS:i:-58 XN:i:0 XM:i:2 XO:i:2 XG:i:12 NM:i:14 MD:Z:18A13^A50A9 YS:i:-43 YT:Z:CP >>> Writing bisulfite mapping results to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz (33350810 sequences in total) Input files are CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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 CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 AATAAAATATATTATATATTGTAAATTTATAATTAAAAATTATAAAATTTAAATTTTTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTATAATTTTTAATTATAAATTTACAATATATAATATATTTTATTTTATATTTTTATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 99 NC_035786.1_GA_converted 38378366 0 60M = 38378351 -75 AATAAAATACATCATATATCATAAATTTATAATTAAAAATTATAAAATTTAAATCTTTAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-12 XS:i:-20 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:36T0C22 YS:i:-12 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 147 NC_035786.1_GA_converted 38378351 0 60M = 38378366 75 AATACAAAAATACAAAATAAAATACATCATATATCATAAATTTATAATTAAAAATTATAA FF:FFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-12 XS:i:-18 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:51T0C7 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 83 NC_035789.1_CT_converted 2210749 30 60M = 2210764 75 GTAAAGATTTAAATTTTATAATTTTTAATTATAAATTTATGATATATGATGTATTTTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:60 YS:i:0 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 163 NC_035789.1_CT_converted 2210764 30 60M = 2210749 -75 TTATAATTTTTAATTATAAATTTATGATATATGATGTATTTTATTTTGTATTTTTGTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFF:FF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:60 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 AATAAAATATATTATATATTGTAAATTTATAATTAAAAATTATAAAATTTAAATTTTTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTATAATTTTTAATTATAAATTTACAATATATAATATATTTTATTTTATATTTTTATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFF:FF YT:Z:UP >>> Writing bisulfite mapping results to CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1116:7274:6198_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1116:7292:4977_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:10809:29700_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1137:29396:17989_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:11107:29371_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:11225:30138_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1163:11921:2566_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1321:3558:21402_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1326:17589:19805_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1263:25852:3427_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 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 GWNJ-1012:512:GW210315000:4:1321:3676:21856_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1341:14109:27336_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1344:28772:19946_1:N:0:ACACGGAC+TGCGAGAC NC_035780.1 2 Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1420:3685:25911_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1420:4282:26694_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1543:16016:18114_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1560:23222:24236_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:8070:12524_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:11577:15217_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1476:16767:13213_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1560:21414:24017_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1610:9634:21120_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1610:9986:27336_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1669:18548:7780_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:9227:11083_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 8000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2213:20980:17754_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2272:29975:21465_1:N:0:GCACAGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2305:17002:1063_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2320:3459:18756_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 17179 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2328:11686:35603_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2354:17047:24533_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2420:1271:31939_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:23330:19006_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:23393:21684_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2377:2917:14622_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2213:20844:17707_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2530:27326:19100_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2531:25247:4319_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 16000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2512:23764:30405_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2661:3323:5462_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2666:5267:22889_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1237:18719:33191_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1374:14977:14465_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1374:16269:22373_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1375:17806:25285_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 22000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2622:26295:3098_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 65668305 Processed 17000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1519:15447:34726_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1142:13765:17190_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1607:10113:7952_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 17162 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1108:9109:27258_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1133:15157:17973_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1638:24975:35728_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1248:28266:11804_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1154:6903:22310_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2107:10926:23202_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2213:10493:35822_1:N:0:ACACGGAC+TGCGAGAC NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1355:19171:25488_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 30000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1433:5909:29168_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2603:1118:5807_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2253:30951:8782_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 23000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2572:18593:20447_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27439657 (82.28%) aligned concordantly 0 times 2638302 (7.91%) aligned concordantly exactly 1 time 3272851 (9.81%) aligned concordantly >1 times 17.72% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27760219 (83.24%) aligned concordantly 0 times 2509945 (7.53%) aligned concordantly exactly 1 time 3080646 (9.24%) aligned concordantly >1 times 16.76% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27436857 (82.27%) aligned concordantly 0 times 2642646 (7.92%) aligned concordantly exactly 1 time 3271307 (9.81%) aligned concordantly >1 times 17.73% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27756125 (83.22%) aligned concordantly 0 times 2511296 (7.53%) aligned concordantly exactly 1 time 3083389 (9.25%) aligned concordantly >1 times 16.78% overall alignment rate Processed 33350810 sequences in total Successfully deleted the temporary files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33350810 Final Cytosine Methylation Report ================================= Total number of C's analysed: 377996480 Total methylated C's in CpG context: 10712877 Total methylated C's in CHG context: 1568527 Total methylated C's in CHH context: 6783945 Total methylated C's in Unknown context: 280453 Total unmethylated C's in CpG context: 47553335 Total unmethylated C's in CHG context: 80054419 Total unmethylated C's in CHH context: 231323377 Total unmethylated C's in Unknown context: 1444504 C methylated in CpG context: 18.4% C methylated in CHG context: 1.9% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 16.3% Processed 29000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 33000000 sequence pairs so far 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27436782 (82.27%) aligned concordantly 0 times 2640330 (7.92%) aligned concordantly exactly 1 time 3273698 (9.82%) aligned concordantly >1 times 17.73% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27760168 (83.24%) aligned concordantly 0 times 2510235 (7.53%) aligned concordantly exactly 1 time 3080407 (9.24%) aligned concordantly >1 times 16.76% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27439753 (82.28%) aligned concordantly 0 times 2637353 (7.91%) aligned concordantly exactly 1 time 3273704 (9.82%) aligned concordantly >1 times 17.72% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27757854 (83.23%) aligned concordantly 0 times 2510199 (7.53%) aligned concordantly exactly 1 time 3082757 (9.24%) aligned concordantly >1 times 16.77% overall alignment rate Processed 33350810 sequences in total Successfully deleted the temporary files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33350810 Final Cytosine Methylation Report ================================= Total number of C's analysed: 377969145 Total methylated C's in CpG context: 10734297 Total methylated C's in CHG context: 1568837 Total methylated C's in CHH context: 6800945 Total methylated C's in Unknown context: 280635 Total unmethylated C's in CpG context: 47549277 Total unmethylated C's in CHG context: 80051614 Total unmethylated C's in CHH context: 231264175 Total unmethylated C's in Unknown context: 1443122 C methylated in CpG context: 18.4% C methylated in CHG context: 1.9% C methylated in CHH context: 2.9% C methylated in Unknown context (CN or CHN): 16.3% Now waiting for all child processes to complete Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2426:26359:31798_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 17176 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2448:13367:2534_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 25000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 33000000 sequence pairs so far 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27758351 (83.23%) aligned concordantly 0 times 2509616 (7.52%) aligned concordantly exactly 1 time 3082843 (9.24%) aligned concordantly >1 times 16.77% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27437955 (82.27%) aligned concordantly 0 times 2638659 (7.91%) aligned concordantly exactly 1 time 3274196 (9.82%) aligned concordantly >1 times 17.73% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27436371 (82.27%) aligned concordantly 0 times 2641663 (7.92%) aligned concordantly exactly 1 time 3272776 (9.81%) aligned concordantly >1 times 17.73% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27753296 (83.22%) aligned concordantly 0 times 2510987 (7.53%) aligned concordantly exactly 1 time 3086527 (9.25%) aligned concordantly >1 times 16.78% overall alignment rate Processed 33350810 sequences in total Successfully deleted the temporary files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33350810 Final Cytosine Methylation Report ================================= Total number of C's analysed: 378067707 Total methylated C's in CpG context: 10735354 Total methylated C's in CHG context: 1569440 Total methylated C's in CHH context: 6767151 Total methylated C's in Unknown context: 280002 Total unmethylated C's in CpG context: 47578239 Total unmethylated C's in CHG context: 80052645 Total unmethylated C's in CHH context: 231364878 Total unmethylated C's in Unknown context: 1443645 C methylated in CpG context: 18.4% C methylated in CHG context: 1.9% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 16.2% Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:23963:29904_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:24080:29982_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2447:12726:28729_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2632:10068:28260_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 33000000 sequence pairs so far 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27435292 (82.26%) aligned concordantly 0 times 2642478 (7.92%) aligned concordantly exactly 1 time 3273040 (9.81%) aligned concordantly >1 times 17.74% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27762484 (83.24%) aligned concordantly 0 times 2506359 (7.52%) aligned concordantly exactly 1 time 3081967 (9.24%) aligned concordantly >1 times 16.76% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27439078 (82.27%) aligned concordantly 0 times 2638650 (7.91%) aligned concordantly exactly 1 time 3273082 (9.81%) aligned concordantly >1 times 17.73% overall alignment rate 33350810 reads; of these: 33350810 (100.00%) were paired; of these: 27753549 (83.22%) aligned concordantly 0 times 2509867 (7.53%) aligned concordantly exactly 1 time 3087394 (9.26%) aligned concordantly >1 times 16.78% overall alignment rate Processed 33350810 sequences in total Successfully deleted the temporary files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33350810 Final Cytosine Methylation Report ================================= Total number of C's analysed: 377955173 Total methylated C's in CpG context: 10719110 Total methylated C's in CHG context: 1568586 Total methylated C's in CHH context: 6787208 Total methylated C's in Unknown context: 281049 Total unmethylated C's in CpG context: 47555899 Total unmethylated C's in CHG context: 80043238 Total unmethylated C's in CHH context: 231281132 Total unmethylated C's in Unknown context: 1445235 C methylated in CpG context: 18.4% C methylated in CHG context: 1.9% C methylated in CHH context: 2.9% C methylated in Unknown context (CN or CHN): 16.3% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF01-CM02-Larvae_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/CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> CF01-CM02-Larvae_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: 133403240 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1511988505 Total methylated C's in CpG context: 42901638 Total methylated C's in CHG context: 6275390 Total methylated C's in CHH context: 27139249 Total methylated C's in Unknown context: 1122139 Total unmethylated C's in CpG context: 190236750 Total unmethylated C's in CHG context: 320201916 Total unmethylated C's in CHH context: 925233562 Total unmethylated C's in Unknown context: 5776506 C methylated in CpG context: 18.4% C methylated in CHG context: 1.9% C methylated in CHH context: 2.8% C methylated in Unknown context (CN or CHN): 16.3% Deleting temporary report files... Bismark completed in 0d 7h 56m 27s ==================== Bismark run complete ====================