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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 28070861) Using the subset file >CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 28070862) Using the subset file >CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 50475 and offset 4 (sequences written out: 28070861) Using the subset file >CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 28070861) Using the subset file >CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 28070861) Using the subset file >CF06-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/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF06-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/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 28070862) Using the subset file >CF06-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/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF06-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/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 50475 and offset 4 (sequences written out: 28070861) Using the subset file >CF06-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/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF06-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/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 28070861) Using the subset file >CF06-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/CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz (28070861 sequences in total) Writing a C -> T converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF06-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 CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz (28070861 sequences in total) Writing a C -> T converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF06-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 CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz (28070862 sequences in total) Writing a C -> T converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF06-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 CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz (28070861 sequences in total) Writing a C -> T converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF06-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 CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF06-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 CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz (28070861 sequences in total) Input files are CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-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)) Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz (28070862 sequences in total) Input files are CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-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:GW210315000:4:1101:31259:1047_1:N:0:ATGTAAGT+CAGAGAGT/1 77 * 0 0 * * 0 0 TTTTAATTTATTATATGTTAATTTTTAATTAATATTTATTTTTTGAATATTAATTTTTAAAATGATTTTTTTTATATTTTTTATTTTTTAAGAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31259:1047_2:N:0:ATGTAAGT+CAGAGAGT/2 141 * 0 0 * * 0 0 AAAAAATATAAAAAAAATCATTTTAAAAATTAATATTCAAAAAATAAATATTAATTAAAAATTAACATATAATAAATTAAAAAAATTAATAAATATA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:FFFFFF:FFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF06-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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 ATATAATATAATATATATATATATTAAATTTTATATATATTATTTTAATTATTTTTAAATATTTTTATAAGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TAAAAATAATTAAAATAATATATATAAAATTTAATATATATATATATTATATTATATTAATATTTTAATATA FFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-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)) Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz (28070861 sequences in total) Input files are CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-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:GW210315000:4:1101:31259:1047_1:N:0:ATGTAAGT+CAGAGAGT/1 99 NC_035783.1_GA_converted 9549297 40 89M2I6M = 9549282 -110 CTTCAATTCATTATACACTAATCTCCAATCAATACCCATCTTCCAAATATTAACCTTCAAAACAATTTCTTCCATATTCTTTATTCCTTAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-29 XN:i:0 XM:i:3 XO:i:1 XG:i:2 NM:i:5 MD:Z:89C0C2C1 YS:i:0 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:31259:1047_2:N:0:ATGTAAGT+CAGAGAGT/2 147 NC_035783.1_GA_converted 9549282 40 97M = 9549297 110 CATATCTATCAACCTCTTCAATTCATTATACACTAATCTCCAATCAATACCCATCTTCCAAATATTAACCTTCAAAACAATTTCTTCCATATTCTTT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFF:FFFFFF:FF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:97 YS:i:-29 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF06-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 CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz (28070861 sequences in total) Input files are CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-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 CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-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:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 ACATAATACAATACATATACACACTAAACCCTATATACATCATTTTAATTATTCCCAAACACTCCCACAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TGGGAATAATTAAAATGATGTATATAGGGTTTAGTGTGTATATGTATTGTATTATGTTAATGTTTTGGTGTA FFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-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:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 ACATAATACAATACATATACACACTAAACCCTATATACATCATTTTAATTATTCCCAAACACTCCCACAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TGGGAATAATTAAAATGATGTATATAGGGTTTAGTGTGTATATGTATTGTATTATGTTAATGTTTTGGTGTA FFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-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:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TGATAAGTAAATGATAAGTTAATGTGTGAAATGGTTTTGATAAA ::FFFFFFFFF,FFFFF:FFFFF,F:FFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TCACACATTAACTTATCATTTACTTATCATCATACTTATCACCT ,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-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:GW210315000:4:1101:31259:1047_1:N:0:ATGTAAGT+CAGAGAGT/1 77 * 0 0 * * 0 0 CTTCAATTCATTATACACTAATCTCCAATCAATACCCATCTTCCAAATATTAACCTTCAAAACAATTTCTTCCATATTCTTTATTCCTTAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31259:1047_2:N:0:ATGTAAGT+CAGAGAGT/2 141 * 0 0 * * 0 0 AAAGAATATGGAAGAAATTGTTTTGAAGGTTAATATTTGGAAGATGGGTATTGATTGGAGATTAGTGTATAATGAATTGAAGAGGTTGATAGATATG FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:FFFFFF:FFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-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:GW210315000:4:1101:29505:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TTTTTTTTTTTTTTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTATTTTTTTTTTTATATTTAATATTTATTTTTTTTATTTTTTATTTTTTTTTATTTTATTTTATTTTAAAATTTATAG FFFF:FFFFFFFFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF,F:F,::FF,FFF:F::FFFF:,F:,F,:::F:F::F:,:F,F:FF:FFF:F:F:F:F::F:F,F,:F,:FF:F, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29505:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TAAAATAAAATAAAAAAAAATAAAAAATAAAAAAAATAAATATTAAATATAAAAAAAAAAATAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAAAAAAATTTAAAAAAAATA FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF06-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:GW210315000:4:1101:29505:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 CCTCTCCTCCTCTCTAATCCCTTTTCTTCCCCTCTCTTCTCTCCTATCCACTCTCTTCCTTATATCTAATACTTATTCCTTTCATCCCCTATTCTCTTCTATCCTACCCTACCCTAAAATCCATAA FFFF:FFFFFFFFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF,F:F,::FF,FFF:F::FFFF:,F:,F,:::F:F::F:,:F,F:FF:FFF:F:F:F:F::F:F,F,:F,:FF:F, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29505:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TAGGGTAGGATAGAAGAGAATAGGGGATGAAAGGAATAAGTATTAGATATAAGGAAGAGAGTGGATAGGAGAGAAGAGAGGGGAAGAAAAGGGATTAGAGAGGAGGAGAGGAGTTTAGAAGAGGTA FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF06-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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31259:1047_1:N:0:ATGTAAGT+CAGAGAGT/1 77 * 0 0 * * 0 0 TTTTAATTTATTATATGTTAATTTTTAATTAATATTTATTTTTTGAATATTAATTTTTAAAATGATTTTTTTTATATTTTTTATTTTTTAAGAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31259:1047_2:N:0:ATGTAAGT+CAGAGAGT/2 141 * 0 0 * * 0 0 AAAAAATATAAAAAAAATCATTTTAAAAATTAATATTCAAAAAATAAATATTAATTAAAAATTAACATATAATAAATTAAAAAAATTAATAAATATA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:FFFFFF:FFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 ATATAATATAATATATATATATATTAAATTTTATATATATTATTTTAATTATTTTTAAATATTTTTATAAGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TAAAAATAATTAAAATAATATATATAAAATTTAATATATATATATATTATATTATATTAATATTTTAATATA FFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TAATAAATAAATAATAAATTAATATACAAAATAATTTTAATAAA ::FFFFFFFFF,FFFFF:FFFFF,F:FFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TTGTATATTAATTTATTATTTATTTATTATTATATTTATTATTT ,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-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)) >>> Writing bisulfite mapping results to CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29505:1047_1:N:0:ATGTAAGT+CATAGAGT/1 83 NC_035783.1_CT_converted 5460679 3 126M = 5460694 141 TTATGGATTTTAGGGTAGGGTAGGATAGAAGAGAATAGGGGATGAAAGGAATAAGTATTAGATATAAGGAAGAGAGTGGATAGGAGAGAAGAGAGGGGAAGAAAAGGGATTAGAGAGGAGGAGAGG ,F:FF:,F:,F,F:F::F:F:F:F:FFF:FF:F,F:,:F::F:F:::,F,:F,:FFFF::F:FFF,FF::,F:F,FFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFF:FFFF AS:i:-60 XN:i:0 XM:i:10 XO:i:0 XG:i:0 NM:i:10 MD:Z:0G1G0A5A0A13G14A32G20T5T26 YS:i:-36 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:29505:1047_2:N:0:ATGTAAGT+CATAGAGT/2 163 NC_035783.1_CT_converted 5460694 3 126M = 5460679 -141 TAGGGTAGGATAGAAGAGAATAGGGGATGAAAGGAATAAGTATTAGATATAAGGAAGAGAGTGGATAGGAGAGAAGAGAGGGGAAGAAAAGGGATTAGAGAGGAGGAGAGGAGTTTAGAAGAGGTA FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: AS:i:-36 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:9G14A32G20T5T28A12 YS:i:-60 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-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:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TAATAAATAAATAATAAATTAATATACAAAATAATTTTAATAAA ::FFFFFFFFF,FFFFF:FFFFF,F:FFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TTGTATATTAATTTATTATTTATTTATTATTATATTTATTATTT ,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-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)) Reading in the sequence files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29505:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TTTTTTTTTTTTTTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTATTTTTTTTTTTATATTTAATATTTATTTTTTTTATTTTTTATTTTTTTTTATTTTATTTTATTTTAAAATTTATAG FFFF:FFFFFFFFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF,F:F,::FF,FFF:F::FFFF:,F:,F,:::F:F::F:,:F,F:FF:FFF:F:F:F:F::F:F,F,:F,:FF:F, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29505:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TAAAATAAAATAAAAAAAAATAAAAAATAAAAAAAATAAATATTAAATATAAAAAAAAAAATAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAAAAAAATTTAAAAAAAATA FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 83 NC_035787.1_GA_converted 61975843 40 44M = 61975858 59 TTTATCAAAACCATTTCACACATTAACTTATCATTTACTTATCA FFFFFFFFFF:FFFFFFF:F,FFFFF:FFFFF,FFFFFFFFF:: AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:44 YS:i:-12 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 163 NC_035787.1_GA_converted 61975858 40 44M = 61975843 -59 TCACACATTAACTTATCATTTACTTATCATCATACTTATCACCT ,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:42A0A0 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz Error, fewer reads in file specified with -2 than in file specified with -1. Last successfully parsed mate: @GWNJ-1012:512:GW210315000:4:1101:7238:8641_1:N:0:ATGTAAGT+CATAGAGT/1/1. Reading in the sequence files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): bowtie2-align exited with value 134 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1103:7057:32972_1:N:0:ATGTAAGT+CATAGAGT NC_035781.1 2 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1305:24551:15452_1:N:0:ATGTAAGT+CATAGAGT NC_007175.2 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2608:13630:32550_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 65668306 Processed 11000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2608:14597:34381_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 65668306 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1336:19967:26177_1:N:0:ATGTAAGT+CATAGAGT NC_007175.2 1 Processed 17000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1665:14000:27148_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 28000000 sequence pairs so far 28070862 reads; of these: 28070862 (100.00%) were paired; of these: 25193935 (89.75%) aligned concordantly 0 times 1352290 (4.82%) aligned concordantly exactly 1 time 1524637 (5.43%) aligned concordantly >1 times 10.25% overall alignment rate 28070862 reads; of these: 28070862 (100.00%) were paired; of these: 25066408 (89.30%) aligned concordantly 0 times 1417950 (5.05%) aligned concordantly exactly 1 time 1586504 (5.65%) aligned concordantly >1 times 10.70% overall alignment rate 28070862 reads; of these: 28070862 (100.00%) were paired; of these: 25067801 (89.30%) aligned concordantly 0 times 1421002 (5.06%) aligned concordantly exactly 1 time 1582059 (5.64%) aligned concordantly >1 times 10.70% overall alignment rate 28070862 reads; of these: 28070862 (100.00%) were paired; of these: 25194749 (89.75%) aligned concordantly 0 times 1347462 (4.80%) aligned concordantly exactly 1 time 1528651 (5.45%) aligned concordantly >1 times 10.25% overall alignment rate Processed 28070862 sequences in total Successfully deleted the temporary files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28070862 Final Cytosine Methylation Report ================================= Total number of C's analysed: 187905513 Total methylated C's in CpG context: 6325008 Total methylated C's in CHG context: 1977466 Total methylated C's in CHH context: 9204996 Total methylated C's in Unknown context: 231574 Total unmethylated C's in CpG context: 19525818 Total unmethylated C's in CHG context: 36262931 Total unmethylated C's in CHH context: 114609294 Total unmethylated C's in Unknown context: 890841 C methylated in CpG context: 24.5% C methylated in CHG context: 5.2% C methylated in CHH context: 7.4% C methylated in Unknown context (CN or CHN): 20.6% Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25191504 (89.74%) aligned concordantly 0 times 1352558 (4.82%) aligned concordantly exactly 1 time 1526799 (5.44%) aligned concordantly >1 times 10.26% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25069375 (89.31%) aligned concordantly 0 times 1419878 (5.06%) aligned concordantly exactly 1 time 1581608 (5.63%) aligned concordantly >1 times 10.69% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25070782 (89.31%) aligned concordantly 0 times 1411918 (5.03%) aligned concordantly exactly 1 time 1588161 (5.66%) aligned concordantly >1 times 10.69% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25192809 (89.75%) aligned concordantly 0 times 1348265 (4.80%) aligned concordantly exactly 1 time 1529787 (5.45%) aligned concordantly >1 times 10.25% overall alignment rate Processed 28070861 sequences in total Successfully deleted the temporary files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28070861 Final Cytosine Methylation Report ================================= Total number of C's analysed: 187686915 Total methylated C's in CpG context: 6320714 Total methylated C's in CHG context: 1974823 Total methylated C's in CHH context: 9182249 Total methylated C's in Unknown context: 230090 Total unmethylated C's in CpG context: 19496815 Total unmethylated C's in CHG context: 36229186 Total unmethylated C's in CHH context: 114483128 Total unmethylated C's in Unknown context: 890772 C methylated in CpG context: 24.5% C methylated in CHG context: 5.2% C methylated in CHH context: 7.4% C methylated in Unknown context (CN or CHN): 20.5% Now waiting for all child processes to complete Processed 11000000 sequence pairs so far Processed 28000000 sequence pairs so far 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25193085 (89.75%) aligned concordantly 0 times 1351336 (4.81%) aligned concordantly exactly 1 time 1526440 (5.44%) aligned concordantly >1 times 10.25% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25072222 (89.32%) aligned concordantly 0 times 1412383 (5.03%) aligned concordantly exactly 1 time 1586256 (5.65%) aligned concordantly >1 times 10.68% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25071518 (89.32%) aligned concordantly 0 times 1418185 (5.05%) aligned concordantly exactly 1 time 1581158 (5.63%) aligned concordantly >1 times 10.68% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25194262 (89.75%) aligned concordantly 0 times 1346745 (4.80%) aligned concordantly exactly 1 time 1529854 (5.45%) aligned concordantly >1 times 10.25% overall alignment rate Processed 28070861 sequences in total Successfully deleted the temporary files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28070861 Final Cytosine Methylation Report ================================= Total number of C's analysed: 187586049 Total methylated C's in CpG context: 6317491 Total methylated C's in CHG context: 1969645 Total methylated C's in CHH context: 9141994 Total methylated C's in Unknown context: 229407 Total unmethylated C's in CpG context: 19498787 Total unmethylated C's in CHG context: 36213931 Total unmethylated C's in CHH context: 114444201 Total unmethylated C's in Unknown context: 892348 C methylated in CpG context: 24.5% C methylated in CHG context: 5.2% C methylated in CHH context: 7.4% C methylated in Unknown context (CN or CHN): 20.5% Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25067507 (89.30%) aligned concordantly 0 times 1416415 (5.05%) aligned concordantly exactly 1 time 1586939 (5.65%) aligned concordantly >1 times 10.70% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25199012 (89.77%) aligned concordantly 0 times 1345665 (4.79%) aligned concordantly exactly 1 time 1526184 (5.44%) aligned concordantly >1 times 10.23% overall alignment rate 28070861 reads; of these: 28070861 (100.00%) were paired; of these: 25069109 (89.31%) aligned concordantly 0 times 1418489 (5.05%) aligned concordantly exactly 1 time 1583263 (5.64%) aligned concordantly >1 times 10.69% overall alignment rate Processed 28070861 sequences in total Successfully deleted the temporary files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28070861 Final Cytosine Methylation Report ================================= Total number of C's analysed: 159746625 Total methylated C's in CpG context: 5390381 Total methylated C's in CHG context: 1793215 Total methylated C's in CHH context: 8883012 Total methylated C's in Unknown context: 192468 Total unmethylated C's in CpG context: 16608223 Total unmethylated C's in CHG context: 30354962 Total unmethylated C's in CHH context: 96716832 Total unmethylated C's in Unknown context: 722877 C methylated in CpG context: 24.5% C methylated in CHG context: 5.6% C methylated in CHH context: 8.4% C methylated in Unknown context (CN or CHN): 21.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF06-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << [E::bgzf_uncompress] Inflate operation failed: invalid distance too far back [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes samtools view: error reading file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam" samtools view: error closing "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam": -1 Failed to close filehandle Merging from file >> CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF06-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/CF06-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-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: 112283445 Final Cytosine Methylation Report ================================= Total number of C's analysed: 722925102 Total methylated C's in CpG context: 24353594 Total methylated C's in CHG context: 7715149 Total methylated C's in CHH context: 36412251 Total methylated C's in Unknown context: 883539 Total unmethylated C's in CpG context: 75129643 Total unmethylated C's in CHG context: 139061010 Total unmethylated C's in CHH context: 440253455 Total unmethylated C's in Unknown context: 3396838 C methylated in CpG context: 24.5% C methylated in CHG context: 5.3% C methylated in CHH context: 7.6% C methylated in Unknown context (CN or CHN): 20.6% Deleting temporary report files... Bismark completed in 0d 5h 0m 26s ==================== Bismark run complete ====================