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/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-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/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-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/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 29953802) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz for PID: 79774 and offset 4 (sequences written out: 29953801) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 29953802) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 29953801) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 29953802) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM04-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/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz for PID: 79774 and offset 4 (sequences written out: 29953801) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM04-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/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 29953802) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM04-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/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 29953801) Using the subset file >CF03-CM04-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/CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz (29953802 sequences in total) Writing a C -> T converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM04-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 CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz (29953801 sequences in total) Writing a C -> T converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM04-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 CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz (29953802 sequences in total) Writing a C -> T converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM04-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 CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz (29953801 sequences in total) Writing a C -> T converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM04-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 CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM04-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 CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz (29953802 sequences in total) Input files are CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-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)) Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz (29953801 sequences in total) Input files are CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM04-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:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TAAAATAATATTAAAAATTATTATAAATAAAAATTAATTAAATAATTTTTTTTTTAATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AAATTATTTAATTAATTTTTATTTATAATAATTTTTAATATTATTTTAAAATTTATTAAAAAA FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM04-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)) Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz (29953802 sequences in total) Input files are CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-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:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 CAAAATAACATCAAAAATCATTATAAACAAAAACCAACTAAATAATTCTCCTTCCAATTCCCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 GAATTATTTAGTTGGTTTTTGTTTATAATGATTTTTGATGTTATTTTGGGGTTTGTTGAAGGG FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM04-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:GW210315000:4:1101:32307:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ATAAAAAATTTATATTAAATTTTTTTTTAAATTATAAAAATTAATTTTTTAATATTTAATATAAAATATTAATATAAAAAATTATATTATATAATATATTTTTAAATTTATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32307:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 ATATATTATATAATATAATTTTTTATATTAATATTTTATATTAAATATTAAAAAATTAATTTTTATAATTTAAAAAAAAATTTAATATAAATTTTTTATAATATTAATATTATA FFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFF:FFFFFFFFFFFFFFFFF,FF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM04-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:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 CAAAATAACATCAAAAATCATTATAAACAAAAACCAACTAAATAATTCTCCTTCCAATTCCCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 GAATTATTTAGTTGGTTTTTGTTTATAATGATTTTTGATGTTATTTTGGGGTTTGTTGAAGGG FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-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:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TTAAATTATATATATTTTTATTAAAAAAAATTAAATATAATAAAAAATTATTTATTTTTTTTTTAAAATTAAAAAAATTATTTTTTATAAAAATTTTATTTATTTATAAAAATTATTAAAATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AATTATAACAATAAATCTATATTAACAACAAAAAAAAACAATAACACCACTTAACACTACTTATACACTATATTCTTAAAATACAAAATATCTATTCAATAATATAATAATTATAAACTCAATACTTTATACTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM04-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:GW210315000:4:1101:32307:1047_1:N:0:TACCGAGG+AGTTCAGG/1 99 NC_035788.1_GA_converted 75071377 0 28M1D86M = 75071362 -130 ACAAAAAATTTATATCAAATTTTTCTCTAAACCACAAAAACCAACTTCCTAATATTTAACACAAAACATCAATATAAAAAACTATATTATATAACACATTTTTAAATCTACAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF AS:i:-32 XS:i:-26 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:11C5T10^A8C66T10 YS:i:-32 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:32307:1047_2:N:0:TACCGAGG+AGTTCAGG/2 147 NC_035788.1_GA_converted 75071362 0 43M1D71M = 75071377 130 TACAACATCAACATCACAAAAAATTTATATCAAATTTTTCTCTAAACCACAAAAACCAACTTCCTAATATTTAACACAAAACATCAATATAAAAAACTATATTATATAACACAT FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF,FFFFFFFFFFFFFFFFF:FFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF AS:i:-32 XS:i:-38 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:4T21C5T10^A8C62 YS:i:-32 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM04-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 CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz (29953801 sequences in total) Input files are CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM04-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 CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM04-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:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TAAAATAATATTAAAAATTATTATAAATAAAAATTAATTAAATAATTTTTTTTTTAATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AAATTATTTAATTAATTTTTATTTATAATAATTTTTAATATTATTTTAAAATTTATTAAAAAA FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TTAAACTATACATATTTTTACTAAAAAAAACTAAATACAATAAAAAACCATTTACTCCCTTTTTAAAATCAAAAAAACCATTTTTTATAAAAACTTTATCCATTTATAAAAATTACCAAAATTTTTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AATTATAATAATAAATTTATATTAATAATAAAAAAAAATAATAATATTATTTAATATTATTTATATATTATATTTTTAAAATATAAAATATTTATTTAATAATATAATAATTATAAATTTAATATTTTATATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM04-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)) Reading in the sequence files CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:32307:1047_1:N:0:TACCGAGG+AGTTCAGG/1 83 NC_035784.1_CT_converted 60751013 2 83M1D31M = 60751028 130 GTTGTAGATTTAAAAATGTGTTATATAATATAGTTTTTTATATTGATGTTTTGTGTTAAATATTAGGAAGTTGGTTTTTGTGGTTTAGAGAAAAATTTGATATAAATTTTTTGT FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-20 XS:i:-26 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:83^T13G5G11 YS:i:-44 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:32307:1047_2:N:0:TACCGAGG+AGTTCAGG/2 163 NC_035784.1_CT_converted 60751028 2 68M1D46M = 60751013 -130 ATGTGTTATATAATATAGTTTTTTATATTGATGTTTTGTGTTAAATATTAGGAAGTTGGTTTTTGTGGTTTAGAGAAAAATTTGATATAAATTTTTTGTGATGTTGATGTTGTA FFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFF:FFFFFFFFFFFFFFFFF,FF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF AS:i:-44 XS:i:-40 XN:i:0 XM:i:6 XO:i:1 XG:i:1 NM:i:7 MD:Z:68^T13G5G17A3A2A0T0 YS:i:-20 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM04-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:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TTAAACTATACATATTTTTACTAAAAAAAACTAAATACAATAAAAAACCATTTACTCCCTTTTTAAAATCAAAAAAACCATTTTTTATAAAAACTTTATCCATTTATAAAAATTACCAAAATTTTTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AATTATAATAATAAATTTATATTAATAATAAAAAAAAATAATAATATTATTTAATATTATTTATATATTATATTTTTAAAATATAAAATATTTATTTAATAATATAATAATTATAAATTTAATATTTTATATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-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:GW210315000:4:1101:28131:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 GTTAGATTTATGAAAATAGATATGGATAAGAATTGAAATTATGTGATAGTATTTGTTAATTTGTTTGAAGTATGTGATAAATGGAATAAAGATGTTGGATTAAAAATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28131:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AACATCTTTATTCCATTTATCACATACTTCAAACAAATTAACAAATACTATCACATAATTTCAATTCTTATCCATATCTATTTTCATAAATCTAACAAAAAAACTTTCACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FF,FFFFFFFF::FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM04-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:GW210315000:4:1101:32307:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ATAAAAAATTTATATTAAATTTTTTTTTAAATTATAAAAATTAATTTTTTAATATTTAATATAAAATATTAATATAAAAAATTATATTATATAATATATTTTTAAATTTATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32307:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 ATATATTATATAATATAATTTTTTATATTAATATTTTATATTAAATATTAAAAAATTAATTTTTATAATTTAAAAAAAAATTTAATATAAATTTTTTATAATATTAATATTATA FFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFF:FFFFFFFFFFFFFFFFF,FF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TTAAATTATATATATTTTTATTAAAAAAAATTAAATATAATAAAAAATTATTTATTTTTTTTTTAAAATTAAAAAAATTATTTTTTATAAAAATTTTATTTATTTATAAAAATTATTAAAATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AATTATAACAATAAATCTATATTAACAACAAAAAAAAACAATAACACCACTTAACACTACTTATACACTATATTCTTAAAATACAAAATATCTATTCAATAATATAATAATTATAAACTCAATACTTTATACTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28131:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ATTAAATTTATAAAAATAAATATAAATAAAAATTAAAATTATATAATAATATTTATTAATTTATTTAAAATATATAATAAATAAAATAAAAATATTAAATTAAAAATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28131:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AATATTTTTATTTTATTTATTATATATTTTAAATAAATTAATAAATATTATTATATAATTTTAATTTTTATTTATATTTATTTTTATAAATTTAATAAAAAAATTTTTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FF,FFFFFFFF::FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM04-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)) >>> Writing bisulfite mapping results to CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28131:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ATTAAATTTATAAAAATAAATATAAATAAAAATTAAAATTATATAATAATATTTATTAATTTATTTAAAATATATAATAAATAAAATAAAAATATTAAATTAAAAATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28131:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AATATTTTTATTTTATTTATTATATATTTTAAATAAATTAATAAATATTATTATATAATTTTAATTTTTATTTATATTTATTTTTATAAATTTAATAAAAAAATTTTTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FF,FFFFFFFF::FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM04-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:GW210315000:4:1101:28131:1047_1:N:0:TACCGAGG+AGTTCAGG/1 83 NC_035789.1_GA_converted 27383970 1 111M = 27383985 126 AATAATTTTTAATCCAACATCTTTATTCCATTTATCACATACTTCAAACAAATTAACAAATACTATCACATAATTTCAATTCTTATCCATATCTATTTTCATAAATCTAAC F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:111 YS:i:0 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:28131:1047_2:N:0:TACCGAGG+AGTTCAGG/2 163 NC_035789.1_GA_converted 27383985 1 111M = 27383970 -126 AACATCTTTATTCCATTTATCACATACTTCAAACAAATTAACAAATACTATCACATAATTTCAATTCTTATCCATATCTATTTTCATAAATCTAACAAAAAAACTTTCACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FF,FFFFFFFF::FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:111 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz and CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1128:3161:31735_1:N:0:TACCGAGG+AGTTCAGG 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 Processed 2000000 sequence pairs so far Processed 2000000 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:GW210315000:4:1318:29432:19961_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1339:17219:24925_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 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:GW210315000:4:1512:4887:31093_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1653:12075:4742_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2328:25843:34601_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2328:25762:33865_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2656:30020:11365_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1146:24985:27226_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1216:29649:21934_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1471:27932:12383_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1471:27028:28291_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2218:6795:33426_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 65668305 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2559:26901:27946_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 22876850 (76.37%) aligned concordantly 0 times 3166810 (10.57%) aligned concordantly exactly 1 time 3910141 (13.05%) aligned concordantly >1 times 23.63% overall alignment rate 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 23492627 (78.43%) aligned concordantly 0 times 2897901 (9.67%) aligned concordantly exactly 1 time 3563273 (11.90%) aligned concordantly >1 times 21.57% overall alignment rate 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 23485325 (78.41%) aligned concordantly 0 times 2897902 (9.67%) aligned concordantly exactly 1 time 3570574 (11.92%) aligned concordantly >1 times 21.59% overall alignment rate 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 22874485 (76.37%) aligned concordantly 0 times 3166352 (10.57%) aligned concordantly exactly 1 time 3912964 (13.06%) aligned concordantly >1 times 23.63% overall alignment rate Processed 29953801 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 29953801 Final Cytosine Methylation Report ================================= Total number of C's analysed: 484126969 Total methylated C's in CpG context: 13269911 Total methylated C's in CHG context: 1402305 Total methylated C's in CHH context: 5472581 Total methylated C's in Unknown context: 222347 Total unmethylated C's in CpG context: 57425148 Total unmethylated C's in CHG context: 99887335 Total unmethylated C's in CHH context: 306669689 Total unmethylated C's in Unknown context: 1671111 C methylated in CpG context: 18.8% C methylated in CHG context: 1.4% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 11.7% Now waiting for all child processes to complete 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 22876380 (76.37%) aligned concordantly 0 times 3165995 (10.57%) aligned concordantly exactly 1 time 3911427 (13.06%) aligned concordantly >1 times 23.63% overall alignment rate 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 23483340 (78.40%) aligned concordantly 0 times 2894860 (9.66%) aligned concordantly exactly 1 time 3575602 (11.94%) aligned concordantly >1 times 21.60% overall alignment rate 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 23490292 (78.42%) aligned concordantly 0 times 2897959 (9.67%) aligned concordantly exactly 1 time 3565551 (11.90%) aligned concordantly >1 times 21.58% overall alignment rate 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 22879048 (76.38%) aligned concordantly 0 times 3165943 (10.57%) aligned concordantly exactly 1 time 3908811 (13.05%) aligned concordantly >1 times 23.62% overall alignment rate Processed 29953802 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 29953802 Final Cytosine Methylation Report ================================= Total number of C's analysed: 483939477 Total methylated C's in CpG context: 13271986 Total methylated C's in CHG context: 1404358 Total methylated C's in CHH context: 5464100 Total methylated C's in Unknown context: 221116 Total unmethylated C's in CpG context: 57393851 Total unmethylated C's in CHG context: 99853118 Total unmethylated C's in CHH context: 306552064 Total unmethylated C's in Unknown context: 1670533 C methylated in CpG context: 18.8% C methylated in CHG context: 1.4% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 11.7% 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 22878889 (76.38%) aligned concordantly 0 times 3163641 (10.56%) aligned concordantly exactly 1 time 3911272 (13.06%) aligned concordantly >1 times 23.62% overall alignment rate 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 23489083 (78.42%) aligned concordantly 0 times 2902305 (9.69%) aligned concordantly exactly 1 time 3562414 (11.89%) aligned concordantly >1 times 21.58% overall alignment rate Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2678:20464:25128_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 23485313 (78.41%) aligned concordantly 0 times 2896364 (9.67%) aligned concordantly exactly 1 time 3572125 (11.93%) aligned concordantly >1 times 21.59% overall alignment rate 29953802 reads; of these: 29953802 (100.00%) were paired; of these: 22874759 (76.37%) aligned concordantly 0 times 3165980 (10.57%) aligned concordantly exactly 1 time 3913063 (13.06%) aligned concordantly >1 times 23.63% overall alignment rate Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2678:15863:34695_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 29953802 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 29953802 Final Cytosine Methylation Report ================================= Total number of C's analysed: 484187113 Total methylated C's in CpG context: 13261329 Total methylated C's in CHG context: 1406751 Total methylated C's in CHH context: 5475691 Total methylated C's in Unknown context: 222092 Total unmethylated C's in CpG context: 57433977 Total unmethylated C's in CHG context: 99903612 Total unmethylated C's in CHH context: 306705753 Total unmethylated C's in Unknown context: 1672284 C methylated in CpG context: 18.8% C methylated in CHG context: 1.4% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 11.7% 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 22878120 (76.38%) aligned concordantly 0 times 3165106 (10.57%) aligned concordantly exactly 1 time 3910575 (13.06%) aligned concordantly >1 times 23.62% overall alignment rate 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 22874070 (76.36%) aligned concordantly 0 times 3166741 (10.57%) aligned concordantly exactly 1 time 3912990 (13.06%) aligned concordantly >1 times 23.64% overall alignment rate 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 23490935 (78.42%) aligned concordantly 0 times 2899674 (9.68%) aligned concordantly exactly 1 time 3563192 (11.90%) aligned concordantly >1 times 21.58% overall alignment rate 29953801 reads; of these: 29953801 (100.00%) were paired; of these: 23483686 (78.40%) aligned concordantly 0 times 2896516 (9.67%) aligned concordantly exactly 1 time 3573599 (11.93%) aligned concordantly >1 times 21.60% overall alignment rate Processed 29953801 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 29953801 Final Cytosine Methylation Report ================================= Total number of C's analysed: 484179462 Total methylated C's in CpG context: 13273645 Total methylated C's in CHG context: 1401962 Total methylated C's in CHH context: 5478289 Total methylated C's in Unknown context: 221567 Total unmethylated C's in CpG context: 57398469 Total unmethylated C's in CHG context: 99900026 Total unmethylated C's in CHH context: 306727071 Total unmethylated C's in Unknown context: 1675379 C methylated in CpG context: 18.8% C methylated in CHG context: 1.4% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 11.7% Right, cleaning up now... Deleting temporary sequence files... Failed to delete temporary FastQ file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Now merging BAM files CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam: No such file or directory Writing report to /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF03-CM04-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/CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Failed to read from temporary mapping report '/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt'