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-CM05-Larvae_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 28490027) Using the subset file >CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 28490027) Using the subset file >CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz for PID: 30942 and offset 4 (sequences written out: 28490027) Using the subset file >CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 28490028) Using the subset file >CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz for PID: 30942 and offset 4 (sequences written out: 28490027) Using the subset file >CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 28490027) Using the subset file >CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 28490028) Using the subset file >CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 28490027) Using the subset file >CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz (28490028 sequences in total) Writing a C -> T converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz (28490027 sequences in total) Writing a C -> T converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz (28490027 sequences in total) Writing a C -> T converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz (28490027 sequences in total) Writing a C -> T converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz (28490028 sequences in total) Input files are CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 AAGAAATATTAAAATATTATTATATATTAAATTATTAATTTAAATTTTAATTTTATTATTATAATATTATTAATTTTATTAAAAATTATATTTTATATTTTTTTTAAAATT FFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 ATAAAATATAATTTTTAATAAAATTAATAATATTATAATAATAAAATTAAAATTTAAATTAATAATTTAATATATAATAATATTTTAATATTTCTTATAAATTAATACTAT FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM05-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 CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz (28490027 sequences in total) Input files are CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 AAAAAATATCAAAACACCACTACACATTAAATCATTAATCCAAATCTTAATCCCATCACCACAACATTACCAACCTTACTAAAAACTATACCCTACATCCCCCCCAAAACC FFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 GTAGGGTATAGTTTTTAGTAAGGTTGGTAATGTTGTGGTGATGGGATTAAGATTTGGATTAATGATTTAATGTGTAGTGGTGTTTTGATATTTTTTATGGATTGGTGTTAT FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM05-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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 AAAAAATATCAAAACACCACTACACATTAAATCATTAATCCAAATCTTAATCCCATCACCACAACATTACCAACCTTACTAAAAACTATACCCTACATCCCCCCCAAAACC FFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 GTAGGGTATAGTTTTTAGTAAGGTTGGTAATGTTGTGGTGATGGGATTAAGATTTGGATTAATGATTTAATGTGTAGTGGTGTTTTGATATTTTTTATGGATTGGTGTTAT FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TTTTAATATATAATTTTATTATTTTAATTAAATATTTAATTATTATAAATATATAAATATATATAAAATAAATAAAAAAAAATATTATTAAATTAAAATGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 ATAATATTTTTTTTTATTTATTTTATATATATTTATATATTTATAATAATTAAATATTTAATTAAAATAATAAAATTATATATTAAAATCAAAAAAACAAAAC F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM05-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-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz (28490027 sequences in total) Input files are CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 AAGAAATATTAAAATATTATTATATATTAAATTATTAATTTAAATTTTAATTTTATTATTATAATATTATTAATTTTATTAAAAATTATATTTTATATTTTTTTTAAAATT FFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 ATAAAATATAATTTTTAATAAAATTAATAATATTATAATAATAAAATTAAAATTTAAATTAATAATTTAATATATAATAATATTTTAATATTTCTTATAAATTAATACTAT FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 99 NC_035786.1_GA_converted 56962935 3 98M2D5M = 56962922 -118 TCTCAATATACAACCTCACCATTTTAATTAAACATTTAATTACTATAAACATATAAATATACACAAAACAAATAAAAAAAAATACTACCAAATTAAAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-29 XN:i:0 XM:i:3 XO:i:1 XG:i:2 NM:i:5 MD:Z:6A91^CC0C2A1 YS:i:-45 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 147 NC_035786.1_GA_converted 56962922 3 5M1I2M1D3M2I90M = 56962935 118 ACCCTACTCTTCCAATCTCAATATACAACCTCACCATTTTAATTAAACATTTAATTACTATAAACATATAAATATACACAAAACAAATAAAAAAAAATACTAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F AS:i:-45 XN:i:0 XM:i:3 XO:i:3 XG:i:4 NM:i:7 MD:Z:1T5^C4T6A81 YS:i:-29 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM05-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)) Reading in the sequence files CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TCTCAATATACAACCTCACCATTTTAATTAAACATTTAATTACTATAAACATATAAATATACACAAAACAAATAAAAAAAAATACTACCAAATTAAAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 GTAGTATTTTTTTTTATTTGTTTTGTGTATATTTATATGTTTATAGTAATTAAATGTTTAATTAAAATGGTGAGGTTGTATATTGAGATTGGAAGAGTAGGGT F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:27950:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATTTTTATAATTTTTAAATAAAAATTAAATTATTAATTAATTAAATATATATTTTTAAAAATTGAATTTTTTTAAAAAAAAATAATATTTATTAATATTTTAAAATATATATAAATAATAAT FFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27950:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TATTTTAAAATATTAATAAATATTATTTTTTTTTAAAAAAATTCAATTTTTAAAAATATATATTTAATTAATTAATAATTTAATTTTTATTTAAAAATTATAAAAATATTAAATATTAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFFFF::FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM05-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:GW210315000:4:1101:27950:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATCCCTATAATCTCCAAACAAAAATTAAATTATCAATCAATCAAATATACATCTTCAAAAATTAAATTTTTTCAAAAAAAAACAACATTCACCAATATTTTAAAACATACACAAACAACAAC FFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27950:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TGTTTTAAAATATTGGTGAATGTTGTTTTTTTTTGAAAAAATTTAATTTTTGAAGATGTATATTTGATTGATTGATAATTTAATTTTTGTTTGGAGATTATAGGGATATTGGGTGTTGGTTGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFFFF::FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM05-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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TTTTAATATATAATTTTATTATTTTAATTAAATATTTAATTATTATAAATATATAAATATATATAAAATAAATAAAAAAAAATATTATTAAATTAAAATGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 ATAATATTTTTTTTTATTTATTTTATATATATTTATATATTTATAATAATTAAATATTTAATTAAAATAATAAAATTATATATTAAAATCAAAAAAACAAAAC F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27950:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATCCCTATAATCTCCAAACAAAAATTAAATTATCAATCAATCAAATATACATCTTCAAAAATTAAATTTTTTCAAAAAAAAACAACATTCACCAATATTTTAAAACATACACAAACAACAAC FFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27950:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TGTTTTAAAATATTGGTGAATGTTGTTTTTTTTTGAAAAAATTTAATTTTTGAAGATGTATATTTGATTGATTGATAATTTAATTTTTGTTTGGAGATTATAGGGATATTGGGTGTTGGTTGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFFFF::FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:27950:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATTTTTATAATTTTTAAATAAAAATTAAATTATTAATTAATTAAATATATATTTTTAAAAATTGAATTTTTTTAAAAAAAAATAATATTTATTAATATTTTAAAATATATATAAATAATAAT FFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27950:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TATTTTAAAATATTAATAAATATTATTTTTTTTTAAAAAAATTCAATTTTTAAAAATATATATTTAATTAATTAATAATTTAATTTTTATTTAAAAATTATAAAAATATTAAATATTAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFFFF::FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz (28490027 sequences in total) Input files are CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:26124:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATGTTAGAATAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAATGTTTTTGT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:F,,F,,,F,F,F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26124:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATAAAAACAAAAACAAACACACACAC FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F::::FF,:,:,:,::F:F,FFF,::FF:,,FFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM05-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:GW210315000:4:1101:26124:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATATTAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATTTTTAT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:F,,F,,,F,F,F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26124:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAAAATAAAAATAAATATATATAT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F::::FF,:,:,:,::F:F,FFF,::FF:,,FFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM05-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:GW210315000:4:1101:26124:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATATTAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATTTTTAT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:F,,F,,,F,F,F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26124:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATAAAAATAAAAATAAATATATATAT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F::::FF,:,:,:,::F:F,FFF,::FF:,,FFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM05-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:GW210315000:4:1101:26124:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 TATGTTAGAATAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAATGTTTTTGT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:F,,F,,,F,F,F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26124:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATAAAAACAAAAACAAACACACACAC FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F::::FF,:,:,:,::F:F,FFF,::FF:,,FFF:F YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz and CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1152:2908:26506_1:N:0:CGGCGTGA+ACAGGCGC NC_007175.2 17115 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:GW210315000:4:1273:20518:32957_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1277:12264:5384_1:N:0:CGGCGTGA+ACAGGCGC 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 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 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 7000000 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 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 9000000 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 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2649:23692:34100_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 1 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1114:1190:3145_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 11000000 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:GW210315000:4:2628:29839:20885_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1222:6198:33833_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1373:9588:17534_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1444:17752:36996_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 65668305 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1460:22761:3490_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1460:22923:3208_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1318:10619:13495_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1373:10077:4601_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1575:8124:10958_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 3 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1677:16034:16830_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1460:22535:3630_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2220:14181:21230_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 65668306 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2221:11894:3490_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 19000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2319:5945:27070_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2469:13675:4758_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2545:14434:34194_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far 28490028 reads; of these: 28490028 (100.00%) were paired; of these: 23790195 (83.50%) aligned concordantly 0 times 2150714 (7.55%) aligned concordantly exactly 1 time 2549119 (8.95%) aligned concordantly >1 times 16.50% overall alignment rate 28490028 reads; of these: 28490028 (100.00%) were paired; of these: 23964642 (84.12%) aligned concordantly 0 times 2075366 (7.28%) aligned concordantly exactly 1 time 2450020 (8.60%) aligned concordantly >1 times 15.88% overall alignment rate 28490028 reads; of these: 28490028 (100.00%) were paired; of these: 23953851 (84.08%) aligned concordantly 0 times 2075084 (7.28%) aligned concordantly exactly 1 time 2461093 (8.64%) aligned concordantly >1 times 15.92% overall alignment rate 28490028 reads; of these: 28490028 (100.00%) were paired; of these: 23786748 (83.49%) aligned concordantly 0 times 2146081 (7.53%) aligned concordantly exactly 1 time 2557199 (8.98%) aligned concordantly >1 times 16.51% overall alignment rate Processed 28490028 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 28490028 Final Cytosine Methylation Report ================================= Total number of C's analysed: 345161024 Total methylated C's in CpG context: 10193698 Total methylated C's in CHG context: 2227908 Total methylated C's in CHH context: 8608513 Total methylated C's in Unknown context: 338986 Total unmethylated C's in CpG context: 41966800 Total unmethylated C's in CHG context: 71775403 Total unmethylated C's in CHH context: 210388702 Total unmethylated C's in Unknown context: 1453165 C methylated in CpG context: 19.5% C methylated in CHG context: 3.0% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 18.9% Processed 25000000 sequence pairs so far Processed 27000000 sequence pairs so far 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23786311 (83.49%) aligned concordantly 0 times 2146310 (7.53%) aligned concordantly exactly 1 time 2557406 (8.98%) aligned concordantly >1 times 16.51% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23789945 (83.50%) aligned concordantly 0 times 2152841 (7.56%) aligned concordantly exactly 1 time 2547241 (8.94%) aligned concordantly >1 times 16.50% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23959901 (84.10%) aligned concordantly 0 times 2078612 (7.30%) aligned concordantly exactly 1 time 2451514 (8.60%) aligned concordantly >1 times 15.90% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23954337 (84.08%) aligned concordantly 0 times 2074029 (7.28%) aligned concordantly exactly 1 time 2461661 (8.64%) aligned concordantly >1 times 15.92% overall alignment rate Processed 28490027 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 28490027 Final Cytosine Methylation Report ================================= Total number of C's analysed: 345398639 Total methylated C's in CpG context: 10191204 Total methylated C's in CHG context: 2231486 Total methylated C's in CHH context: 8605970 Total methylated C's in Unknown context: 340312 Total unmethylated C's in CpG context: 41948125 Total unmethylated C's in CHG context: 71849533 Total unmethylated C's in CHH context: 210572321 Total unmethylated C's in Unknown context: 1453234 C methylated in CpG context: 19.5% C methylated in CHG context: 3.0% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 19.0% Processed 28000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2677:16188:19257_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23959616 (84.10%) aligned concordantly 0 times 2077203 (7.29%) aligned concordantly exactly 1 time 2453208 (8.61%) aligned concordantly >1 times 15.90% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23955272 (84.08%) aligned concordantly 0 times 2072907 (7.28%) aligned concordantly exactly 1 time 2461848 (8.64%) aligned concordantly >1 times 15.92% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23787792 (83.50%) aligned concordantly 0 times 2151623 (7.55%) aligned concordantly exactly 1 time 2550612 (8.95%) aligned concordantly >1 times 16.50% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23781157 (83.47%) aligned concordantly 0 times 2150401 (7.55%) aligned concordantly exactly 1 time 2558469 (8.98%) aligned concordantly >1 times 16.53% overall alignment rate Processed 28490027 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 28490027 Final Cytosine Methylation Report ================================= Total number of C's analysed: 345630828 Total methylated C's in CpG context: 10199405 Total methylated C's in CHG context: 2225852 Total methylated C's in CHH context: 8620321 Total methylated C's in Unknown context: 339574 Total unmethylated C's in CpG context: 41986064 Total unmethylated C's in CHG context: 71890469 Total unmethylated C's in CHH context: 210708717 Total unmethylated C's in Unknown context: 1454667 C methylated in CpG context: 19.5% C methylated in CHG context: 3.0% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 18.9% Now waiting for all child processes to complete Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23787767 (83.50%) aligned concordantly 0 times 2146584 (7.53%) aligned concordantly exactly 1 time 2555676 (8.97%) aligned concordantly >1 times 16.50% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23790310 (83.50%) aligned concordantly 0 times 2153424 (7.56%) aligned concordantly exactly 1 time 2546293 (8.94%) aligned concordantly >1 times 16.50% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23953602 (84.08%) aligned concordantly 0 times 2074870 (7.28%) aligned concordantly exactly 1 time 2461555 (8.64%) aligned concordantly >1 times 15.92% overall alignment rate 28490027 reads; of these: 28490027 (100.00%) were paired; of these: 23960650 (84.10%) aligned concordantly 0 times 2077272 (7.29%) aligned concordantly exactly 1 time 2452105 (8.61%) aligned concordantly >1 times 15.90% overall alignment rate Processed 28490027 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 28490027 Final Cytosine Methylation Report ================================= Total number of C's analysed: 345384573 Total methylated C's in CpG context: 10186062 Total methylated C's in CHG context: 2233245 Total methylated C's in CHH context: 8608782 Total methylated C's in Unknown context: 340951 Total unmethylated C's in CpG context: 41978200 Total unmethylated C's in CHG context: 71831085 Total unmethylated C's in CHH context: 210547199 Total unmethylated C's in Unknown context: 1452048 C methylated in CpG context: 19.5% C methylated in CHG context: 3.0% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 19.0% Right, cleaning up now... Deleting temporary sequence files... Failed to delete temporary FastQ file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Now merging BAM files CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Failed to close output filehandle 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-CM05-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-CM05-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-CM05-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-CM05-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-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF03-CM05-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-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt'