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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz for PID: 99768 and offset 4 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz for PID: 99768 and offset 4 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to EF05-EM06-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/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to EF05-EM06-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/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 49328754) Using the subset file >EF05-EM06-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/EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz (49328754 sequences in total) Writing a C -> T converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to EF05-EM06-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 EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz (49328754 sequences in total) Writing a C -> T converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to EF05-EM06-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 EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz (49328754 sequences in total) Writing a C -> T converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to EF05-EM06-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 EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz (49328754 sequences in total) Writing a C -> T converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to EF05-EM06-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 EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to EF05-EM06-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 EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz (49328754 sequences in total) Input files are EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:30734:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAATTAAATATTTAAATTTTAATTATAATAAATTTAAATTATTAAAATAAATATTAATAATTTTATTATTAAATATTTAATAATTTAATAAAAATAAATATTATAATTTTTATATTTTAAAAATATTAATAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30734:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TTATTAATATTTTTAAAATATAAAAATTATAATATTTATTTTTATTAAATTATTAAATATTTAATAATAAAATTATTAATATTTATTTTAATAATTTAAATTTATTATAATTAAAATTTAAATATTTAATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFF::FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz (49328754 sequences in total) Input files are EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TTTTTATTAATATTAATATTAATAAAATTATAATTTTAAATATTTTAATTAAAATATATTAATAAATTATTTTATTATTTTATTATTTAAATTTATGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 ATAAAATAATAAAATAATTTATTAATATATTTTAATTAAAATATTTAAAATTATAATTTTATTAATATTAATATTAATAAAAAAATTTTTATTATAAT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM06-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:GW210315000:4:1101:30734:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAATTAAATATTCAAATTCCAACTACAACAAACCTAAATCATCAAAACAAATATTAACAATTCTACTACTAAACACTCAACAATTTAATAAAAATAAATATCACAATCCTCATATCTCAAAAACATCAACAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30734:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TTGTTGATGTTTTTGAGATATGAGGATTGTGATATTTATTTTTATTAAATTGTTGAGTGTTTAGTAGTAGAATTGTTAATATTTGTTTTGATGATTTAGGTTTGTTGTAGTTGGAATTTGAATATTTAATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFF::FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 99 NC_035784.1_GA_converted 20135259 1 98M = 20135244 -113 CCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:95T1T0 YS:i:0 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 147 NC_035784.1_GA_converted 20135244 1 98M = 20135259 113 ATTATAATAAAAACCCCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:98 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM06-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:GW210315000:4:1101:30734:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAATTAAATATTCAAATTCCAACTACAACAAACCTAAATCATCAAAACAAATATTAACAATTCTACTACTAAACACTCAACAATTTAATAAAAATAAATATCACAATCCTCATATCTCAAAAACATCAACAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30734:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TTGTTGATGTTTTTGAGATATGAGGATTGTGATATTTATTTTTATTAAATTGTTGAGTGTTTAGTAGTAGAATTGTTAATATTTGTTTTGATGATTTAGGTTTGTTGTAGTTGGAATTTGAATATTTAATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFF::FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 CCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 ATAAAGTAATAAAGTAGTTTGTTGGTGTGTTTTAGTTGAAATGTTTAGAGTTGTGATTTTATTAATGTTAATATTAATGGAGGGGTTTTTATTATAAT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TTTTTATTAATATTAATATTAATAAAATTATAATTTTAAATATTTTAATTAAAATATATTAATAAATTATTTTATTATTTTATTATTTAAATTTATGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 ATAAAATAATAAAATAATTTATTAATATATTTTAATTAAAATATTTAAAATTATAATTTTATTAATATTAATATTAATAAAAAAATTTTTATTATAAT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30734:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAATTAAATATTTAAATTTTAATTATAATAAATTTAAATTATTAAAATAAATATTAATAATTTTATTATTAAATATTTAATAATTTAATAAAAATAAATATTATAATTTTTATATTTTAAAAATATTAATAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30734:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TTATTAATATTTTTAAAATATAAAAATTATAATATTTATTTTTATTAAATTATTAAATATTTAATAATAAAATTATTAATATTTATTTTAATAATTTAAATTTATTATAATTAAAATTTAAATATTTAATTATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFF::FFFF YT:Z:UP >>> Writing bisulfite mapping results to EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz (49328754 sequences in total) Input files are EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TGATATTATTGAATATATTTTATGTATGTATTTGTTTAATATTATTAAAATTTATGTTTGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TAATAATATTAAACAAATACATACATAAAATATATTCAATAATATCATATAAAAACACCAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAATATTATTAAATATATTTTATATATATATTTATTTAATATTATTAAAATTTATATTTACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TAATAATATTAAATAAATATATATATAAAATATATTTAATAATATTATATAAAAATATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM06-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:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAATATTATTAAATATATTTTATATATATATTTATTTAATATTATTAAAATTTATATTTACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TAATAATATTAAATAAATATATATATAAAATATATTTAATAATATTATATAAAAATATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 83 NC_035788.1_GA_converted 21765157 1 62M = 21765172 77 AACAAACATAAATTTTAATAATATTAAACAAATACATACATAAAATATATTCAATAATATCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0T61 YS:i:0 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 163 NC_035788.1_GA_converted 21765172 1 62M = 21765157 -77 TAATAATATTAAACAAATACATACATAAAATATATTCAATAATATCATATAAAAACACCAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:62 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz (49328754 sequences in total) Input files are EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:29776:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAAAAATATATTTATATTTTATTTATAATTTTTTTTATATATTTAAAAAATGGGTTGAATATGATTTTTTGTGGTTTTAGTTTTTTGGTTAAAATTTGTTTATAGTTTTTTTTTATTTTTTTTAATGTATTATTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF::F:FFF:FFF:FF,F:FFFFFFFFFFF:F:FF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29776:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 AAAATTCCAAAATAACAATAATACATTAAAAAAAATAAAAAAAAACTATAAACAAATTTTAACCAAAAAACTAAAACCACAAAAAATCATATTCAACCCATTTTTTAAATATATAAAAAAAATTATAAATAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF05-EM06-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:GW210315000:4:1101:29776:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 CAAAAACACACTCACATCCTACCCATAATCCTTCCTATACACCCAAAAAATAAATTAAATATAATTTTTTATAATTTTAATTTTTTAATTAAAATTTATTTATAATTTTTTTTTATTTTTTTTAATATATTATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF::F:FFF:FFF:FF,F:FFFFFFFFFFF:F:FF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29776:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 AAAATTTTAAAATAATAATAATATATTAAAAAAAATAAAAAAAAATTATAAATAAATTTTAATTAAAAAATTAAAATTATAAAAAATTATATTTAATTTATTTTTTGGGTGTATAGGAAGGATTATGGGTAGGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF05-EM06-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:GW210315000:4:1101:29776:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 CAAAAACACACTCACATCCTACCCATAATCCTTCCTATACACCCAAAAAATAAATTAAATATAATTTTTTATAATTTTAATTTTTTAATTAAAATTTATTTATAATTTTTTTTTATTTTTTTTAATATATTATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF::F:FFF:FFF:FF,F:FFFFFFFFFFF:F:FF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29776:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 AAAATTTTAAAATAATAATAATATATTAAAAAAAATAAAAAAAAATTATAAATAAATTTTAATTAAAAAATTAAAATTATAAAAAATTATATTTAATTTATTTTTTGGGTGTATAGGAAGGATTATGGGTAGGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF05-EM06-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:GW210315000:4:1101:29776:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TAAAAATATATTTATATTTTATTTATAATTTTTTTTATATATTTAAAAAATGGGTTGAATATGATTTTTTGTGGTTTTAGTTTTTTGGTTAAAATTTGTTTATAGTTTTTTTTTATTTTTTTTAATGTATTATTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF::F:FFF:FFF:FF,F:FFFFFFFFFFF:F:FF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29776:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 AAAATTCCAAAATAACAATAATACATTAAAAAAAATAAAAAAAAACTATAAACAAATTTTAACCAAAAAACTAAAACCACAAAAAATCATATTCAACCCATTTTTTAAATATATAAAAAAAATTATAAATAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFF YT:Z:UP >>> Writing bisulfite mapping results to EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1234:3586:1689_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17136 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:GW210315000:4:1246:8811:27649_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 65668305 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:GW210315000:4:1417:30734:1517_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1432:20582:21981_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1417:29957:2237_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1432:20446:13573_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 1 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 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1664:13485:21496_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 7000000 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2251:28971:18192_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2316:5502:6010_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 65668307 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2245:7292:5447_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 65668305 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 10000000 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 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:25192:17065_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:23348:13808_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:25247:16877_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2406:23827:33708_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2647:7636:16470_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 65668338 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1115:8856:12320_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17136 Processed 16000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 17000000 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:2:1168:31584:9878_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1256:10981:13714_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 1 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1304:30391:34522_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17115 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1305:28999:18490_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17115 Processed 19000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1332:23863:32330_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17112 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1256:9634:12289_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 1 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1378:31548:21371_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 1 Processed 24000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1419:18285:9298_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 23000000 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 24000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1608:29378:20619_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 2 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1647:31792:35164_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1647:32976:22467_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2223:26223:10645_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 65668306 Processed 36000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2255:11297:5494_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 1 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2244:19045:7294_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 42000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2311:14253:31939_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 45000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2517:8024:22279_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 48000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 46000000 sequence pairs so far 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41001432 (83.12%) aligned concordantly 0 times 3841879 (7.79%) aligned concordantly exactly 1 time 4485443 (9.09%) aligned concordantly >1 times 16.88% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41604484 (84.34%) aligned concordantly 0 times 3565358 (7.23%) aligned concordantly exactly 1 time 4158912 (8.43%) aligned concordantly >1 times 15.66% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41607356 (84.35%) aligned concordantly 0 times 3576196 (7.25%) aligned concordantly exactly 1 time 4145202 (8.40%) aligned concordantly >1 times 15.65% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 40993703 (83.10%) aligned concordantly 0 times 3837659 (7.78%) aligned concordantly exactly 1 time 4497392 (9.12%) aligned concordantly >1 times 16.90% overall alignment rate Processed 49328754 sequences in total Successfully deleted the temporary files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 49328754 Final Cytosine Methylation Report ================================= Total number of C's analysed: 692762642 Total methylated C's in CpG context: 18883427 Total methylated C's in CHG context: 6078589 Total methylated C's in CHH context: 25144821 Total methylated C's in Unknown context: 470051 Total unmethylated C's in CpG context: 76680898 Total unmethylated C's in CHG context: 128968056 Total unmethylated C's in CHH context: 437006851 Total unmethylated C's in Unknown context: 2668361 C methylated in CpG context: 19.8% C methylated in CHG context: 4.5% C methylated in CHH context: 5.4% C methylated in Unknown context (CN or CHN): 15.0% Processed 44000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2430:10728:26772_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17136 Processed 46000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2443:11975:36448_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 1 Processed 49000000 sequence pairs so far 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 40998360 (83.11%) aligned concordantly 0 times 3844109 (7.79%) aligned concordantly exactly 1 time 4486285 (9.09%) aligned concordantly >1 times 16.89% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 40993377 (83.10%) aligned concordantly 0 times 3838203 (7.78%) aligned concordantly exactly 1 time 4497174 (9.12%) aligned concordantly >1 times 16.90% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41606879 (84.35%) aligned concordantly 0 times 3564256 (7.23%) aligned concordantly exactly 1 time 4157619 (8.43%) aligned concordantly >1 times 15.65% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41607055 (84.35%) aligned concordantly 0 times 3578953 (7.26%) aligned concordantly exactly 1 time 4142746 (8.40%) aligned concordantly >1 times 15.65% overall alignment rate Processed 49328754 sequences in total Successfully deleted the temporary files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 49328754 Final Cytosine Methylation Report ================================= Total number of C's analysed: 692700300 Total methylated C's in CpG context: 18865549 Total methylated C's in CHG context: 6080043 Total methylated C's in CHH context: 25136435 Total methylated C's in Unknown context: 470111 Total unmethylated C's in CpG context: 76640095 Total unmethylated C's in CHG context: 128960773 Total unmethylated C's in CHH context: 437017405 Total unmethylated C's in Unknown context: 2668229 C methylated in CpG context: 19.8% C methylated in CHG context: 4.5% C methylated in CHH context: 5.4% C methylated in Unknown context (CN or CHN): 15.0% Processed 43000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2645:6415:10504_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 65668306 Processed 44000000 sequence pairs so far Processed 49000000 sequence pairs so far 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 40994244 (83.10%) aligned concordantly 0 times 3836047 (7.78%) aligned concordantly exactly 1 time 4498463 (9.12%) aligned concordantly >1 times 16.90% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41605481 (84.34%) aligned concordantly 0 times 3578467 (7.25%) aligned concordantly exactly 1 time 4144806 (8.40%) aligned concordantly >1 times 15.66% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41608130 (84.35%) aligned concordantly 0 times 3562848 (7.22%) aligned concordantly exactly 1 time 4157776 (8.43%) aligned concordantly >1 times 15.65% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 40996988 (83.11%) aligned concordantly 0 times 3846111 (7.80%) aligned concordantly exactly 1 time 4485655 (9.09%) aligned concordantly >1 times 16.89% overall alignment rate Processed 49328754 sequences in total Successfully deleted the temporary files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 49328754 Final Cytosine Methylation Report ================================= Total number of C's analysed: 692586375 Total methylated C's in CpG context: 18867510 Total methylated C's in CHG context: 6067892 Total methylated C's in CHH context: 25153367 Total methylated C's in Unknown context: 469655 Total unmethylated C's in CpG context: 76637674 Total unmethylated C's in CHG context: 128935278 Total unmethylated C's in CHH context: 436924654 Total unmethylated C's in Unknown context: 2670615 C methylated in CpG context: 19.8% C methylated in CHG context: 4.5% C methylated in CHH context: 5.4% C methylated in Unknown context (CN or CHN): 15.0% Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41606818 (84.35%) aligned concordantly 0 times 3574426 (7.25%) aligned concordantly exactly 1 time 4147510 (8.41%) aligned concordantly >1 times 15.65% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 40996304 (83.11%) aligned concordantly 0 times 3844732 (7.79%) aligned concordantly exactly 1 time 4487718 (9.10%) aligned concordantly >1 times 16.89% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 41603727 (84.34%) aligned concordantly 0 times 3563120 (7.22%) aligned concordantly exactly 1 time 4161907 (8.44%) aligned concordantly >1 times 15.66% overall alignment rate 49328754 reads; of these: 49328754 (100.00%) were paired; of these: 40994339 (83.10%) aligned concordantly 0 times 3832946 (7.77%) aligned concordantly exactly 1 time 4501469 (9.13%) aligned concordantly >1 times 16.90% overall alignment rate Processed 49328754 sequences in total Successfully deleted the temporary files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 49328754 Final Cytosine Methylation Report ================================= Total number of C's analysed: 692715717 Total methylated C's in CpG context: 18874600 Total methylated C's in CHG context: 6073487 Total methylated C's in CHH context: 25178080 Total methylated C's in Unknown context: 469222 Total unmethylated C's in CpG context: 76667988 Total unmethylated C's in CHG context: 128955794 Total unmethylated C's in CHH context: 436965768 Total unmethylated C's in Unknown context: 2669632 C methylated in CpG context: 19.8% C methylated in CHG context: 4.5% C methylated in CHH context: 5.4% C methylated in Unknown context (CN or CHN): 14.9% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF05-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF05-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 197315016 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2770765034 Total methylated C's in CpG context: 75491086 Total methylated C's in CHG context: 24300011 Total methylated C's in CHH context: 100612703 Total methylated C's in Unknown context: 1879039 Total unmethylated C's in CpG context: 306626655 Total unmethylated C's in CHG context: 515819901 Total unmethylated C's in CHH context: 1747914678 Total unmethylated C's in Unknown context: 10676837 C methylated in CpG context: 19.8% C methylated in CHG context: 4.5% C methylated in CHH context: 5.4% C methylated in Unknown context (CN or CHN): 15.0% Deleting temporary report files... Bismark completed in 0d 13h 27m 13s ==================== Bismark run complete ====================