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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz for PID: 25157 and offset 4 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM03-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/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz for PID: 25157 and offset 4 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM03-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/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 32015468) Using the subset file >EF07-EM03-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/EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM03-Larvae_R1_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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz (32015468 sequences in total) Writing a C -> T converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM03-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 EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz (32015468 sequences in total) Writing a C -> T converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM03-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 EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz (32015468 sequences in total) Writing a C -> T converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM03-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 EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz (32015468 sequences in total) Writing a C -> T converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM03-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 EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM03-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 EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz (32015468 sequences in total) Input files are EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz (32015468 sequences in total) Input files are EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM03-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:GW210315000:4:1101:26304:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATTAGTTTTTTGTTGTTTGTTATGAGTGAGGAGTGGAAGTTAATATTTATGAAAAATGGTTATGAAGTTTGTGGTTATTTATTGGATGATATGGGTGTAGATAGTATATGTAGATGTAATTAATTGAAGAATTGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26304:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAAAAAACCACCATCAAACAACTTAATATTCTTTCAATTCTTCAATTAATTACATCTACATATACTATCTACACCCATATCATCCAATAAATAACCACAAACTTCATAACCATTTTTCATAAATATTAACTTCCA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF07-EM03-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 EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz (32015468 sequences in total) Input files are EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25889:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATAGTTATATAATATAAATTTTTTTATTTTTTTTATTATATTTAATTAAAATATATTTTTTTATAAAAATTAAATTATATAATATTTTTATTAAATTATTTTTTTATATTAAATGAAAAATTTTA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25889:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 CAAACAACCAAACAAAAAACAATTCAATCAAAATCAAAAATACCCACAATACCCACAATTCAAAAATCAAAAAACAAATCAAAAATATACAATACCTCCCAAAAAACCAAACACTCAATAAATCAAATAAATCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATGAATTTAAAATGAATTTTAATGAATTTAAAATAAATTTTTAATGAATTT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 TTATTTTAAATTCATTAAAATTCATTTTAAATTCATTAAAAATTCATTTTA FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM03-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:GW210315000:4:1101:26304:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ACTAATTTTTTATTATTTATTATAAATAAAAAATAAAAATTAATATTTATAAAAAATAATTATAAAATTTATAATTATTTATTAAATAATATAAATATAAATAATATATATAAATATAATTAATTAAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26304:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAAAAAATTATTATTAAATAATTTAATATTTTTTTAATTTTTTAATTAATTATATTTATATATATTATTTATATTTATATTATTTAATAAATAATTATAAATTTTATAATTATTTTTTATAAATATTAATTTTTA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25889:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATAATCACATAACATAAACTTCTTTATTTCTCCTATCATATTTAATCAAAATATATCTCTCTACAAAAATTAAACCATATAACACTTCTACTAAATTACTTTTTTATATTAAATAAAAAATTTTA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25889:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 TAAATAATTAAATAAAAAATAATTTAATTAAAATTAAAAATATTTATAATATTTATAATTTAAAAATTAAAAAATAAATTAAAAATATATAATATTTTTTAAAAAATTAAATATTTAATAAATTAAATAAATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 99 NC_035787.1_GA_converted 74474415 1 20M1D31M = 74474400 -67 ACAAACTCAAAACAAACCCCAACAAACTCAAAACAAACTCCTAACAAACCC FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:20^A31 YS:i:-8 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 147 NC_035787.1_GA_converted 74474400 1 35M1D16M = 74474415 67 CAAAACAAACCCCTAACAAACTCAAAACAAACCCCAACAAACTCAAAACAA FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:35^A16 YS:i:-8 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25889:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATAATCACATAACATAAACTTCTTTATTTCTCCTATCATATTTAATCAAAATATATCTCTCTACAAAAATTAAACCATATAACACTTCTACTAAATTACTTTTTTATATTAAATAAAAAATTTTA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25889:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 TAAATAATTAAATAAAAAATAATTTAATTAAAATTAAAAATATTTATAATATTTATAATTTAAAAATTAAAAAATAAATTAAAAATATATAATATTTTTTAAAAAATTAAATATTTAATAAATTAAATAAATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM03-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:GW210315000:4:1101:26304:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ACTAATTTTTTATTATTTATTATAAATAAAAAATAAAAATTAATATTTATAAAAAATAATTATAAAATTTATAATTATTTATTAAATAATATAAATATAAATAATATATATAAATATAATTAATTAAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26304:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAAAAAATTATTATTAAATAATTTAATATTTTTTTAATTTTTTAATTAATTATATTTATATATATTATTTATATTTATATTATTTAATAAATAATTATAAATTTTATAATTATTTTTTATAAATATTAATTTTTA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 83 NC_035786.1_CT_converted 12194239 1 29M1D22M = 12194254 67 GGGTTTGTTAGGAGTTTGTTTTGAGTTTGTTGGGGTTTGTTTTGAGTTTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:29^T22 YS:i:-8 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 163 NC_035786.1_CT_converted 12194254 1 14M1D37M = 12194239 -67 TTGTTTTGAGTTTGTTGGGGTTTGTTTTGAGTTTGTTAGGGGTTTGTTTTG FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:14^T37 YS:i:-8 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-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)) Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz (32015468 sequences in total) Input files are EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-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 EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-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:GW210315000:4:1101:26304:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATTAGTTTTTTGTTGTTTGTTATGAGTGAGGAGTGGAAGTTAATATTTATGAAAAATGGTTATGAAGTTTGTGGTTATTTATTGGATGATATGGGTGTAGATAGTATATGTAGATGTAATTAATTGAAGAATTGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26304:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAAAAAACCACCATCAAACAACTTAATATTCTTTCAATTCTTCAATTAATTACATCTACATATACTATCTACACCCATATCATCCAATAAATAACCACAAACTTCATAACCATTTTTCATAAATATTAACTTCCA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATGAATTTAAAATGAATTTTAATGAATTTAAAATAAATTTTTAATGAATTT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 TTATTTTAAATTCATTAAAATTCATTTTAAATTCATTAAAAATTCATTTTA FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25889:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ATAGTTATATAATATAAATTTTTTTATTTTTTTTATTATATTTAATTAAAATATATTTTTTTATAAAAATTAAATTATATAATATTTTTATTAAATTATTTTTTTATATTAAATGAAAAATTTTA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25889:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 CAAACAACCAAACAAAAAACAATTCAATCAAAATCAAAAATACCCACAATACCCACAATTCAAAAATCAAAAAACAAATCAAAAATATACAATACCTCCCAAAAAACCAAACACTCAATAAATCAAATAAATCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 AGGTAGTATAGAAATATTTAGAATAATTATATGTTTTGAGGGTTAAGGTTGGTATTAATTTTTAGTTTTATGAATAGGTTTGGAAGGAGTTTAAGATTTTATATGGTAGGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAATCTTAAACTCCTTCCAAACCTATTCATAAAACTAAAAATTAATACCAACCTTAACCCTCAAAACATATAATTATTCTAAATATTTCTATACTACCTCCAAATCAAACCACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM03-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)) Reading in the sequence files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 AAATAATATAAAAATATTTAAAATAATTATACATTTTAAAAATTAAAATTAATATTAATTTTTAATTTTACAAATAAACTTAAAAAAAATTTAAAATTTTATACAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAATTTTAAATTTTTTTTAAGTTTATTTGTAAAATTAAAAATTAATATTAATTTTAATTTTTAAAATGTATAATTATTTTAAATATTTTTATATTATTTTTAAATTAAATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 AAATAATATAAAAATATTTAAAATAATTATACATTTTAAAAATTAAAATTAATATTAATTTTTAATTTTACAAATAAACTTAAAAAAAATTTAAAATTTTATACAATAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAATTTTAAATTTTTTTTAAGTTTATTTGTAAAATTAAAAATTAATATTAATTTTAATTTTTAAAATGTATAATTATTTTAAATATTTTTATATTATTTTTAAATTAAATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-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:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 AGGTAGTATAGAAATATTTAGAATAATTATATGTTTTGAGGGTTAAGGTTGGTATTAATTTTTAGTTTTATGAATAGGTTTGGAAGGAGTTTAAGATTTTATATGGTAGGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAATCTTAAACTCCTTCCAAACCTATTCATAAAACTAAAAATTAATACCAACCTTAACCCTCAAAACATATAATTATTCTAAATATTTCTATACTACCTCCAAATCAAACCACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1104:11234:26365_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668306 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1104:12075:24471_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668306 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1119:16251:8437_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668307 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1144:13060:26897_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1244:9100:10708_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668307 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1421:32090:11036_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 3 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:GW210315000:4:1518:16640:36135_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1518:16604:36166_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1578:12192:28839_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1576:25635:1924_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668307 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1576:25934:1720_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668307 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2361:11650:31313_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2468:31331:13166_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668307 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2419:8241:35149_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 17112 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2575:21875:30358_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668307 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1131:9842:10081_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1135:10312:22514_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2641:21233:23985_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 17112 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1165:21115:16329_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1174:28230:17347_1:N:0:CCGTGAAG+ATCCACTG NC_035781.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1131:9760:9940_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 1 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1164:26964:6793_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1165:21025:17738_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1215:28628:33098_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1239:8449:31939_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 2 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1419:29369:5134_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668308 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1674:28348:25567_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 17178 Processed 22000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2115:4670:36166_1:N:0:CCGTGAAG+ATCCGCTG NC_035780.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1606:10366:4319_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2145:7166:32252_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2145:7229:32268_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 3 Processed 23000000 sequence pairs so far 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:2:1663:27389:31735_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2147:16712:13150_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2312:26955:29105_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2332:16866:28510_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2332:16794:30514_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2343:22724:25598_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2232:2365:3521_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2312:27335:29387_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2346:10764:34695_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2354:26946:30718_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668306 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26736956 (83.51%) aligned concordantly 0 times 2397045 (7.49%) aligned concordantly exactly 1 time 2881467 (9.00%) aligned concordantly >1 times 16.49% overall alignment rate Processed 32000000 sequence pairs so far 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26735638 (83.51%) aligned concordantly 0 times 2389817 (7.46%) aligned concordantly exactly 1 time 2890013 (9.03%) aligned concordantly >1 times 16.49% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27141366 (84.78%) aligned concordantly 0 times 2201417 (6.88%) aligned concordantly exactly 1 time 2672685 (8.35%) aligned concordantly >1 times 15.22% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27146788 (84.79%) aligned concordantly 0 times 2205455 (6.89%) aligned concordantly exactly 1 time 2663225 (8.32%) aligned concordantly >1 times 15.21% overall alignment rate Processed 32015468 sequences in total Successfully deleted the temporary files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 32015468 Final Cytosine Methylation Report ================================= Total number of C's analysed: 368077577 Total methylated C's in CpG context: 9734861 Total methylated C's in CHG context: 1191843 Total methylated C's in CHH context: 5179246 Total methylated C's in Unknown context: 191273 Total unmethylated C's in CpG context: 43299501 Total unmethylated C's in CHG context: 75478985 Total unmethylated C's in CHH context: 233193141 Total unmethylated C's in Unknown context: 1362005 C methylated in CpG context: 18.4% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 12.3% Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2613:16848:8187_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668306 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2641:28682:4351_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 17184 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2639:27769:27164_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 17184 Processed 32000000 sequence pairs so far 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26734200 (83.50%) aligned concordantly 0 times 2397744 (7.49%) aligned concordantly exactly 1 time 2883524 (9.01%) aligned concordantly >1 times 16.50% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26734823 (83.51%) aligned concordantly 0 times 2390326 (7.47%) aligned concordantly exactly 1 time 2890319 (9.03%) aligned concordantly >1 times 16.49% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27144672 (84.79%) aligned concordantly 0 times 2208633 (6.90%) aligned concordantly exactly 1 time 2662163 (8.32%) aligned concordantly >1 times 15.21% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27141925 (84.78%) aligned concordantly 0 times 2200909 (6.87%) aligned concordantly exactly 1 time 2672634 (8.35%) aligned concordantly >1 times 15.22% overall alignment rate Processed 32015468 sequences in total Successfully deleted the temporary files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 32015468 Final Cytosine Methylation Report ================================= Total number of C's analysed: 368037290 Total methylated C's in CpG context: 9726961 Total methylated C's in CHG context: 1189857 Total methylated C's in CHH context: 5159053 Total methylated C's in Unknown context: 191607 Total unmethylated C's in CpG context: 43316681 Total unmethylated C's in CHG context: 75487700 Total unmethylated C's in CHH context: 233157038 Total unmethylated C's in Unknown context: 1361784 C methylated in CpG context: 18.3% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 12.3% 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27147603 (84.80%) aligned concordantly 0 times 2207086 (6.89%) aligned concordantly exactly 1 time 2660779 (8.31%) aligned concordantly >1 times 15.20% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26733233 (83.50%) aligned concordantly 0 times 2391695 (7.47%) aligned concordantly exactly 1 time 2890540 (9.03%) aligned concordantly >1 times 16.50% overall alignment rate Processed 32000000 sequence pairs so far 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26734614 (83.51%) aligned concordantly 0 times 2398209 (7.49%) aligned concordantly exactly 1 time 2882645 (9.00%) aligned concordantly >1 times 16.49% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27143626 (84.78%) aligned concordantly 0 times 2199217 (6.87%) aligned concordantly exactly 1 time 2672625 (8.35%) aligned concordantly >1 times 15.22% overall alignment rate Processed 32015468 sequences in total Successfully deleted the temporary files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 32015468 Final Cytosine Methylation Report ================================= Total number of C's analysed: 368287558 Total methylated C's in CpG context: 9741972 Total methylated C's in CHG context: 1191925 Total methylated C's in CHH context: 5184130 Total methylated C's in Unknown context: 192132 Total unmethylated C's in CpG context: 43331291 Total unmethylated C's in CHG context: 75528913 Total unmethylated C's in CHH context: 233309327 Total unmethylated C's in Unknown context: 1361668 C methylated in CpG context: 18.4% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 12.4% Now waiting for all child processes to complete 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27141997 (84.78%) aligned concordantly 0 times 2198775 (6.87%) aligned concordantly exactly 1 time 2674696 (8.35%) aligned concordantly >1 times 15.22% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26735254 (83.51%) aligned concordantly 0 times 2399893 (7.50%) aligned concordantly exactly 1 time 2880321 (9.00%) aligned concordantly >1 times 16.49% overall alignment rate 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 27142880 (84.78%) aligned concordantly 0 times 2208260 (6.90%) aligned concordantly exactly 1 time 2664328 (8.32%) aligned concordantly >1 times 15.22% overall alignment rate Processed 32000000 sequence pairs so far 32015468 reads; of these: 32015468 (100.00%) were paired; of these: 26735269 (83.51%) aligned concordantly 0 times 2392705 (7.47%) aligned concordantly exactly 1 time 2887494 (9.02%) aligned concordantly >1 times 16.49% overall alignment rate Processed 32015468 sequences in total Successfully deleted the temporary files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 32015468 Final Cytosine Methylation Report ================================= Total number of C's analysed: 368273612 Total methylated C's in CpG context: 9733783 Total methylated C's in CHG context: 1189469 Total methylated C's in CHH context: 5185090 Total methylated C's in Unknown context: 191501 Total unmethylated C's in CpG context: 43325748 Total unmethylated C's in CHG context: 75539567 Total unmethylated C's in CHH context: 233299955 Total unmethylated C's in Unknown context: 1362620 C methylated in CpG context: 18.3% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 12.3% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF07-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF07-EM03-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/EF07-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM03-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: 128061872 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1472676037 Total methylated C's in CpG context: 38937577 Total methylated C's in CHG context: 4763094 Total methylated C's in CHH context: 20707519 Total methylated C's in Unknown context: 766513 Total unmethylated C's in CpG context: 173273221 Total unmethylated C's in CHG context: 302035165 Total unmethylated C's in CHH context: 932959461 Total unmethylated C's in Unknown context: 5448077 C methylated in CpG context: 18.3% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in Unknown context (CN or CHN): 12.3% Deleting temporary report files... Bismark completed in 0d 11h 11m 11s ==================== Bismark run complete ====================