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/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 1 (sequences written out: 13217052) Using the subset file >CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 3 (sequences written out: 13217052) Using the subset file >CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 2 (sequences written out: 13217052) Using the subset file >CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 79732 and offset 4 (sequences written out: 13217051) Using the subset file >CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 3 (sequences written out: 13217052) Using the subset file >CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 1 (sequences written out: 13217052) Using the subset file >CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 2 (sequences written out: 13217052) Using the subset file >CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 79732 and offset 4 (sequences written out: 13217051) Using the subset file >CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz (13217052 sequences in total) Writing a C -> T converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz (13217052 sequences in total) Writing a C -> T converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz (13217051 sequences in total) Writing a C -> T converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz (13217052 sequences in total) Writing a C -> T converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz (13217052 sequences in total) Input files are CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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 CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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)) Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz (13217052 sequences in total) Input files are CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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 CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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)) Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz (13217052 sequences in total) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ATTTGGTTATGTTGGTATGAGATTGTGAATTGTTAATTAAGTAGGGGTATTAGTTAAGTAAATTGGGGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ACTAATACCCCTACTTAATTAACAATTCACAATCTCATACCAACATAACCAAATTACAAAAAATAATTA FFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:32018:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TTTAAATATAATTTAATTATTAATTTTTTATTATTTTAATTATATATATTTTATAATAAATAAATATAATATTGTGTGAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32018:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATTTATTTATTATAAAATATATATAATTAAAATAATAAAAAATTAATAATTAAATTATATTTAAAATATATTATTAAATA :FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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)) Input files are CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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 CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz (13217051 sequences in total) Input files are CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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 CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TATTAATTAATAATAAAATATATAAATTAAATAAATTTATATATAAAAATAATATTTTATTATTAATTAATAATATTTATAATTTATTATTTTTAAATATTATTTTTAAAAATATTAAATTATTTTAAATTAATA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATAACCATAAAAAAAACAAATATATTAACAACATAACATTTATCTTTATCTCACACAAAATACATAAACACATATTATAATCAAATATAAAATTAACCCTTTCCATAACCCAAATAATCAATACTTATTACAAAA FFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:32181:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TAAATTATAAATAATATATAAAAATTTATTTATATTTTAAAATTAAATATTTTTATTAAT FFFFFFF:FF:FFF,F,,FF:FFFFFF:FF,FF,FF:F:F:FF,FFF:F,F::FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32181:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TAATATTAAAATATAAATAAAATTTTAAAAATTATTTATAATTTATTAATAAAAATATTT ,:F,,FFF,F,:,,F::FFFF,FFF,FFF:,,FF,FF,,FF,,,,FF,:FF,F:,,FF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ATTTAATTATATTAATATAAAATTATAAATTATTAATTAAATAAAAATATTAATTAAATAAATTAAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATTAATATTTTTATTTAATTAATAATTTATAATTTTATATTAATATAATTAAATTATAAAAAATAGTTG FFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TACTAACCAACAATAAAATACATAAACTAAATAAACTCACACATAAAAACAATATCCCACTACTAATCAACAATACTTACAACCTACCATTTCCAAACATCATCTTTAAAAATATCAAACCATTCTAAATCAATA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATAATTATAAAAAAAATAAATATATTAATAATATAATATTTATTTTTATTTTATATAAAATATATAAATATATATTATAATTAAATATAAAATTAATTTTTTTTATAATTTAAATAATTAATATTTATTATAAAA FFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:32018:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TCTAAACACAACCCAATCACCAACTCTTTACCATCTTAATCACACATACTTTATAACAAACAAATATAATATTATATAAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32018:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATTTGTTTGTTATAAAGTATGTGTGATTAAGATGGTAAAGAGTTGGTGATTGGGTTGTGTTTAGAATATATTATTGAATA :FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:32181:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 CAAATCACAAACAACATACAAAAACTTATTTATATTCCAAAACTAAACACCTTTACCAAC FFFFFFF:FF:FFF,F,,FF:FFFFFF:FF,FF,FF:F:F:FF,FFF:F,F::FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32181:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TAGTATTGGAATATAAATAAGATTTTGAAAGTTGTTTGTGATTTGTTGGTAAAGGTGTTT ,:F,,FFF,F,:,,F::FFFF,FFF,FFF:,,FF,FF,,FF,,,,FF,:FF,F:,,FF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TACTAACCAACAATAAAATACATAAACTAAATAAACTCACACATAAAAACAATATCCCACTACTAATCAACAATACTTACAACCTACCATTTCCAAACATCATCTTTAAAAATATCAAACCATTCTAAATCAATA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATAATTATAAAAAAAATAAATATATTAATAATATAATATTTATTTTTATTTTATATAAAATATATAAATATATATTATAATTAAATATAAAATTAATTTTTTTTATAATTTAAATAATTAATATTTATTATAAAA FFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:32018:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TCTAAACACAACCCAATCACCAACTCTTTACCATCTTAATCACACATACTTTATAACAAACAAATATAATATTATATAAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32018:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATTTGTTTGTTATAAAGTATGTGTGATTAAGATGGTAAAGAGTTGGTGATTGGGTTGTGTTTAGAATATATTATTGAATA :FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ATTTAATTATATTAATATAAAATTATAAATTATTAATTAAATAAAAATATTAATTAAATAAATTAAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATTAATATTTTTATTTAATTAATAATTTATAATTTTATATTAATATAATTAAATTATAAAAAATAGTTG FFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:32181:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 CAAATCACAAACAACATACAAAAACTTATTTATATTCCAAAACTAAACACCTTTACCAAC FFFFFFF:FF:FFF,F,,FF:FFFFFF:FF,FF,FF:F:F:FF,FFF:F,F::FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32181:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TAGTATTGGAATATAAATAAGATTTTGAAAGTTGTTTGTGATTTGTTGGTAAAGGTGTTT ,:F,,FFF,F,:,,F::FFFF,FFF,FFF:,,FF,FF,,FF,,,,FF,:FF,F:,,FF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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:GW210315000:4:1101:32181:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TAAATTATAAATAATATATAAAAATTTATTTATATTTTAAAATTAAATATTTTTATTAAT FFFFFFF:FF:FFF,F,,FF:FFFFFF:FF,FF,FF:F:F:FF,FFF:F,F::FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32181:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TAATATTAAAATATAAATAAAATTTTAAAAATTATTTATAATTTATTAATAAAAATATTT ,:F,,FFF,F,:,,F::FFFF,FFF,FFF:,,FF,FF,,FF,,,,FF,:FF,F:,,FF,: YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TATTAATTAATAATAAAATATATAAATTAAATAAATTTATATATAAAAATAATATTTTATTATTAATTAATAATATTTATAATTTATTATTTTTAAATATTATTTTTAAAAATATTAAATTATTTTAAATTAATA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATAACCATAAAAAAAACAAATATATTAACAACATAACATTTATCTTTATCTCACACAAAATACATAAACACATATTATAATCAAATATAAAATTAACCCTTTCCATAACCCAAATAATCAATACTTATTACAAAA FFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ATTTGGTTATGTTGGTATGAGATTGTGAATTGTTAATTAAGTAGGGGTATTAGTTAAGTAAATTGGGGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ACTAATACCCCTACTTAATTAACAATTCACAATCTCATACCAACATAACCAAATTACAAAAAATAATTA FFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:32018:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TTTAAATATAATTTAATTATTAATTTTTTATTATTTTAATTATATATATTTTATAATAAATAAATATAATATTGTGTGAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:32018:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ATTTATTTATTATAAAATATATATAATTAAAATAATAAAAAATTAATAATTAAATTATATTTAAAATATATTATTAAATA :FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP >>> Writing bisulfite mapping results to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz Reading in the sequence files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz Reading in the sequence files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz Reading in the sequence files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.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 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 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 13000000 sequence pairs so far 13217051 reads; of these: 13217051 (100.00%) were paired; of these: 13146062 (99.46%) aligned concordantly 0 times 32021 (0.24%) aligned concordantly exactly 1 time 38968 (0.29%) aligned concordantly >1 times 0.54% overall alignment rate 13217051 reads; of these: 13217051 (100.00%) were paired; of these: 13146470 (99.47%) aligned concordantly 0 times 32029 (0.24%) aligned concordantly exactly 1 time 38552 (0.29%) aligned concordantly >1 times 0.53% overall alignment rate 13217051 reads; of these: 13217051 (100.00%) were paired; of these: 13154611 (99.53%) aligned concordantly 0 times 27542 (0.21%) aligned concordantly exactly 1 time 34898 (0.26%) aligned concordantly >1 times 0.47% overall alignment rate 13217051 reads; of these: 13217051 (100.00%) were paired; of these: 13155428 (99.53%) aligned concordantly 0 times 27163 (0.21%) aligned concordantly exactly 1 time 34460 (0.26%) aligned concordantly >1 times 0.47% overall alignment rate Processed 13217051 sequences in total Successfully deleted the temporary files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz, CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz, CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 13217051 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4320699 Total methylated C's in CpG context: 94771 Total methylated C's in CHG context: 16338 Total methylated C's in CHH context: 303784 Total methylated C's in Unknown context: 6239 Total unmethylated C's in CpG context: 418673 Total unmethylated C's in CHG context: 738695 Total unmethylated C's in CHH context: 2748438 Total unmethylated C's in Unknown context: 18559 C methylated in CpG context: 18.5% C methylated in CHG context: 2.2% C methylated in CHH context: 10.0% C methylated in Unknown context (CN or CHN): 25.2% Now waiting for all child processes to complete Processed 12000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13146522 (99.47%) aligned concordantly 0 times 31666 (0.24%) aligned concordantly exactly 1 time 38864 (0.29%) aligned concordantly >1 times 0.53% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13155000 (99.53%) aligned concordantly 0 times 27408 (0.21%) aligned concordantly exactly 1 time 34644 (0.26%) aligned concordantly >1 times 0.47% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13155448 (99.53%) aligned concordantly 0 times 27127 (0.21%) aligned concordantly exactly 1 time 34477 (0.26%) aligned concordantly >1 times 0.47% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13146303 (99.46%) aligned concordantly 0 times 31767 (0.24%) aligned concordantly exactly 1 time 38982 (0.29%) aligned concordantly >1 times 0.54% overall alignment rate Processed 13217052 sequences in total Successfully deleted the temporary files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 13217052 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4302393 Total methylated C's in CpG context: 94348 Total methylated C's in CHG context: 16841 Total methylated C's in CHH context: 303621 Total methylated C's in Unknown context: 6221 Total unmethylated C's in CpG context: 419943 Total unmethylated C's in CHG context: 735961 Total unmethylated C's in CHH context: 2731679 Total unmethylated C's in Unknown context: 18692 C methylated in CpG context: 18.3% C methylated in CHG context: 2.2% C methylated in CHH context: 10.0% C methylated in Unknown context (CN or CHN): 25.0% 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13146772 (99.47%) aligned concordantly 0 times 31825 (0.24%) aligned concordantly exactly 1 time 38455 (0.29%) aligned concordantly >1 times 0.53% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13155166 (99.53%) aligned concordantly 0 times 27183 (0.21%) aligned concordantly exactly 1 time 34703 (0.26%) aligned concordantly >1 times 0.47% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13146335 (99.46%) aligned concordantly 0 times 32041 (0.24%) aligned concordantly exactly 1 time 38676 (0.29%) aligned concordantly >1 times 0.54% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13154418 (99.53%) aligned concordantly 0 times 27707 (0.21%) aligned concordantly exactly 1 time 34927 (0.26%) aligned concordantly >1 times 0.47% overall alignment rate Processed 13217052 sequences in total Successfully deleted the temporary files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 13217052 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4333647 Total methylated C's in CpG context: 95912 Total methylated C's in CHG context: 16095 Total methylated C's in CHH context: 303022 Total methylated C's in Unknown context: 6275 Total unmethylated C's in CpG context: 421190 Total unmethylated C's in CHG context: 740920 Total unmethylated C's in CHH context: 2756508 Total unmethylated C's in Unknown context: 18834 C methylated in CpG context: 18.5% C methylated in CHG context: 2.1% C methylated in CHH context: 9.9% C methylated in Unknown context (CN or CHN): 25.0% Processed 13000000 sequence pairs so far 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13146188 (99.46%) aligned concordantly 0 times 31903 (0.24%) aligned concordantly exactly 1 time 38961 (0.29%) aligned concordantly >1 times 0.54% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13146761 (99.47%) aligned concordantly 0 times 31632 (0.24%) aligned concordantly exactly 1 time 38659 (0.29%) aligned concordantly >1 times 0.53% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13155083 (99.53%) aligned concordantly 0 times 27154 (0.21%) aligned concordantly exactly 1 time 34815 (0.26%) aligned concordantly >1 times 0.47% overall alignment rate 13217052 reads; of these: 13217052 (100.00%) were paired; of these: 13154915 (99.53%) aligned concordantly 0 times 27039 (0.20%) aligned concordantly exactly 1 time 35098 (0.27%) aligned concordantly >1 times 0.47% overall alignment rate Processed 13217052 sequences in total Successfully deleted the temporary files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz, CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz, CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 13217052 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4320400 Total methylated C's in CpG context: 96180 Total methylated C's in CHG context: 15948 Total methylated C's in CHH context: 299422 Total methylated C's in Unknown context: 6235 Total unmethylated C's in CpG context: 421596 Total unmethylated C's in CHG context: 740556 Total unmethylated C's in CHH context: 2746698 Total unmethylated C's in Unknown context: 18695 C methylated in CpG context: 18.6% C methylated in CHG context: 2.1% C methylated in CHH context: 9.8% C methylated in Unknown context (CN or CHN): 25.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.bam <<< Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.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/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED_bismark_bt2_PE_report.txt Now merging temporary reports CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.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/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED_bismark_bt2_PE_report.txt <<< Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.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: 52868207 Final Cytosine Methylation Report ================================= Total number of C's analysed: 17277139 Total methylated C's in CpG context: 381211 Total methylated C's in CHG context: 65222 Total methylated C's in CHH context: 1209849 Total methylated C's in Unknown context: 24970 Total unmethylated C's in CpG context: 1681402 Total unmethylated C's in CHG context: 2956132 Total unmethylated C's in CHH context: 10983323 Total unmethylated C's in Unknown context: 74780 C methylated in CpG context: 18.5% C methylated in CHG context: 2.2% C methylated in CHH context: 9.9% C methylated in Unknown context (CN or CHN): 25.0% Deleting temporary report files... Bismark completed in 0d 3h 9m 39s ==================== Bismark run complete ====================