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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 99793 and offset 4 (sequences written out: 28825747) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 28825747) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 28825748) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 28825747) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 99793 and offset 4 (sequences written out: 28825747) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz to EF06-EM02-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/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 28825748) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz to EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 28825747) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz to EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 28825747) Using the subset file >EF06-EM02-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/EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz to EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz (28825748 sequences in total) Writing a C -> T converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to EF06-EM02-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 EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz to EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz (28825747 sequences in total) Writing a C -> T converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to EF06-EM02-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 EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz to EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz (28825747 sequences in total) Writing a C -> T converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to EF06-EM02-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 EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz to EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz (28825747 sequences in total) Writing a C -> T converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to EF06-EM02-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 EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz to EF06-EM02-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 EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz (28825748 sequences in total) Input files are EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-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)) Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz (28825747 sequences in total) Input files are EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz (28825747 sequences in total) Input files are EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF06-EM02-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:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 AAAAAATTTTAATATATAAAAAATTGTTTAAAATTTTTATAATGAAAGAAAATAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 ATTATAAAAATTTTAAACAATTTTTTATATATTAAAATTTTTTTATATATTTTAAATT F:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM02-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:GW210315000:4:1101:28854:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TTATGTAGTATGTTGTGGTAGATTTAGAAATATTAAGTTGAGAATAGGAGAGTTTATTATTATGTTGTGTGTTGGTTTTAATTTGTTTGATATTTGTAATTTGTTTTTTTGAGAATTAGAATTTAAATTGTATTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28854:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 AACAATACAATTTAAATTCTAATTCTCAAAAAAACAAATTACAAATATCAAACAAATTAAAACCAACACACAACATAATAATAAACTCTCCTATTCTCAACTTAATATTTCTAAATCTACCACAACATACTACAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF06-EM02-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:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TTTGTTATTGAAATAAATTAATTTTTTTTTTAGTGTTTTTGTATGGTAGAATATTGGTTTGTTTGTTGTGTTAATGGTGTATTTTGTATTTTTGGAGATAAATAGTATTATGTTTTTTTGGTATATTATGTGGGT FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 ATTCACCACAACACAAACATTTTTAATTTAAAAAAAACCTTACCACACCTACACCATACCTTAAACTTTATAACCCACATAATATACCAAAAAAACATAATACTATTTATCTCCAAAAATACAAAATACACCATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz (28825747 sequences in total) Input files are EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF06-EM02-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 EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29125:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TGTAGGGTGAGATTGTGGTGTTGGTTTATAGTTATTTTGGTGGTTTGTTTTGGTTGAGATTGGAAGAGTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29125:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 TCAACCAAAACAAACCACCAAAATAACTATAAACCAACACCACAATCTCACCCTACATTTCTACCTACAACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 AAAAAATTCCAACATACAAAAAATCATCCAAAACCTCTACAACAAAAAAAAACAACTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 GTTGTAGAGGTTTTGGATGATTTTTTGTATGTTGGAATTTTTTTGTATGTTTTGGATT F:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM02-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:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 CCCACTACCAAAACAAACTAACCCCCTCTTTAATATTTTTATATAATAAAATATTAACTTATTTATTATATTAATAATATATTTTATATTTTTAAAAATAAATAATATTATATTTTTTTAATATATTATATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 ATTTATTATAATATAAATATTTTTAATTTAAAAAAAATTTTATTATATTTATATTATATTTTAAATTTTATAATTTATATAATATATTAAAAAAATATAATATTATTTATTTTTAAAAATATAAAATATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM02-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:GW210315000:4:1101:28854:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TTATATAATATATCATAATAAATTTAAAAATATTAAATTAAAAATAAAAAAATTTATTATTATATCATATATTAATTTTAATTTATTTAATATTCATAATTTATTTTTTTAAAAATTAAAATTTAAATTATATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28854:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 AATAATATAATTTAAATTTTAATTTTTAAAAAAATAAATTATGAATATTAAATAAATTAAAATTAATATATGATATAATAATAAATTTTTTTATTTTTAATTTAATATTTTTAAATTTATTATGATATATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF06-EM02-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:GW210315000:4:1101:28854:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TTATATAATATATCATAATAAATTTAAAAATATTAAATTAAAAATAAAAAAATTTATTATTATATCATATATTAATTTTAATTTATTTAATATTCATAATTTATTTTTTTAAAAATTAAAATTTAAATTATATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28854:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 AATAATATAATTTAAATTTTAATTTTTAAAAAAATAAATTATGAATATTAAATAAATTAAAATTAATATATGATATAATAATAAATTTTTTTATTTTTAATTTAATATTTTTAAATTTATTATGATATATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF06-EM02-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:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 CCCACTACCAAAACAAACTAACCCCCTCTTTAATATTTTTATATAATAAAATATTAACTTATTTATTATATTAATAATATATTTTATATTTTTAAAAATAAATAATATTATATTTTTTTAATATATTATATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 ATTTATTATAATATAAATATTTTTAATTTAAAAAAAATTTTATTATATTTATATTATATTTTAAATTTTATAATTTATATAATATATTAAAAAAATATAATATTATTTATTTTTAAAAATATAAAATATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-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:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 83 NC_035789.1_CT_converted 8475991 42 58M = 8476006 73 GAGTTGTTTTTTTTTGTTGTAGAGGTTTTGGATGATTTTTTGTATGTTGGAATTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:51T6 YS:i:-6 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 163 NC_035789.1_CT_converted 8476006 42 58M = 8475991 -73 GTTGTAGAGGTTTTGGATGATTTTTTGTATGTTGGAATTTTTTTGTATGTTTTGGATT F:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:36T21 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29125:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TATAAAATAAAATTATAATATTAATTTATAATTATTTTAATAATTTATTTTAATTAAAATCAAAAAAACATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29125:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 TTAATTAAAATAAATTATTAAAATAATTATAAATTAATATTATAATTTTATTTTATATTTTTATTTATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF06-EM02-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:GW210315000:4:1101:28854:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TTATGTAGTATGTTGTGGTAGATTTAGAAATATTAAGTTGAGAATAGGAGAGTTTATTATTATGTTGTGTGTTGGTTTTAATTTGTTTGATATTTGTAATTTGTTTTTTTGAGAATTAGAATTTAAATTGTATTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28854:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 AACAATACAATTTAAATTCTAATTCTCAAAAAAACAAATTACAAATATCAAACAAATTAAAACCAACACACAACATAATAATAAACTCTCCTATTCTCAACTTAATATTTCTAAATCTACCACAACATACTACAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TTTGTTATTGAAATAAATTAATTTTTTTTTTAGTGTTTTTGTATGGTAGAATATTGGTTTGTTTGTTGTGTTAATGGTGTATTTTGTATTTTTGGAGATAAATAGTATTATGTTTTTTTGGTATATTATGTGGGT FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 ATTCACCACAACACAAACATTTTTAATTTAAAAAAAACCTTACCACACCTACACCATACCTTAAACTTTATAACCCACATAATATACCAAAAAAACATAATACTATTTATCTCCAAAAATACAAAATACACCATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 AAAAAATTTTAATATATAAAAAATTGTTTAAAATTTTTATAATGAAAGAAAATAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 ATTATAAAAATTTTAAACAATTTTTTATATATTAAAATTTTTTTATATATTTTAAATT F:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29125:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TATAAAATAAAATTATAATATTAATTTATAATTATTTTAATAATTTATTTTAATTAAAATCAAAAAAACATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29125:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 TTAATTAAAATAAATTATTAAAATAATTATAAATTAATATTATAATTTTATTTTATATTTTTATTTATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF06-EM02-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)) Reading in the sequence files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29125:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 TGTAGGGTGAGATTGTGGTGTTGGTTTATAGTTATTTTGGTGGTTTGTTTTGGTTGAGATTGGAAGAGTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29125:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 TCAACCAAAACAAACCACCAAAATAACTATAAACCAACACCACAATCTCACCCTACATTTCTACCTACAACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1168:11641:3615_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 1 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 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1372:15176:24048_1:N:0:GCAGAATT+TGGCCGGT NC_035786.1 57830728 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1636:4689:28933_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 65668306 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1646:19895:36636_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1636:3658:28526_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 65668306 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 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2261:18756:21418_1:N:0:ACAGAATT+TGGCCGGT NC_035780.1 65668305 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2346:22372:15937_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2349:31376:22263_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 3 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2360:20247:6684_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 3 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2645:9968:35196_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1318:30038:15969_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1318:30409:33771_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1349:16586:22294_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1320:15176:21887_1:N:0:GCAGAAGT+TGGCCGGT NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1229:22290:27821_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1242:4734:13448_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1424:28203:9846_1:N:0:GCAGAATT+TGGCCGGT NC_035786.1 57830724 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1424:28248:10269_1:N:0:GCAGAATT+TGGCCGGT NC_035786.1 57830724 Processed 16000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1605:3016:7310_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1462:12807:1282_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 2 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1652:17626:11851_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1565:6515:5729_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 22000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2276:10520:20400_1:N:0:ACAGAATT+TGGCCGGT NC_035780.1 2 Processed 22000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2351:7157:35086_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2375:19904:2018_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2424:27670:12367_1:N:0:GCAGAATT+TGGCCGGT NC_035786.1 57830724 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2414:31846:18568_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 17173 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2529:22173:20509_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 2 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2650:20419:24549_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2619:1850:30342_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 17115 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2608:8784:29230_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 24151363 (83.78%) aligned concordantly 0 times 2172096 (7.54%) aligned concordantly exactly 1 time 2502288 (8.68%) aligned concordantly >1 times 16.22% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 23927468 (83.01%) aligned concordantly 0 times 2268955 (7.87%) aligned concordantly exactly 1 time 2629324 (9.12%) aligned concordantly >1 times 16.99% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 24139254 (83.74%) aligned concordantly 0 times 2173246 (7.54%) aligned concordantly exactly 1 time 2513247 (8.72%) aligned concordantly >1 times 16.26% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 23921660 (82.99%) aligned concordantly 0 times 2265875 (7.86%) aligned concordantly exactly 1 time 2638212 (9.15%) aligned concordantly >1 times 17.01% overall alignment rate Processed 28825747 sequences in total Successfully deleted the temporary files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28825747 Final Cytosine Methylation Report ================================= Total number of C's analysed: 344479565 Total methylated C's in CpG context: 10570464 Total methylated C's in CHG context: 1830095 Total methylated C's in CHH context: 7007856 Total methylated C's in Unknown context: 329482 Total unmethylated C's in CpG context: 41497030 Total unmethylated C's in CHG context: 72619210 Total unmethylated C's in CHH context: 210954910 Total unmethylated C's in Unknown context: 1424042 C methylated in CpG context: 20.3% C methylated in CHG context: 2.5% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 18.8% Now waiting for all child processes to complete Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 27000000 sequence pairs so far 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 23923792 (82.99%) aligned concordantly 0 times 2263437 (7.85%) aligned concordantly exactly 1 time 2638518 (9.15%) aligned concordantly >1 times 17.01% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 24144168 (83.76%) aligned concordantly 0 times 2169700 (7.53%) aligned concordantly exactly 1 time 2511879 (8.71%) aligned concordantly >1 times 16.24% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 23928253 (83.01%) aligned concordantly 0 times 2268931 (7.87%) aligned concordantly exactly 1 time 2628563 (9.12%) aligned concordantly >1 times 16.99% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 24149183 (83.78%) aligned concordantly 0 times 2174009 (7.54%) aligned concordantly exactly 1 time 2502555 (8.68%) aligned concordantly >1 times 16.22% overall alignment rate Processed 28825747 sequences in total Successfully deleted the temporary files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28825747 Final Cytosine Methylation Report ================================= Total number of C's analysed: 344180975 Total methylated C's in CpG context: 10565113 Total methylated C's in CHG context: 1831220 Total methylated C's in CHH context: 7010886 Total methylated C's in Unknown context: 329619 Total unmethylated C's in CpG context: 41440610 Total unmethylated C's in CHG context: 72558810 Total unmethylated C's in CHH context: 210774336 Total unmethylated C's in Unknown context: 1424327 C methylated in CpG context: 20.3% C methylated in CHG context: 2.5% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 18.8% 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 23929637 (83.01%) aligned concordantly 0 times 2267878 (7.87%) aligned concordantly exactly 1 time 2628232 (9.12%) aligned concordantly >1 times 16.99% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 24147406 (83.77%) aligned concordantly 0 times 2174318 (7.54%) aligned concordantly exactly 1 time 2504023 (8.69%) aligned concordantly >1 times 16.23% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 24138801 (83.74%) aligned concordantly 0 times 2171223 (7.53%) aligned concordantly exactly 1 time 2515723 (8.73%) aligned concordantly >1 times 16.26% overall alignment rate 28825747 reads; of these: 28825747 (100.00%) were paired; of these: 23926603 (83.00%) aligned concordantly 0 times 2261069 (7.84%) aligned concordantly exactly 1 time 2638075 (9.15%) aligned concordantly >1 times 17.00% overall alignment rate Processed 28825747 sequences in total Successfully deleted the temporary files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28825747 Final Cytosine Methylation Report ================================= Total number of C's analysed: 344110483 Total methylated C's in CpG context: 10581183 Total methylated C's in CHG context: 1831680 Total methylated C's in CHH context: 7018008 Total methylated C's in Unknown context: 328071 Total unmethylated C's in CpG context: 41432231 Total unmethylated C's in CHG context: 72538149 Total unmethylated C's in CHH context: 210709232 Total unmethylated C's in Unknown context: 1424810 C methylated in CpG context: 20.3% C methylated in CHG context: 2.5% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 18.7% Processed 28000000 sequence pairs so far 28825748 reads; of these: 28825748 (100.00%) were paired; of these: 24141541 (83.75%) aligned concordantly 0 times 2171998 (7.53%) aligned concordantly exactly 1 time 2512209 (8.72%) aligned concordantly >1 times 16.25% overall alignment rate 28825748 reads; of these: 28825748 (100.00%) were paired; of these: 24148941 (83.78%) aligned concordantly 0 times 2174734 (7.54%) aligned concordantly exactly 1 time 2502073 (8.68%) aligned concordantly >1 times 16.22% overall alignment rate 28825748 reads; of these: 28825748 (100.00%) were paired; of these: 23929459 (83.01%) aligned concordantly 0 times 2270146 (7.88%) aligned concordantly exactly 1 time 2626143 (9.11%) aligned concordantly >1 times 16.99% overall alignment rate 28825748 reads; of these: 28825748 (100.00%) were paired; of these: 23927159 (83.01%) aligned concordantly 0 times 2263626 (7.85%) aligned concordantly exactly 1 time 2634963 (9.14%) aligned concordantly >1 times 16.99% overall alignment rate Processed 28825748 sequences in total Successfully deleted the temporary files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 28825748 Final Cytosine Methylation Report ================================= Total number of C's analysed: 344275347 Total methylated C's in CpG context: 10564751 Total methylated C's in CHG context: 1829223 Total methylated C's in CHH context: 7012836 Total methylated C's in Unknown context: 328596 Total unmethylated C's in CpG context: 41461294 Total unmethylated C's in CHG context: 72571653 Total unmethylated C's in CHH context: 210835590 Total unmethylated C's in Unknown context: 1424143 C methylated in CpG context: 20.3% C methylated in CHG context: 2.5% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 18.7% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF06-EM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF06-EM02-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/EF06-EM02-Larvae_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> EF06-EM02-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: 115302989 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1377046370 Total methylated C's in CpG context: 42281511 Total methylated C's in CHG context: 7322218 Total methylated C's in CHH context: 28049586 Total methylated C's in Unknown context: 1315768 Total unmethylated C's in CpG context: 165831165 Total unmethylated C's in CHG context: 290287822 Total unmethylated C's in CHH context: 843274068 Total unmethylated C's in Unknown context: 5697322 C methylated in CpG context: 20.3% C methylated in CHG context: 2.5% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 18.8% Deleting temporary report files... Bismark completed in 0d 7h 11m 58s ==================== Bismark run complete ====================