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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 93372 and offset 4 (sequences written out: 33334331) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 3 (sequences written out: 33334332) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 2 (sequences written out: 33334332) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 1 (sequences written out: 33334332) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 93372 and offset 4 (sequences written out: 33334331) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 3 (sequences written out: 33334332) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to EF03-EM03-Zygote_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/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 1 (sequences written out: 33334332) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to EF03-EM03-Zygote_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/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz for PID: 0 and offset 2 (sequences written out: 33334332) Using the subset file >EF03-EM03-Zygote_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/EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to EF03-EM03-Zygote_R1_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz (33334331 sequences in total) Writing a C -> T converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz (33334332 sequences in total) Writing a C -> T converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz (33334332 sequences in total) Writing a C -> T converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz (33334332 sequences in total) Writing a C -> T converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz to EF03-EM03-Zygote_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 EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz (33334331 sequences in total) Input files are EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:27371:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TATAATAATATTATAATAATAATAAATATAATAGGTTTAAAAAATTTAAATAAAATTAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27371:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 AATTTTTTAAACCTATTATATTTATTATTATTATAATATTATTATATTTAATTTTTAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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)) Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz (33334332 sequences in total) Input files are EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27371:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 CATAACAACACCACAATAATAATAAACACAATAAACTCAAAAAATCCAAATAAAACCAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27371:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 GATTTTTTGAGTTTATTGTGTTTATTATTATTGTGGTGTTGTTATGTTTGGTTTTTAGTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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)) Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz (33334332 sequences in total) Input files are EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27299:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TAGTGTAGATTATTAATGGTGTGTTTAGTTAGTTATTGGTAATTTTTTTGGTG FFFFFFFFFFFFF:FFFFF:FFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27299:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 CAATAACTAACTAAACACACCATTAATAATCTACACTACCTACTATACCTACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27371:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 CATAACAACACCACAATAATAATAAACACAATAAACTCAAAAAATCCAAATAAAACCAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27371:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 GATTTTTTGAGTTTATTGTGTTTATTATTATTGTGGTGTTGTTATGTTTGGTTTTTAGTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TGTGGTTGTGGTGGAGGTAGATGTGGTGGTTGATTGTTGTGATGTTGTAGTATTTGTTTTTTTTGAGGTTATTGTATTTTGTGTTGAAGTGGTGGTTTTTGATGTTTTGTGGTTATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TCAAAAACCACCACTTCAACACAAAATACAATAACCTCAAAAAAAACAAATACTACAACATCACAACAATCAACCACCACATCTACCTCCACCACAACCACAAATAAACTTATACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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)) Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz (33334332 sequences in total) Input files are EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27299:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TAATATAAATTATTAATAATATATTTAATTAATTATTAATAATTTTTTTAATA FFFFFFFFFFFFF:FFFFF:FFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27299:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TAATAATTAATTAAATATATTATTAATAATTTATATTATTTATTATATTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:27371:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TATAATAATATTATAATAATAATAAATATAATAGGTTTAAAAAATTTAAATAAAATTAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27371:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 AATTTTTTAAACCTATTATATTTATTATTATTATAATATTATTATATTTAATTTTTAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27299:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TAATATAAATTATTAATAATATATTTAATTAATTATTAATAATTTTTTTAATA FFFFFFFFFFFFF:FFFFF:FFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27299:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TAATAATTAATTAAATATATTATTAATAATTTATATTATTTATTATATTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ATATATATAAATAAAAATTAAATAAAAAAAATTGATTAATTAATTAATAAATTATTATAAATTATTATAATAATAAATAAATATTATTATATAAAATAAAATTATTAATAAAATTTATATTTATTAAAATAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTATTTTAATAAATATAAATTTTATTAATAATTTTATTTTATATAATAATATTTATTTATTATTATAATAATTTATAATAATTTATTAATTAATTAATCAATTTTTTTTATTTAATTTTTATTTATATATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TATAATTATAATAAAAATAAATATAATAATTAATTATTATAATATTATAATATTTATTTTTTTTAAAATTATTATATTTTATATTAAAATAATAATTTTTAATATTTTATAATTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTAAAAATTATTATTTTAATATAAAATATAATAATTTTAAAAAAAATAAATATTATAATATTATAATAATTAATTATTATATTTATTTTTATTATAATTATAAATAAATTTATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ACACATATAAATAAAAACCAAATAAAAAAAACTAACTAATTAACCAACAAATTATTATAAACCACCACAACAATAAACAAACACTACTACATAAAATAAAACCATCAATAAAACCTATACCCACCAAAATAATAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTATTTTGGTGGGTATAGGTTTTATTGATGGTTTTATTTTATGTAGTAGTGTTTGTTTATTGTTGTGGTGGTTTATAATAATTTGTTGGTTAATTAGTTAGTTTTTTTTATTTGGTTTTTATTTATATGTGTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:27299:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TAGTGTAGATTATTAATGGTGTGTTTAGTTAGTTATTGGTAATTTTTTTGGTG FFFFFFFFFFFFF:FFFFF:FFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27299:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 CAATAACTAACTAAACACACCATTAATAATCTACACTACCTACTATACCTACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TATAATTATAATAAAAATAAATATAATAATTAATTATTATAATATTATAATATTTATTTTTTTTAAAATTATTATATTTTATATTAAAATAATAATTTTTAATATTTTATAATTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTAAAAATTATTATTTTAATATAAAATATAATAATTTTAAAAAAAATAAATATTATAATATTATAATAATTAATTATTATATTTATTTTTATTATAATTATAAATAAATTTATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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)) Reading in the sequence files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ACACATATAAATAAAAACCAAATAAAAAAAACTAACTAATTAACCAACAAATTATTATAAACCACCACAACAATAAACAAACACTACTACATAAAATAAAACCATCAATAAAACCTATACCCACCAAAATAATAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTATTTTGGTGGGTATAGGTTTTATTGATGGTTTTATTTTATGTAGTAGTGTTTGTTTATTGTTGTGGTGGTTTATAATAATTTGTTGGTTAATTAGTTAGTTTTTTTTATTTGGTTTTTATTTATATGTGTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_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:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TGTGGTTGTGGTGGAGGTAGATGTGGTGGTTGATTGTTGTGATGTTGTAGTATTTGTTTTTTTTGAGGTTATTGTATTTTGTGTTGAAGTGGTGGTTTTTGATGTTTTGTGGTTATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TCAAAAACCACCACTTCAACACAAAATACAATAACCTCAAAAAAAACAAATACTACAACATCACAACAATCAACCACCACATCTACCTCCACCACAACCACAAATAAACTTATACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ATATATATAAATAAAAATTAAATAAAAAAAATTGATTAATTAATTAATAAATTATTATAAATTATTATAATAATAAATAAATATTATTATATAAAATAAAATTATTAATAAAATTTATATTTATTAAAATAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTATTTTAATAAATATAAATTTTATTAATAATTTTATTTTATATAATAATATTTATTTATTATTATAATAATTTATAATAATTTATTAATTAATTAATCAATTTTTTTTATTTAATTTTTATTTATATATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz Reading in the sequence files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1107:6958:14450_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1173:2401:20400_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1173:1714:34053_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1213:6750:35477_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1233:8666:22701_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 17209 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1235:23836:23672_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1313:15564:2801_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1373:7039:2284_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far 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 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1450:21721:19758_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 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 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1558:29884:26475_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2235:23863:25347_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2364:12897:12179_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2374:18430:35070_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 17129 Processed 25000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2447:30544:21605_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2374:18358:34976_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 17129 Processed 25000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2409:27661:36871_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 25000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2378:12536:13839_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2432:5565:21433_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 1 Processed 29000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2643:25265:25300_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2558:25373:19194_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 30000000 sequence pairs so far 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30336518 (91.01%) aligned concordantly 0 times 1408388 (4.23%) aligned concordantly exactly 1 time 1589426 (4.77%) aligned concordantly >1 times 8.99% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30336978 (91.01%) aligned concordantly 0 times 1406919 (4.22%) aligned concordantly exactly 1 time 1590435 (4.77%) aligned concordantly >1 times 8.99% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30948990 (92.84%) aligned concordantly 0 times 1112706 (3.34%) aligned concordantly exactly 1 time 1272636 (3.82%) aligned concordantly >1 times 7.16% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30949692 (92.85%) aligned concordantly 0 times 1110553 (3.33%) aligned concordantly exactly 1 time 1274087 (3.82%) aligned concordantly >1 times 7.15% overall alignment rate Processed 33334332 sequences in total Successfully deleted the temporary files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz, EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz, EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33334332 Final Cytosine Methylation Report ================================= Total number of C's analysed: 123144105 Total methylated C's in CpG context: 3227859 Total methylated C's in CHG context: 863730 Total methylated C's in CHH context: 4858898 Total methylated C's in Unknown context: 148859 Total unmethylated C's in CpG context: 11838660 Total unmethylated C's in CHG context: 21812288 Total unmethylated C's in CHH context: 80542670 Total unmethylated C's in Unknown context: 673566 C methylated in CpG context: 21.4% C methylated in CHG context: 3.8% C methylated in CHH context: 5.7% C methylated in Unknown context (CN or CHN): 18.1% Processed 30000000 sequence pairs so far Processed 33000000 sequence pairs so far 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30948867 (92.84%) aligned concordantly 0 times 1110733 (3.33%) aligned concordantly exactly 1 time 1274732 (3.82%) aligned concordantly >1 times 7.16% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30947688 (92.84%) aligned concordantly 0 times 1113698 (3.34%) aligned concordantly exactly 1 time 1272946 (3.82%) aligned concordantly >1 times 7.16% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30336856 (91.01%) aligned concordantly 0 times 1408674 (4.23%) aligned concordantly exactly 1 time 1588802 (4.77%) aligned concordantly >1 times 8.99% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30336498 (91.01%) aligned concordantly 0 times 1408335 (4.22%) aligned concordantly exactly 1 time 1589499 (4.77%) aligned concordantly >1 times 8.99% overall alignment rate Processed 33334332 sequences in total Successfully deleted the temporary files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33334332 Final Cytosine Methylation Report ================================= Total number of C's analysed: 123208808 Total methylated C's in CpG context: 3232087 Total methylated C's in CHG context: 866229 Total methylated C's in CHH context: 4848491 Total methylated C's in Unknown context: 148640 Total unmethylated C's in CpG context: 11846271 Total unmethylated C's in CHG context: 21837159 Total unmethylated C's in CHH context: 80578571 Total unmethylated C's in Unknown context: 673311 C methylated in CpG context: 21.4% C methylated in CHG context: 3.8% C methylated in CHH context: 5.7% C methylated in Unknown context (CN or CHN): 18.1% Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2643:24695:28322_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far 33334331 reads; of these: 33334331 (100.00%) were paired; of these: 30336403 (91.01%) aligned concordantly 0 times 1409721 (4.23%) aligned concordantly exactly 1 time 1588207 (4.76%) aligned concordantly >1 times 8.99% overall alignment rate 33334331 reads; of these: 33334331 (100.00%) were paired; of these: 30949148 (92.84%) aligned concordantly 0 times 1111008 (3.33%) aligned concordantly exactly 1 time 1274175 (3.82%) aligned concordantly >1 times 7.16% overall alignment rate 33334331 reads; of these: 33334331 (100.00%) were paired; of these: 30950856 (92.85%) aligned concordantly 0 times 1111609 (3.33%) aligned concordantly exactly 1 time 1271866 (3.82%) aligned concordantly >1 times 7.15% overall alignment rate 33334331 reads; of these: 33334331 (100.00%) were paired; of these: 30336187 (91.01%) aligned concordantly 0 times 1408499 (4.23%) aligned concordantly exactly 1 time 1589645 (4.77%) aligned concordantly >1 times 8.99% overall alignment rate Processed 33334331 sequences in total Successfully deleted the temporary files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz, EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz, EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33334331 Final Cytosine Methylation Report ================================= Total number of C's analysed: 123131075 Total methylated C's in CpG context: 3230847 Total methylated C's in CHG context: 867544 Total methylated C's in CHH context: 4848156 Total methylated C's in Unknown context: 149238 Total unmethylated C's in CpG context: 11835784 Total unmethylated C's in CHG context: 21825269 Total unmethylated C's in CHH context: 80523475 Total unmethylated C's in Unknown context: 671986 C methylated in CpG context: 21.4% C methylated in CHG context: 3.8% C methylated in CHH context: 5.7% C methylated in Unknown context (CN or CHN): 18.2% Now waiting for all child processes to complete Processed 33000000 sequence pairs so far 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30334486 (91.00%) aligned concordantly 0 times 1406976 (4.22%) aligned concordantly exactly 1 time 1592870 (4.78%) aligned concordantly >1 times 9.00% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30336092 (91.01%) aligned concordantly 0 times 1406492 (4.22%) aligned concordantly exactly 1 time 1591748 (4.78%) aligned concordantly >1 times 8.99% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30947021 (92.84%) aligned concordantly 0 times 1111190 (3.33%) aligned concordantly exactly 1 time 1276121 (3.83%) aligned concordantly >1 times 7.16% overall alignment rate 33334332 reads; of these: 33334332 (100.00%) were paired; of these: 30948669 (92.84%) aligned concordantly 0 times 1111735 (3.34%) aligned concordantly exactly 1 time 1273928 (3.82%) aligned concordantly >1 times 7.16% overall alignment rate Processed 33334332 sequences in total Successfully deleted the temporary files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 33334332 Final Cytosine Methylation Report ================================= Total number of C's analysed: 123075823 Total methylated C's in CpG context: 3225444 Total methylated C's in CHG context: 863956 Total methylated C's in CHH context: 4850477 Total methylated C's in Unknown context: 148593 Total unmethylated C's in CpG context: 11827249 Total unmethylated C's in CHG context: 21804630 Total unmethylated C's in CHH context: 80504067 Total unmethylated C's in Unknown context: 674476 C methylated in CpG context: 21.4% C methylated in CHG context: 3.8% C methylated in CHH context: 5.7% C methylated in Unknown context (CN or CHN): 18.1% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.bam <<< Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_PE_report.txt Now merging temporary reports EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF03-EM03-Zygote_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/EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_PE_report.txt <<< Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> EF03-EM03-Zygote_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: 133337327 Final Cytosine Methylation Report ================================= Total number of C's analysed: 492559811 Total methylated C's in CpG context: 12916237 Total methylated C's in CHG context: 3461459 Total methylated C's in CHH context: 19406022 Total methylated C's in Unknown context: 595330 Total unmethylated C's in CpG context: 47347964 Total unmethylated C's in CHG context: 87279346 Total unmethylated C's in CHH context: 322148783 Total unmethylated C's in Unknown context: 2693339 C methylated in CpG context: 21.4% C methylated in CHG context: 3.8% C methylated in CHH context: 5.7% C methylated in Unknown context (CN or CHN): 18.1% Deleting temporary report files... Bismark completed in 0d 6h 41m 33s ==================== Bismark run complete ====================