Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools' Reference genome folder provided is /gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ (absolute path is '/gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array'): /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 95487 and offset 4 (sequences written out: 36378494) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 36378494) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 36378495) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 36378495) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 95487 and offset 4 (sequences written out: 36378494) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF08-CM03-Zygote_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/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 36378495) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF08-CM03-Zygote_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/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 36378494) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 36378495) Using the subset file >CF08-CM03-Zygote_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/CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (36378494 sequences in total) Writing a C -> T converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF08-CM03-Zygote_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 CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (36378495 sequences in total) Writing a C -> T converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF08-CM03-Zygote_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 CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (36378494 sequences in total) Writing a C -> T converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF08-CM03-Zygote_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 CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (36378495 sequences in total) Writing a C -> T converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF08-CM03-Zygote_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 CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (36378495 sequences in total) Input files are CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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 CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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 CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (36378494 sequences in total) Input files are CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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 CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (36378494 sequences in total) Input files are CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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 CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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)) Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (36378495 sequences in total) Input files are CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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 CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31458:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TGTAAGTTTTTTTTTTTTTATTAATGTTATGATATAATTATTTGAATTGTTTTTAGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FFFF,:FFFFF,FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31458:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 CAAATAATTATATCATAACATTAATAAAAAAAAAAAAACTTACAACTAACAAATACCTA FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 GGTGATTTGATTGGTGTGTTATGGAT FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATCAAATCACCCCATCTCACACACCA FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 ATGGAATAGGTTAATGTAGGAATGTGTGTAGTTTGTTGGT FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ACATTCCTACATTAACCTATTCCATCATAATAAACTACCC FFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31512:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TAGTTGGATGTGGGTGTTGTAGTTGTATTTGGAG FFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31512:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 CAACACCCACATCCAACTAACCAACATACCAAAC FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 ATAAAATAAATTAATATAAAAATATATATAATTTATTAAT FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATATTTTTATATTAATTTATTTTATTATAATAAATTATTT FFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:31512:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 CAATTAAATATAAATATTATAATTATATTTAAAA FFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31512:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 TAATATTTATATTTAATTGATTAATATATTAAAT FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 AATAATTTAATTAATATATTATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATTAAATTATTTTATTTTATATATTA FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:31458:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TATAAATTTTTTTTTTTTTATTAACATTATAATATAATTATTTAAATTATTTTTAAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FFFF,:FFFFF,FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31458:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 TAAATAATTATATTATAATGTTAATAAAAAAAAAAAAATTTATAATTAATAAATATTTA FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:31458:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TATAAATTTTTTTTTTTTTATTAACATTATAATATAATTATTTAAATTATTTTTAAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FFFF,:FFFFF,FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31458:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 TAAATAATTATATTATAATGTTAATAAAAAAAAAAAAATTTATAATTAATAAATATTTA FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 ATAAAATAAATTAATATAAAAATATATATAATTTATTAAT FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATATTTTTATATTAATTTATTTTATTATAATAAATTATTT FFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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)) Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:31512:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 CAATTAAATATAAATATTATAATTATATTTAAAA FFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31512:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 TAATATTTATATTTAATTGATTAATATATTAAAT FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 AATAATTTAATTAATATATTATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATTAAATTATTTTATTTTATATATTA FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 ATGGAATAGGTTAATGTAGGAATGTGTGTAGTTTGTTGGT FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ACATTCCTACATTAACCTATTCCATCATAATAAACTACCC FFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31458:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TGTAAGTTTTTTTTTTTTTATTAATGTTATGATATAATTATTTGAATTGTTTTTAGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FFFF,:FFFFF,FF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31458:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 CAAATAATTATATCATAACATTAATAAAAAAAAAAAAACTTACAACTAACAAATACCTA FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 GGTGATTTGATTGGTGTGTTATGGAT FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATCAAATCACCCCATCTCACACACCA FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31512:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TAGTTGGATGTGGGTGTTGTAGTTGTATTTGGAG FFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31512:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 CAACACCCACATCCAACTAACCAACATACCAAAC FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1101:30969:27946_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17147 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 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1406:10710:33254_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17179 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1406:10420:33411_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17179 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1453:18132:6464_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17166 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1522:25409:20447_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 7000000 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:GW210315000:4:2135:4363:6355_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17193 Processed 9000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2124:28221:25661_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17120 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2343:27019:35665_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17166 Processed 10000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2521:18132:1141_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 13000000 sequence pairs so far Processed 14000000 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 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2520:23936:35744_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 16000000 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 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1211:4426:18771_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1261:15103:1783_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17147 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1155:2573:27117_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17185 Processed 20000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1173:24207:17989_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1252:25626:36761_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17190 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1259:20735:18521_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17147 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1203:3188:27117_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17194 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1213:21658:4053_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 21000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1359:23077:21887_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1372:21242:10191_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17151 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1474:16016:13636_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17151 Processed 23000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 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:2:1621:22652:2738_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 23000000 sequence pairs so far Processed 23000000 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:2:1525:21160:26052_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1541:28302:16063_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17184 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1554:3685:6057_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1562:24099:25786_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 25000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2203:2871:32456_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17194 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2204:2437:16642_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17194 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2223:1307:26553_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 26000000 sequence pairs so far Processed 28000000 sequence pairs so far 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 27000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2203:6623:32252_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17194 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2210:21142:26960_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2213:1072:14465_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2366:20699:9471_1:N:0:GACCTGAC+CTCACCAA NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2424:26142:13385_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2425:31232:4038_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2455:10474:19539_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17193 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2323:10963:14559_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17166 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2529:5150:22842_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2351:31693:21214_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17186 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2351:32045:21230_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17186 Processed 34000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2641:31123:2754_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 33000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2501:19678:15342_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 36000000 sequence pairs so far 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 33555440 (92.24%) aligned concordantly 0 times 1297685 (3.57%) aligned concordantly exactly 1 time 1525370 (4.19%) aligned concordantly >1 times 7.76% overall alignment rate 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 33552480 (92.23%) aligned concordantly 0 times 1302288 (3.58%) aligned concordantly exactly 1 time 1523727 (4.19%) aligned concordantly >1 times 7.77% overall alignment rate 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 32426388 (89.14%) aligned concordantly 0 times 1833149 (5.04%) aligned concordantly exactly 1 time 2118958 (5.82%) aligned concordantly >1 times 10.86% overall alignment rate 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 32430236 (89.15%) aligned concordantly 0 times 1825187 (5.02%) aligned concordantly exactly 1 time 2123072 (5.84%) aligned concordantly >1 times 10.85% overall alignment rate Processed 36378495 sequences in total Successfully deleted the temporary files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36378495 Final Cytosine Methylation Report ================================= Total number of C's analysed: 144949579 Total methylated C's in CpG context: 3312751 Total methylated C's in CHG context: 800362 Total methylated C's in CHH context: 5644646 Total methylated C's in Unknown context: 137077 Total unmethylated C's in CpG context: 13515796 Total unmethylated C's in CHG context: 24474621 Total unmethylated C's in CHH context: 97201403 Total unmethylated C's in Unknown context: 770725 C methylated in CpG context: 19.7% C methylated in CHG context: 3.2% C methylated in CHH context: 5.5% C methylated in Unknown context (CN or CHN): 15.1% 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 32429776 (89.15%) aligned concordantly 0 times 1823602 (5.01%) aligned concordantly exactly 1 time 2125117 (5.84%) aligned concordantly >1 times 10.85% overall alignment rate 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 32424449 (89.13%) aligned concordantly 0 times 1831622 (5.03%) aligned concordantly exactly 1 time 2122424 (5.83%) aligned concordantly >1 times 10.87% overall alignment rate 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 33552944 (92.23%) aligned concordantly 0 times 1298746 (3.57%) aligned concordantly exactly 1 time 1526805 (4.20%) aligned concordantly >1 times 7.77% overall alignment rate 36378495 reads; of these: 36378495 (100.00%) were paired; of these: 33550482 (92.23%) aligned concordantly 0 times 1302414 (3.58%) aligned concordantly exactly 1 time 1525599 (4.19%) aligned concordantly >1 times 7.77% overall alignment rate Processed 36378495 sequences in total Successfully deleted the temporary files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36378495 Final Cytosine Methylation Report ================================= Total number of C's analysed: 145015629 Total methylated C's in CpG context: 3318345 Total methylated C's in CHG context: 797491 Total methylated C's in CHH context: 5658655 Total methylated C's in Unknown context: 137440 Total unmethylated C's in CpG context: 13513236 Total unmethylated C's in CHG context: 24490563 Total unmethylated C's in CHH context: 97237339 Total unmethylated C's in Unknown context: 771857 C methylated in CpG context: 19.7% C methylated in CHG context: 3.2% C methylated in CHH context: 5.5% C methylated in Unknown context (CN or CHN): 15.1% Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2641:31024:2581_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 33549610 (92.22%) aligned concordantly 0 times 1302179 (3.58%) aligned concordantly exactly 1 time 1526705 (4.20%) aligned concordantly >1 times 7.78% overall alignment rate 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 32422808 (89.13%) aligned concordantly 0 times 1831462 (5.03%) aligned concordantly exactly 1 time 2124224 (5.84%) aligned concordantly >1 times 10.87% overall alignment rate 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 33555507 (92.24%) aligned concordantly 0 times 1295982 (3.56%) aligned concordantly exactly 1 time 1527005 (4.20%) aligned concordantly >1 times 7.76% overall alignment rate 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 32427547 (89.14%) aligned concordantly 0 times 1825916 (5.02%) aligned concordantly exactly 1 time 2125031 (5.84%) aligned concordantly >1 times 10.86% overall alignment rate Processed 36378494 sequences in total Successfully deleted the temporary files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36378494 Final Cytosine Methylation Report ================================= Total number of C's analysed: 145015874 Total methylated C's in CpG context: 3310808 Total methylated C's in CHG context: 800587 Total methylated C's in CHH context: 5667077 Total methylated C's in Unknown context: 137358 Total unmethylated C's in CpG context: 13516986 Total unmethylated C's in CHG context: 24480990 Total unmethylated C's in CHH context: 97239426 Total unmethylated C's in Unknown context: 771308 C methylated in CpG context: 19.7% C methylated in CHG context: 3.2% C methylated in CHH context: 5.5% C methylated in Unknown context (CN or CHN): 15.1% 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 32424742 (89.13%) aligned concordantly 0 times 1835014 (5.04%) aligned concordantly exactly 1 time 2118738 (5.82%) aligned concordantly >1 times 10.87% overall alignment rate 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 33556239 (92.24%) aligned concordantly 0 times 1296252 (3.56%) aligned concordantly exactly 1 time 1526003 (4.19%) aligned concordantly >1 times 7.76% overall alignment rate 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 32430439 (89.15%) aligned concordantly 0 times 1825140 (5.02%) aligned concordantly exactly 1 time 2122915 (5.84%) aligned concordantly >1 times 10.85% overall alignment rate 36378494 reads; of these: 36378494 (100.00%) were paired; of these: 33550467 (92.23%) aligned concordantly 0 times 1301644 (3.58%) aligned concordantly exactly 1 time 1526383 (4.20%) aligned concordantly >1 times 7.77% overall alignment rate Processed 36378494 sequences in total Successfully deleted the temporary files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36378494 Final Cytosine Methylation Report ================================= Total number of C's analysed: 145012145 Total methylated C's in CpG context: 3317366 Total methylated C's in CHG context: 799890 Total methylated C's in CHH context: 5659607 Total methylated C's in Unknown context: 136717 Total unmethylated C's in CpG context: 13511007 Total unmethylated C's in CHG context: 24483823 Total unmethylated C's in CHH context: 97240452 Total unmethylated C's in Unknown context: 771956 C methylated in CpG context: 19.7% C methylated in CHG context: 3.2% C methylated in CHH context: 5.5% C methylated in Unknown context (CN or CHN): 15.0% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF08-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF08-CM03-Zygote_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/CF08-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM03-Zygote_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: 145513978 Final Cytosine Methylation Report ================================= Total number of C's analysed: 579993227 Total methylated C's in CpG context: 13259270 Total methylated C's in CHG context: 3198330 Total methylated C's in CHH context: 22629985 Total methylated C's in Unknown context: 548592 Total unmethylated C's in CpG context: 54057025 Total unmethylated C's in CHG context: 97929997 Total unmethylated C's in CHH context: 388918620 Total unmethylated C's in Unknown context: 3085846 C methylated in CpG context: 19.7% C methylated in CHG context: 3.2% C methylated in CHH context: 5.5% C methylated in Unknown context (CN or CHN): 15.1% Deleting temporary report files... Bismark completed in 0d 7h 43m 59s ==================== Bismark run complete ====================