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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 99808 and offset 4 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 99808 and offset 4 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF07-CM02-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/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF07-CM02-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/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 52667030) Using the subset file >CF07-CM02-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/CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (52667030 sequences in total) Writing a C -> T converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF07-CM02-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 CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (52667030 sequences in total) Writing a C -> T converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF07-CM02-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 CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (52667030 sequences in total) Writing a C -> T converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF07-CM02-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 CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (52667030 sequences in total) Writing a C -> T converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF07-CM02-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 CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF07-CM02-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 CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (52667030 sequences in total) Input files are CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF07-CM02-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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27154:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ATTTTATTTTTAATATTTTTTTTTTAATAATAATTAAATAAAATTTTTTAATAATAGATTAAATTTAAAAATAAATAATATAATTTAAT ::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27154:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 TTATTTTTAAATTTAATCTATTATTAAAAAATTTTATTTAATTATTATTAAAAAAAAAATATTAAAAATAAAATAATATAATTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF07-CM02-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)) Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (52667030 sequences in total) Input files are CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF07-CM02-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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27154:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ATTCCACTTCTAATATTCCCCTCCCAACAATAACCAAATAAAATTTTCCAATAACAAACCAAATTCAAAAATAAATAACACAATTCAAC ::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27154:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 TTATTTTTGAATTTGGTTTGTTATTGGAAAATTTTATTTGGTTATTGTTGGGAGGGGAATATTAGAAGTGGAATGGTATAGTTTGGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF07-CM02-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:GW210315000:4:1101:27154:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ATTCCACTTCTAATATTCCCCTCCCAACAATAACCAAATAAAATTTTCCAATAACAAACCAAATTCAAAAATAAATAACACAATTCAAC ::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27154:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 TTATTTTTGAATTTGGTTTGTTATTGGAAAATTTTATTTGGTTATTGTTGGGAGGGGAATATTAGAAGTGGAATGGTATAGTTTGGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF07-CM02-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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27914:1047_1:N:0:GGTACCTT+GACGTCAT/1 77 * 0 0 * * 0 0 AATAAAAAAAATAAATTTAAATTATATTAATATTATAAAATATTAATATATATTTTATATTAATAATTTTTAATTTATATAATATGATTATTAAAATAATAAAAAATATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27914:1047_2:N:0:GGTACCTT+GACGTCAT/2 141 * 0 0 * * 0 0 TATTTTAATAATCATATTATATAAATTAAAAATTATTAATATAAAATATATATTAATATTTTATAATATTAATATAATTTAAATTTATTTTTTTTATTAAATATTTTTAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF07-CM02-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:GW210315000:4:1101:27154:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ATTTTATTTTTAATATTTTTTTTTTAATAATAATTAAATAAAATTTTTTAATAATAGATTAAATTTAAAAATAAATAATATAATTTAAT ::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27154:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 TTATTTTTAAATTTAATCTATTATTAAAAAATTTTATTTAATTATTATTAAAAAAAAAATATTAAAAATAAAATAATATAATTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27914:1047_1:N:0:GGTACCTT+GACGTCAT/1 77 * 0 0 * * 0 0 AACAAAAAAAATAAATTTAAATTATATTAATACTATAAAACACCAATACACACCCCACACTAACAATTTCTAACCTATACAATATAATCACCAAAATAACAAAAAATATACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27914:1047_2:N:0:GGTACCTT+GACGTCAT/2 141 * 0 0 * * 0 0 TATTTTGGTGATTATATTGTATAGGTTAGAAATTGTTAGTGTGGGGTGTGTATTGGTGTTTTATAGTATTAATATAATTTAAATTTATTTTTTTTGTTAGGTATTTTTAGTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF07-CM02-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)) >>> Writing bisulfite mapping results to CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27914:1047_1:N:0:GGTACCTT+GACGTCAT/1 77 * 0 0 * * 0 0 AACAAAAAAAATAAATTTAAATTATATTAATACTATAAAACACCAATACACACCCCACACTAACAATTTCTAACCTATACAATATAATCACCAAAATAACAAAAAATATACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27914:1047_2:N:0:GGTACCTT+GACGTCAT/2 141 * 0 0 * * 0 0 TATTTTGGTGATTATATTGTATAGGTTAGAAATTGTTAGTGTGGGGTGTGTATTGGTGTTTTATAGTATTAATATAATTTAAATTTATTTTTTTTGTTAGGTATTTTTAGTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF07-CM02-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)) Reading in the sequence files CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27914:1047_1:N:0:GGTACCTT+GACGTCAT/1 77 * 0 0 * * 0 0 AATAAAAAAAATAAATTTAAATTATATTAATATTATAAAATATTAATATATATTTTATATTAATAATTTTTAATTTATATAATATGATTATTAAAATAATAAAAAATATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27914:1047_2:N:0:GGTACCTT+GACGTCAT/2 141 * 0 0 * * 0 0 TATTTTAATAATCATATTATATAAATTAAAAATTATTAATATAAAATATATATTAATATTTTATAATATTAATATAATTTAAATTTATTTTTTTTATTAAATATTTTTAATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (52667030 sequences in total) Input files are CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 GATTAGTGTTATAATTTTATTTTGTATTTTTGTTTGTAGTTAGTTTTGGTGATATATGGAAATATGTTTTTGGTTTATTGGAGATATTTATGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAAACCAAAAACATATTTCCATATATCACCAAAACTAACTACAAACAAAAATACAAAATAAAATTATAACACTAATCCACAACCACCCCAAT F:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF07-CM02-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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 AATTAATATTATAATTTTATTTTATATTTTTATTTATAATTAATTTTAATAATATATAAAAATATATTTTTAATTTATTAAAAATATTTATAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAAATTAAAAATATATTTTTATATATTATTAAAATTAATTATAAATAAAAATATAAAATAAAATTATAATATTAATTTATAATTATTTTAAT F:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF07-CM02-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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 AATTAATATTATAATTTTATTTTATATTTTTATTTATAATTAATTTTAATAATATATAAAAATATATTTTTAATTTATTAAAAATATTTATAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAAATTAAAAATATATTTTTATATATTATTAAAATTAATTATAAATAAAAATATAAAATAAAATTATAATATTAATTTATAATTATTTTAAT F:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 GATTAGTGTTATAATTTTATTTTGTATTTTTGTTTGTAGTTAGTTTTGGTGATATATGGAAATATGTTTTTGGTTTATTGGAGATATTTATGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAAACCAAAAACATATTTCCATATATCACCAAAACTAACTACAAACAAAAATACAAAATAAAATTATAACACTAATCCACAACCACCCCAAT F:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (52667030 sequences in total) Input files are CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-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 CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-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)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 GTGAAAGTGTGGATGTAGTTTGTTGTTTAATTTTATTTGTGGTAATGTTGTGTAGATGTTTTGGTATGTAATAATGTTTATTATTTTTATTTTTTTGGGGTTGGATGGTATGATATTGTTGTGTGAATATGTTGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAACCAACATATTCACACAACAATATCATACCATCCAACCCCAAAAAAATAAAAATAATAAACATTATTACATACCAAAACATCTACACAACATTACCACAAATAAAATTAAACAACAAACTACATCCACACTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF07-CM02-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:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ATAAAAATATAAATATAATTTATTATTTAATTTTATTTATAATAATATTATATAAATATTTTAATATATAATAATATTTATTATTTTTATTTTTTTAAAATTAAATAATATAATATTATTATATAAATATATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAATTAATATATTTATATAATAATATTATATTATTTAATTTTAAAAAAATAAAAATAATAAATATTATTATATATTAAAATATTTATATAATATTATTATAAATAAAATTAAATAATAAATTATATTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF07-CM02-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:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ATAAAAATATAAATATAATTTATTATTTAATTTTATTTATAATAATATTATATAAATATTTTAATATATAATAATATTTATTATTTTTATTTTTTTAAAATTAAATAATATAATATTATTATATAAATATATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAATTAATATATTTATATAATAATATTATATTATTTAATTTTAAAAAAATAAAAATAATAAATATTATTATATATTAAAATATTTATATAATATTATTATAAATAAAATTAAATAATAAATTATATTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-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:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 GTGAAAGTGTGGATGTAGTTTGTTGTTTAATTTTATTTGTGGTAATGTTGTGTAGATGTTTTGGTATGTAATAATGTTTATTATTTTTATTTTTTTGGGGTTGGATGGTATGATATTGTTGTGTGAATATGTTGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATAACCAACATATTCACACAACAATATCATACCATCCAACCCCAAAAAAATAAAAATAATAAACATTATTACATACCAAAACATCTACACAACATTACCACAAATAAAATTAAACAACAAACTACATCCACACTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1152:20256:34726_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17178 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1275:3206:28087_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1157:26503:36620_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 2000000 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:GW210315000:4:2160:25663:20697_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 1 Processed 4000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2525:5674:35869_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1439:10981:1063_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17194 Processed 14000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:24352:18646_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 15000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1162:29848:31767_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17191 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1177:2058:26631_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 6000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2206:4426:11005_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1320:10764:32534_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17118 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2217:13693:17472_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2268:3622:3004_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17195 Processed 8000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2217:13557:16955_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2217:13991:17613_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1519:22019:1141_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17175 Processed 29000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1549:23095:34225_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 1 Processed 12000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1623:16170:36385_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 32000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1116:21495:30890_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2277:10312:17879_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2525:2871:31015_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2526:4752:23531_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1141:19199:23719_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2320:30897:34898_1:N:0:GGTACCTT+GACGTCTT NC_035781.1 2 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2323:10041:28964_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 17000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1162:29604:31970_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17191 Processed 17000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1144:10691:4257_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 46000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1178:2663:3317_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 22000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2550:1154:5901_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 23000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1425:17815:12962_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 25000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1275:17246:2425_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17192 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2671:9317:9142_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17188 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50075505 (95.08%) aligned concordantly 0 times 1183689 (2.25%) aligned concordantly exactly 1 time 1407836 (2.67%) aligned concordantly >1 times 4.92% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49493395 (93.97%) aligned concordantly 0 times 1467817 (2.79%) aligned concordantly exactly 1 time 1705818 (3.24%) aligned concordantly >1 times 6.03% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50047394 (95.03%) aligned concordantly 0 times 1208905 (2.30%) aligned concordantly exactly 1 time 1410731 (2.68%) aligned concordantly >1 times 4.97% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49464411 (93.92%) aligned concordantly 0 times 1494474 (2.84%) aligned concordantly exactly 1 time 1708145 (3.24%) aligned concordantly >1 times 6.08% overall alignment rate Processed 52667030 sequences in total Successfully deleted the temporary files CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 52667030 Final Cytosine Methylation Report ================================= Total number of C's analysed: 151957855 Total methylated C's in CpG context: 3624261 Total methylated C's in CHG context: 534250 Total methylated C's in CHH context: 3990790 Total methylated C's in Unknown context: 143738 Total unmethylated C's in CpG context: 15846744 Total unmethylated C's in CHG context: 28835373 Total unmethylated C's in CHH context: 99126437 Total unmethylated C's in Unknown context: 685532 C methylated in CpG context: 18.6% C methylated in CHG context: 1.8% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 17.3% Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1346:29414:14544_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17118 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1503:30300:20650_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17191 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1505:26856:18975_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17191 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1512:10176:30639_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1550:26820:19038_1:N:0:GGTACCTT+GGCGTCTT NC_035780.1 2 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1612:20094:5040_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 27000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1558:18945:24283_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 30000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2165:30101:1047_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17195 Processed 36000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1658:22381:32393_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17115 Processed 33000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2125:14525:10833_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 39000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2263:29107:34021_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17112 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2154:18059:12226_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 36000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2407:3387:17440_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 39000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2421:7862:26569_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2421:8621:31078_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 44000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2440:5475:24251_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17197 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2452:30725:3004_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2322:12481:34820_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2323:8811:30373_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2467:2844:3443_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2560:20437:20102_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2426:20003:33004_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2624:17454:27899_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2636:5394:8234_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2648:32289:26725_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 46000000 sequence pairs so far Processed 52000000 sequence pairs so far 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49495855 (93.98%) aligned concordantly 0 times 1466091 (2.78%) aligned concordantly exactly 1 time 1705084 (3.24%) aligned concordantly >1 times 6.02% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49464614 (93.92%) aligned concordantly 0 times 1493008 (2.83%) aligned concordantly exactly 1 time 1709408 (3.25%) aligned concordantly >1 times 6.08% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50077032 (95.08%) aligned concordantly 0 times 1181819 (2.24%) aligned concordantly exactly 1 time 1408179 (2.67%) aligned concordantly >1 times 4.92% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50049044 (95.03%) aligned concordantly 0 times 1210042 (2.30%) aligned concordantly exactly 1 time 1407944 (2.67%) aligned concordantly >1 times 4.97% overall alignment rate Processed 52667030 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 52667030 Final Cytosine Methylation Report ================================= Total number of C's analysed: 151981159 Total methylated C's in CpG context: 3628494 Total methylated C's in CHG context: 535231 Total methylated C's in CHH context: 3984273 Total methylated C's in Unknown context: 143894 Total unmethylated C's in CpG context: 15859528 Total unmethylated C's in CHG context: 28856370 Total unmethylated C's in CHH context: 99117263 Total unmethylated C's in Unknown context: 686094 C methylated in CpG context: 18.6% C methylated in CHG context: 1.8% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 17.3% Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2674:19931:36511_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2675:19325:23970_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 47000000 sequence pairs so far 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49488539 (93.96%) aligned concordantly 0 times 1468030 (2.79%) aligned concordantly exactly 1 time 1710461 (3.25%) aligned concordantly >1 times 6.04% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50045854 (95.02%) aligned concordantly 0 times 1209754 (2.30%) aligned concordantly exactly 1 time 1411422 (2.68%) aligned concordantly >1 times 4.98% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50076798 (95.08%) aligned concordantly 0 times 1181428 (2.24%) aligned concordantly exactly 1 time 1408804 (2.67%) aligned concordantly >1 times 4.92% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49462311 (93.92%) aligned concordantly 0 times 1490835 (2.83%) aligned concordantly exactly 1 time 1713884 (3.25%) aligned concordantly >1 times 6.08% overall alignment rate Processed 52667030 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 52667030 Final Cytosine Methylation Report ================================= Total number of C's analysed: 152024558 Total methylated C's in CpG context: 3632644 Total methylated C's in CHG context: 535707 Total methylated C's in CHH context: 3988619 Total methylated C's in Unknown context: 143403 Total unmethylated C's in CpG context: 15857261 Total unmethylated C's in CHG context: 28859655 Total unmethylated C's in CHH context: 99150672 Total unmethylated C's in Unknown context: 684081 C methylated in CpG context: 18.6% C methylated in CHG context: 1.8% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 17.3% Now waiting for all child processes to complete Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2530:18032:31000_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50075318 (95.08%) aligned concordantly 0 times 1183612 (2.25%) aligned concordantly exactly 1 time 1408100 (2.67%) aligned concordantly >1 times 4.92% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 50045289 (95.02%) aligned concordantly 0 times 1211867 (2.30%) aligned concordantly exactly 1 time 1409874 (2.68%) aligned concordantly >1 times 4.98% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49490035 (93.97%) aligned concordantly 0 times 1466765 (2.78%) aligned concordantly exactly 1 time 1710230 (3.25%) aligned concordantly >1 times 6.03% overall alignment rate 52667030 reads; of these: 52667030 (100.00%) were paired; of these: 49458786 (93.91%) aligned concordantly 0 times 1494590 (2.84%) aligned concordantly exactly 1 time 1713654 (3.25%) aligned concordantly >1 times 6.09% overall alignment rate Processed 52667030 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 52667030 Final Cytosine Methylation Report ================================= Total number of C's analysed: 152176200 Total methylated C's in CpG context: 3635356 Total methylated C's in CHG context: 533943 Total methylated C's in CHH context: 3984008 Total methylated C's in Unknown context: 143489 Total unmethylated C's in CpG context: 15868952 Total unmethylated C's in CHG context: 28880852 Total unmethylated C's in CHH context: 99273089 Total unmethylated C's in Unknown context: 686297 C methylated in CpG context: 18.6% C methylated in CHG context: 1.8% C methylated in CHH context: 3.9% C methylated in Unknown context (CN or CHN): 17.3% Right, cleaning up now... Deleting temporary sequence files... Failed to delete temporary FastQ file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Failed to delete temporary FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Now merging BAM files CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF07-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Failed to close output filehandle Deleting temporary BAM files... Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam: No such file or directory Writing report to /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF07-CM02-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/CF07-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Failed to read from temporary mapping report '/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF07-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt'