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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 72354 and offset 4 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF06-CM01-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/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 72354 and offset 4 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF06-CM01-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/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF06-CM01-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/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 36834069) Using the subset file >CF06-CM01-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/CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (36834069 sequences in total) Writing a C -> T converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (36834069 sequences in total) Writing a C -> T converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (36834069 sequences in total) Writing a C -> T converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (36834069 sequences in total) Writing a C -> T converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (36834069 sequences in total) Input files are CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (36834069 sequences in total) Input files are CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (36834069 sequences in total) Input files are CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-CM01-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 CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (36834069 sequences in total) Input files are CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-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 CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-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:GW210315000:4:1101:30065:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TAGAGAGATAAAAAGGGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGATAGAGAGATAAAAAGGGAGAGAAAG :FFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:,FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30065:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 TATCTCTCTATCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCCCTTTTTATCTCTCTATCTCTATCTCCACAC FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FFFFFF,F:,::FFF:FFFFF,FFF,F,FFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ATATTAAATTATTATTTTATTAATTAAATTTTTATTATATTTATTTTTTATAATATTAAATATTAGTTAATTATATTTATTTATAATAATTAAATTATTATAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 TTTAATTATTATAAATAAATATAATTAACTAATATTTAATATTATAAAAAATAAATATAATAAAAATTTAATTAATAAAATAATAATTTAATATAAAATTTATACTTAT FFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:28782:1047_1:N:0:TAGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TAAAATTTTATTAATTAATATATTAATTAATATTAATTTATAAATAATTATATTTAAAAATATTTTTTTATTTATTTTATTTTTTTATAAAATTAAAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28782:1047_2:N:0:TAGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AAAATAAAATAAATAAAAAAATATTTTTAAATATAATTATTTATAAATTAATATTAATTAATATATTAATTAATAAAATTTTATAAAAAAATAAAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TATATTAAGAGATAATGTGGGTTTTAAGATATAGAAGTAATATATGTTTGGATATTATTTTAGATGAAGTTAAATTATTTTAAATAGAGTGATTGGTATTAAGGTGGGATGTAAATGTTAATAGAAATAATTTTT FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATAAAAATTCCATAAAATATAATAAAATAAACTATTTTAATCAACTAATACATAATCAACATATTAATATATAAAAATTATTTCTATTAACATTTACATCCCACCTTAATACCAATCACTCTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ACACCAAACCACCATTCCACCAACCAAACTTTTACTACATTTATCCTTCATAATATCAAACATTAACTAATCATATTCATCCACAACAACCAAACCACTATAACCACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 TTTGGTTGTTGTGGATGAATATGATTAGTTAATGTTTGATATTATGAAGGATAAATGTAGTAAAAGTTTGGTTGGTGGAATGGTGGTTTGGTGTAAGGTTTATGTTTGT FFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:30065:1047_1:N:0:TGGATCGA+TATCGCAC/1 99 NC_035785.1_GA_converted 10654590 2 85M = 10654582 -93 TAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAATAAAAAAAAAAAAAAAA :FFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:,FFFFFFFFF AS:i:-36 XS:i:-46 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:0A7A4C27C18A15T8 YS:i:-38 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:30065:1047_2:N:0:TGGATCGA+TATCGCAC/2 147 NC_035785.1_GA_converted 10654582 2 21M1D64M = 10654590 93 ATATAAAAATAAAAATAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAATA FF:FFFFFF,F,FFF,FFFFF:FFF::,:F,FFFFFF,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFF AS:i:-38 XS:i:-29 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:3A5A5A5^C2A24C36 YS:i:-36 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:28782:1047_1:N:0:TAGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 CAAAATCCCATCAATCAATATATTAACCAATACCAATTCACAAACAATTATACTTAAAAACACCTCTCTATCTACTTCATTTTCTTACAAAATCAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28782:1047_2:N:0:TAGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AAAATGAAGTAGATAGAGAGGTGTTTTTAAGTATAATTGTTTGTGAATTGGTATTGGTTAATATATTGATTGATGGGATTTTGTAAGAAAATGAAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TATATTAAAAAATAATATAAATTTTAAAATATAAAAATAATATATATTTAAATATTATTTTAAATAAAATTAAATTATTTTAAATAAAATAATTAATATTAAAATAAAATATAAATATTAATAAAAATAATTTTT FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATAAAAATTTTATAAAATATAATAAAATAAATTATTTTAATTAATTAATATATAATTAATATATTAATATATAAAAATTATTTTTATTAATATTTATATTTTATTTTAATATTAATTATTTTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM01-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:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TATATTAAAAAATAATATAAATTTTAAAATATAAAAATAATATATATTTAAATATTATTTTAAATAAAATTAAATTATTTTAAATAAAATAATTAATATTAAAATAAAATATAAATATTAATAAAAATAATTTTT FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATAAAAATTTTATAAAATATAATAAAATAAATTATTTTAATTAATTAATATATAATTAATATATTAATATATAAAAATTATTTTTATTAATATTTATATTTTATTTTAATATTAATTATTTTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-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:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ACACCAAACCACCATTCCACCAACCAAACTTTTACTACATTTATCCTTCATAATATCAAACATTAACTAATCATATTCATCCACAACAACCAAACCACTATAACCACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 TTTGGTTGTTGTGGATGAATATGATTAGTTAATGTTTGATATTATGAAGGATAAATGTAGTAAAAGTTTGGTTGGTGGAATGGTGGTTTGGTGTAAGGTTTATGTTTGT FFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-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:GW210315000:4:1101:28782:1047_1:N:0:TAGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 CAAAATCCCATCAATCAATATATTAACCAATACCAATTCACAAACAATTATACTTAAAAACACCTCTCTATCTACTTCATTTTCTTACAAAATCAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28782:1047_2:N:0:TAGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AAAATGAAGTAGATAGAGAGGTGTTTTTAAGTATAATTGTTTGTGAATTGGTATTGGTTAATATATTGATTGATGGGATTTTGTAAGAAAATGAAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-CM01-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:GW210315000:4:1101:30065:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAATAAAAAAAAAAAAAAAA :FFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:,FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30065:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 TATTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTATTTTTATTTTTATAT FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FFFFFF,F:,::FFF:FFFFF,FFF,F,FFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-CM01-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:GW210315000:4:1101:30065:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TAGAGAGATAAAAAGGGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGATAGAGAGATAAAAAGGGAGAGAAAG :FFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:,FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30065:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 TATCTCTCTATCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCCCTTTTTATCTCTCTATCTCTATCTCCACAC FFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FFFFFF,F:,::FFF:FFFFF,FFF,F,FFFFFF:FF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28782:1047_1:N:0:TAGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TAAAATTTTATTAATTAATATATTAATTAATATTAATTTATAAATAATTATATTTAAAAATATTTTTTTATTTATTTTATTTTTTTATAAAATTAAAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28782:1047_2:N:0:TAGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AAAATAAAATAAATAAAAAAATATTTTTAAATATAATTATTTATAAATTAATATTAATTAATATATTAATTAATAAAATTTTATAAAAAAATAAAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ATATTAAATTATTATTTTATTAATTAAATTTTTATTATATTTATTTTTTATAATATTAAATATTAGTTAATTATATTTATTTATAATAATTAAATTATTATAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 TTTAATTATTATAAATAAATATAATTAACTAATATTTAATATTATAAAAAATAAATATAATAAAAATTTAATTAATAAAATAATAATTTAATATAAAATTTATACTTAT FFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TATATTAAGAGATAATGTGGGTTTTAAGATATAGAAGTAATATATGTTTGGATATTATTTTAGATGAAGTTAAATTATTTTAAATAGAGTGATTGGTATTAAGGTGGGATGTAAATGTTAATAGAAATAATTTTT FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATAAAAATTCCATAAAATATAATAAAATAAACTATTTTAATCAACTAATACATAATCAACATATTAATATATAAAAATTATTTCTATTAACATTTACATCCCACCTTAATACCAATCACTCTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1122:17264:16799_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17173 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1135:19162:30013_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17114 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1135:19135:29590_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17114 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 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1436:19786:11303_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1515:31304:32127_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17195 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1473:13178:28197_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1527:7970:1642_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2158:29324:19241_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17114 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2202:17535:5838_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2202:17544:5885_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2272:30680:20306_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:26539:9565_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17152 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:26521:9533_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17152 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2326:31141:19633_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17189 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2324:10013:9283_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2303:9227:21919_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17137 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2308:27263:9972_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17152 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2343:31060:16924_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17141 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2343:28772:19946_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17141 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2526:5918:30530_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:11062:25191_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 3 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2535:31629:18818_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2635:1434:28526_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2631:13946:11240_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2621:14615:1251_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 65668307 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 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:GW210315000:4:2668:10420:36166_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1257:1154:6903_1:N:0:TGGATCGA+TGTCGCAC NC_035789.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1260:26169:34695_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1270:4119:20901_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1249:15076:19147_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1274:27480:35524_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1329:3332:6605_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1336:29803:30405_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1419:31177:12900_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1517:29432:31297_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1520:28809:10175_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1577:14172:24408_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1563:2230:36229_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1564:1307:2002_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1572:15582:36652_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17107 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1631:2311:17957_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1636:7401:3317_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2102:12057:14325_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2111:29188:7827_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17122 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2130:21377:8547_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 65668307 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2164:19452:13479_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2164:19479:13432_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2162:1678:28166_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17178 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2237:20916:7216_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2237:23556:16861_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2237:25238:23218_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 31000000 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:2:2273:22625:13150_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2273:22083:13463_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2330:2817:33708_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2444:20365:9330_1:N:0:TGGATCGT+TATCGCAC NC_007175.2 17173 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 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:2:2504:4363:15217_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17123 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2557:2763:9909_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:25762:21057_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2615:23023:28714_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 1 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2654:8205:8406_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2603:25265:32503_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32245232 (87.54%) aligned concordantly 0 times 2179301 (5.92%) aligned concordantly exactly 1 time 2409536 (6.54%) aligned concordantly >1 times 12.46% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33009282 (89.62%) aligned concordantly 0 times 1799838 (4.89%) aligned concordantly exactly 1 time 2024949 (5.50%) aligned concordantly >1 times 10.38% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33003864 (89.60%) aligned concordantly 0 times 1799712 (4.89%) aligned concordantly exactly 1 time 2030493 (5.51%) aligned concordantly >1 times 10.40% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32238545 (87.52%) aligned concordantly 0 times 2180814 (5.92%) aligned concordantly exactly 1 time 2414710 (6.56%) aligned concordantly >1 times 12.48% overall alignment rate Processed 36834069 sequences in total Successfully deleted the temporary files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36834069 Final Cytosine Methylation Report ================================= Total number of C's analysed: 212356689 Total methylated C's in CpG context: 6004388 Total methylated C's in CHG context: 1362045 Total methylated C's in CHH context: 7554153 Total methylated C's in Unknown context: 232955 Total unmethylated C's in CpG context: 21602666 Total unmethylated C's in CHG context: 39229322 Total unmethylated C's in CHH context: 136604115 Total unmethylated C's in Unknown context: 1118227 C methylated in CpG context: 21.7% C methylated in CHG context: 3.4% C methylated in CHH context: 5.2% C methylated in Unknown context (CN or CHN): 17.2% 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32239502 (87.53%) aligned concordantly 0 times 2181170 (5.92%) aligned concordantly exactly 1 time 2413397 (6.55%) aligned concordantly >1 times 12.47% overall alignment rate Processed 36000000 sequence pairs so far 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33008215 (89.61%) aligned concordantly 0 times 1798047 (4.88%) aligned concordantly exactly 1 time 2027807 (5.51%) aligned concordantly >1 times 10.39% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33009150 (89.62%) aligned concordantly 0 times 1802506 (4.89%) aligned concordantly exactly 1 time 2022413 (5.49%) aligned concordantly >1 times 10.38% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32243820 (87.54%) aligned concordantly 0 times 2182095 (5.92%) aligned concordantly exactly 1 time 2408154 (6.54%) aligned concordantly >1 times 12.46% overall alignment rate Processed 36834069 sequences in total Successfully deleted the temporary files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36834069 Final Cytosine Methylation Report ================================= Total number of C's analysed: 212365790 Total methylated C's in CpG context: 6015674 Total methylated C's in CHG context: 1358724 Total methylated C's in CHH context: 7557963 Total methylated C's in Unknown context: 233162 Total unmethylated C's in CpG context: 21584997 Total unmethylated C's in CHG context: 39235978 Total unmethylated C's in CHH context: 136612454 Total unmethylated C's in Unknown context: 1118266 C methylated in CpG context: 21.8% C methylated in CHG context: 3.3% C methylated in CHH context: 5.2% C methylated in Unknown context (CN or CHN): 17.3% Now waiting for all child processes to complete Processed 36000000 sequence pairs so far 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32237957 (87.52%) aligned concordantly 0 times 2181189 (5.92%) aligned concordantly exactly 1 time 2414923 (6.56%) aligned concordantly >1 times 12.48% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32244622 (87.54%) aligned concordantly 0 times 2179320 (5.92%) aligned concordantly exactly 1 time 2410127 (6.54%) aligned concordantly >1 times 12.46% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33008061 (89.61%) aligned concordantly 0 times 1796911 (4.88%) aligned concordantly exactly 1 time 2029097 (5.51%) aligned concordantly >1 times 10.39% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33008587 (89.61%) aligned concordantly 0 times 1800092 (4.89%) aligned concordantly exactly 1 time 2025390 (5.50%) aligned concordantly >1 times 10.39% overall alignment rate Processed 36834069 sequences in total Successfully deleted the temporary files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36834069 Final Cytosine Methylation Report ================================= Total number of C's analysed: 212267057 Total methylated C's in CpG context: 6010906 Total methylated C's in CHG context: 1362198 Total methylated C's in CHH context: 7565681 Total methylated C's in Unknown context: 233735 Total unmethylated C's in CpG context: 21592469 Total unmethylated C's in CHG context: 39208027 Total unmethylated C's in CHH context: 136527776 Total unmethylated C's in Unknown context: 1119586 C methylated in CpG context: 21.8% C methylated in CHG context: 3.4% C methylated in CHH context: 5.3% C methylated in Unknown context (CN or CHN): 17.3% 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32245374 (87.54%) aligned concordantly 0 times 2179411 (5.92%) aligned concordantly exactly 1 time 2409284 (6.54%) aligned concordantly >1 times 12.46% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33011445 (89.62%) aligned concordantly 0 times 1794813 (4.87%) aligned concordantly exactly 1 time 2027811 (5.51%) aligned concordantly >1 times 10.38% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 32242180 (87.53%) aligned concordantly 0 times 2177078 (5.91%) aligned concordantly exactly 1 time 2414811 (6.56%) aligned concordantly >1 times 12.47% overall alignment rate 36834069 reads; of these: 36834069 (100.00%) were paired; of these: 33012388 (89.62%) aligned concordantly 0 times 1798881 (4.88%) aligned concordantly exactly 1 time 2022800 (5.49%) aligned concordantly >1 times 10.38% overall alignment rate Processed 36834069 sequences in total Successfully deleted the temporary files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 36834069 Final Cytosine Methylation Report ================================= Total number of C's analysed: 212189987 Total methylated C's in CpG context: 6002804 Total methylated C's in CHG context: 1356827 Total methylated C's in CHH context: 7548412 Total methylated C's in Unknown context: 234282 Total unmethylated C's in CpG context: 21582494 Total unmethylated C's in CHG context: 39192809 Total unmethylated C's in CHH context: 136506641 Total unmethylated C's in Unknown context: 1114348 C methylated in CpG context: 21.8% C methylated in CHG context: 3.3% C methylated in CHH context: 5.2% C methylated in Unknown context (CN or CHN): 17.4% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF06-CM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF06-CM01-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/CF06-CM01-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-CM01-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: 147336276 Final Cytosine Methylation Report ================================= Total number of C's analysed: 849179523 Total methylated C's in CpG context: 24033772 Total methylated C's in CHG context: 5439794 Total methylated C's in CHH context: 30226209 Total methylated C's in Unknown context: 934134 Total unmethylated C's in CpG context: 86362626 Total unmethylated C's in CHG context: 156866136 Total unmethylated C's in CHH context: 546250986 Total unmethylated C's in Unknown context: 4470427 C methylated in CpG context: 21.8% C methylated in CHG context: 3.4% C methylated in CHH context: 5.2% C methylated in Unknown context (CN or CHN): 17.3% Deleting temporary report files... Bismark completed in 0d 7h 49m 47s ==================== Bismark run complete ====================