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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 59135531) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 59135532) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 59135532) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 25141 and offset 4 (sequences written out: 59135531) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 59135532) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM01-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/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 59135532) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM01-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/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 25141 and offset 4 (sequences written out: 59135531) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM01-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/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 59135531) Using the subset file >EF07-EM01-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/EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (59135531 sequences in total) Writing a C -> T converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM01-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 EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (59135532 sequences in total) Writing a C -> T converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM01-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 EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (59135532 sequences in total) Writing a C -> T converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM01-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 EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (59135531 sequences in total) Writing a C -> T converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM01-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 EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF07-EM01-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 EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (59135532 sequences in total) Input files are EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TTAATTTAAAAATTAAATTTTAATTAAATTATAAATAATATTTAATATAATTTTATAATAAATATAGTTTATAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TTATTATAAAATTATATTAAATATTATTTATAATTTAATTAAAATTTAATTTTTAAATTAAATTTATAAATTTATC FFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM01-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)) Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (59135532 sequences in total) Input files are EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ATTTAATTTAATAATTTATTTAAAATTATTAAATTAAATTATATTTATAAATAATTTTAATAAAATTAATAATATTATTTTTAATAAATAAAAAAAATAAAAATTTTAATAATTTATTATTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 ATTAAAATTTTTATTTTTTTTATTTATTAAAAATAATATTATTAATTTTATTAAAATTATTTATAAATATAATTTAATTTAATAATTTTAAATAAATTATTAAATTAAATAATTTTTATATAATT FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM01-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)) Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (59135531 sequences in total) Input files are EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TCAATTTAAAAATCAAATCCTAACTAAACTATAAACAATATTTAACACAACTTTATAATAAACATAATTTATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TTATTATAAAGTTGTGTTAAATATTGTTTATAGTTTAGTTAGGATTTGATTTTTAAATTGAATTTATAAGTTTGTT FFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27552:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TGTGTTGGTATGGATTTTGTTGATTTATAGGAATTGATTATTATTTTTTGTTAGATGGTATTTAAAGGTGATGTTAGTGATGTGTAGTTTATTGTATTATTGATTGTTGTTAATTAGTATGGTTTTAATTTGTGG FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27552:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TACCATTCTACTTATCAAAAAAAACATAAATTTCTTTCATCCACAAATTAAAACCATACTAATTAACAACAATCAATAATACAATAAACTACACATCACTAACATCACCTTTAAATACCATCTAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ACCTAACTCAACAACCTACTCAAAATCATCAAATTAAACCACACCTATAAACAATTCTAACAAAACCAATAATATCACCTTCAACAAACAAAAAAAATAAAAATCCCAATAATTCATCATCTACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 ATTGGGATTTTTATTTTTTTTGTTTGTTGAAGGTGATATTATTGGTTTTGTTAGAATTGTTTATAGGTGTGGTTTAATTTGATGATTTTGAGTAGGTTGTTGAGTTAGGTGATTTTTGTATAGTT FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM01-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:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TCAATTTAAAAATCAAATCCTAACTAAACTATAAACAATATTTAACACAACTTTATAATAAACATAATTTATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TTATTATAAAGTTGTGTTAAATATTGTTTATAGTTTAGTTAGGATTTGATTTTTAAATTGAATTTATAAGTTTGTT FFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ACCTAACTCAACAACCTACTCAAAATCATCAAATTAAACCACACCTATAAACAATTCTAACAAAACCAATAATATCACCTTCAACAAACAAAAAAAATAAAAATCCCAATAATTCATCATCTACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 ATTGGGATTTTTATTTTTTTTGTTTGTTGAAGGTGATATTATTGGTTTTGTTAGAATTGTTTATAGGTGTGGTTTAATTTGATGATTTTGAGTAGGTTGTTGAGTTAGGTGATTTTTGTATAGTT FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ATTTAATTTAATAATTTATTTAAAATTATTAAATTAAATTATATTTATAAATAATTTTAATAAAATTAATAATATTATTTTTAATAAATAAAAAAAATAAAAATTTTAATAATTTATTATTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 ATTAAAATTTTTATTTTTTTTATTTATTAAAAATAATATTATTAATTTTATTAAAATTATTTATAAATATAATTTAATTTAATAATTTTAAATAAATTATTAAATTAAATAATTTTTATATAATT FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27552:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TATATTAATATAAATTTTATTAATTTATAAAAATTAATTATTATTTTTTATTAAATAATACTTAAAAATAATATTAATAATATATAATTTATTATATTATTAATTATTATTAATTAATATAATTTTAATTTATAA FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27552:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TATTATTTTATTTATTAAAAAAAATATAAATTTTTTTTATTTATAAATTAAAATTATATTAATTAATAATAATTAATAATATAATAAATTATATATTATTAATATTATTTTTAAGTATTATTTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF07-EM01-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:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TTAATTTAAAAATTAAATTTTAATTAAATTATAAATAATATTTAATATAATTTTATAATAAATATAGTTTATAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TTATTATAAAATTATATTAAATATTATTTATAATTTAATTAAAATTTAATTTTTAAATTAAATTTATAAATTTATC FFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Reading in the sequence files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27552:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TATATTAATATAAATTTTATTAATTTATAAAAATTAATTATTATTTTTTATTAAATAATACTTAAAAATAATATTAATAATATATAATTTATTATATTATTAATTATTATTAATTAATATAATTTTAATTTATAA FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27552:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TATTATTTTATTTATTAAAAAAAATATAAATTTTTTTTATTTATAAATTAAAATTATATTAATTAATAATAATTAATAATATAATAAATTATATATTATTAATATTATTTTTAAGTATTATTTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27552:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TGTGTTGGTATGGATTTTGTTGATTTATAGGAATTGATTATTATTTTTTGTTAGATGGTATTTAAAGGTGATGTTAGTGATGTGTAGTTTATTGTATTATTGATTGTTGTTAATTAGTATGGTTTTAATTTGTGG FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27552:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TACCATTCTACTTATCAAAAAAAACATAAATTTCTTTCATCCACAAATTAAAACCATACTAATTAACAACAATCAATAATACAATAAACTACACATCACTAACATCACCTTTAAATACCATCTAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (59135531 sequences in total) Input files are EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM01-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 EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27896:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TTTAATTAAAATAAATTATTAAAATAATTATAAATTAATATTATTATAAAATTTATAATTATTTAAATATTTATTATATTTATTTTTTATAATATTAGTAAAAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27896:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TAAAAAATAAATATAATAAATATTTAAATAATTATAAATTTTATAATAATATTAATTTATAATTATTTTAATAATTTATTTTAATTAAATAAAATTAATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27896:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 CTCAACCAAAACAAACCACCAAAATAACTATAAACCAACATTATTACAAAACTTACAACCACTCAAACATTTACTACATTTATCCTTCATAATATCAATAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27896:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TGAAGGATAAATGTAGTAAATGTTTGAGTGGTTGTAAGTTTTGTAATAATGTTGGTTTATAGTTATTTTGGTGGTTTGTTTTGGTTGAGTGAGGTTGATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27896:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 CTCAACCAAAACAAACCACCAAAATAACTATAAACCAACATTATTACAAAACTTACAACCACTCAAACATTTACTACATTTATCCTTCATAATATCAATAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27896:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TGAAGGATAAATGTAGTAAATGTTTGAGTGGTTGTAAGTTTTGTAATAATGTTGGTTTATAGTTATTTTGGTGGTTTGTTTTGGTTGAGTGAGGTTGATTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM01-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:GW210315000:4:1101:27896:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 TTTAATTAAAATAAATTATTAAAATAATTATAAATTAATATTATTATAAAATTTATAATTATTTAAATATTTATTATATTTATTTTTTATAATATTAGTAAAAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27896:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TAAAAAATAAATATAATAAATATTTAAATAATTATAAATTTTATAATAATATTAATTTATAATTATTTTAATAATTTATTTTAATTAAATAAAATTAATTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1205:23854:9455_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17193 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:GW210315000:4:1501:21169:22091_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1501:21133:22091_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1559:24858:34554_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17178 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1564:4020:8265_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1615:26684:2707_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2162:26151:6950_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 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:GW210315000:4:2173:32298:3505_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2238:18701:5008_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2412:14317:7686_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2406:11071:27806_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2409:8214:17221_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1102:18593:31532_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1159:31286:21136_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1102:23303:29293_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1171:21314:3583_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Processed 22000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1173:1994:16501_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17146 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1225:15655:24815_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 23000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1146:32027:10927_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1153:22245:8328_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1154:23737:23719_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1263:29351:3881_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1237:27208:12352_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1245:9733:1157_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1171:31096:13980_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 23000000 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:2:1245:9525:1047_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Processed 26000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1415:7374:16047_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Processed 29000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1470:22092:12414_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 2 Processed 30000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1513:23204:24079_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17173 Processed 31000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1526:10113:8390_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1529:27489:36918_1:N:0:GTCGGAGC+TTATAACC NC_035789.1 1 Processed 29000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1572:29143:10755_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1505:30445:25504_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1559:25084:13213_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 38000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1678:27326:1846_1:N:0:GTCGGAGC+TTATAACC NC_035781.1 2 Processed 39000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:1443:11005_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 40000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2202:11397:36511_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2125:22525:20306_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17173 Processed 38000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2212:10890:12712_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17173 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:17363:15217_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 39000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2128:25120:23954_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2172:3450:24439_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 45000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2338:32841:2065_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2445:7898:20494_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17186 Processed 51000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2336:15338:19319_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17173 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2519:11234:6762_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17177 Processed 48000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2445:7274:4789_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17186 Processed 51000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:24749:2926_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 59000000 sequence pairs so far 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 56563345 (95.65%) aligned concordantly 0 times 1150890 (1.95%) aligned concordantly exactly 1 time 1421296 (2.40%) aligned concordantly >1 times 4.35% overall alignment rate 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 55601396 (94.02%) aligned concordantly 0 times 1604533 (2.71%) aligned concordantly exactly 1 time 1929602 (3.26%) aligned concordantly >1 times 5.98% overall alignment rate 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 55582667 (93.99%) aligned concordantly 0 times 1619474 (2.74%) aligned concordantly exactly 1 time 1933390 (3.27%) aligned concordantly >1 times 6.01% overall alignment rate 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 56554722 (95.64%) aligned concordantly 0 times 1158172 (1.96%) aligned concordantly exactly 1 time 1422637 (2.41%) aligned concordantly >1 times 4.36% overall alignment rate Processed 59135531 sequences in total Successfully deleted the temporary files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 59135531 Final Cytosine Methylation Report ================================= Total number of C's analysed: 134598854 Total methylated C's in CpG context: 2729808 Total methylated C's in CHG context: 377935 Total methylated C's in CHH context: 2867139 Total methylated C's in Unknown context: 106216 Total unmethylated C's in CpG context: 14323971 Total unmethylated C's in CHG context: 24518597 Total unmethylated C's in CHH context: 89781404 Total unmethylated C's in Unknown context: 626921 C methylated in CpG context: 16.0% C methylated in CHG context: 1.5% C methylated in CHH context: 3.1% C methylated in Unknown context (CN or CHN): 14.5% Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2622:6849:14325_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 54000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2630:17743:9549_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17186 Processed 55000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2573:23972:9627_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2663:32307:34115_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 55586335 (94.00%) aligned concordantly 0 times 1620441 (2.74%) aligned concordantly exactly 1 time 1928755 (3.26%) aligned concordantly >1 times 6.00% overall alignment rate 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 56551298 (95.63%) aligned concordantly 0 times 1158637 (1.96%) aligned concordantly exactly 1 time 1425596 (2.41%) aligned concordantly >1 times 4.37% overall alignment rate 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 56562433 (95.65%) aligned concordantly 0 times 1150869 (1.95%) aligned concordantly exactly 1 time 1422229 (2.41%) aligned concordantly >1 times 4.35% overall alignment rate Processed 57000000 sequence pairs so far 59135531 reads; of these: 59135531 (100.00%) were paired; of these: 55603218 (94.03%) aligned concordantly 0 times 1604895 (2.71%) aligned concordantly exactly 1 time 1927418 (3.26%) aligned concordantly >1 times 5.97% overall alignment rate Processed 59135531 sequences in total Successfully deleted the temporary files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 59135531 Final Cytosine Methylation Report ================================= Total number of C's analysed: 134508997 Total methylated C's in CpG context: 2726032 Total methylated C's in CHG context: 377890 Total methylated C's in CHH context: 2853560 Total methylated C's in Unknown context: 106286 Total unmethylated C's in CpG context: 14329910 Total unmethylated C's in CHG context: 24516992 Total unmethylated C's in CHH context: 89704613 Total unmethylated C's in Unknown context: 625874 C methylated in CpG context: 16.0% C methylated in CHG context: 1.5% C methylated in CHH context: 3.1% C methylated in Unknown context (CN or CHN): 14.5% Now waiting for all child processes to complete Processed 59000000 sequence pairs so far 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 55581519 (93.99%) aligned concordantly 0 times 1621910 (2.74%) aligned concordantly exactly 1 time 1932103 (3.27%) aligned concordantly >1 times 6.01% overall alignment rate 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 56550341 (95.63%) aligned concordantly 0 times 1158734 (1.96%) aligned concordantly exactly 1 time 1426457 (2.41%) aligned concordantly >1 times 4.37% overall alignment rate 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 55599477 (94.02%) aligned concordantly 0 times 1604515 (2.71%) aligned concordantly exactly 1 time 1931540 (3.27%) aligned concordantly >1 times 5.98% overall alignment rate 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 56562899 (95.65%) aligned concordantly 0 times 1147169 (1.94%) aligned concordantly exactly 1 time 1425464 (2.41%) aligned concordantly >1 times 4.35% overall alignment rate Processed 59135532 sequences in total Successfully deleted the temporary files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 59135532 Final Cytosine Methylation Report ================================= Total number of C's analysed: 134574543 Total methylated C's in CpG context: 2723030 Total methylated C's in CHG context: 377986 Total methylated C's in CHH context: 2861348 Total methylated C's in Unknown context: 105743 Total unmethylated C's in CpG context: 14344071 Total unmethylated C's in CHG context: 24527804 Total unmethylated C's in CHH context: 89740304 Total unmethylated C's in Unknown context: 627253 C methylated in CpG context: 16.0% C methylated in CHG context: 1.5% C methylated in CHH context: 3.1% C methylated in Unknown context (CN or CHN): 14.4% Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2676:17535:19742_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 56550744 (95.63%) aligned concordantly 0 times 1158742 (1.96%) aligned concordantly exactly 1 time 1426046 (2.41%) aligned concordantly >1 times 4.37% overall alignment rate 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 55581192 (93.99%) aligned concordantly 0 times 1619791 (2.74%) aligned concordantly exactly 1 time 1934549 (3.27%) aligned concordantly >1 times 6.01% overall alignment rate 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 56560811 (95.65%) aligned concordantly 0 times 1150379 (1.95%) aligned concordantly exactly 1 time 1424342 (2.41%) aligned concordantly >1 times 4.35% overall alignment rate 59135532 reads; of these: 59135532 (100.00%) were paired; of these: 55600340 (94.02%) aligned concordantly 0 times 1602799 (2.71%) aligned concordantly exactly 1 time 1932393 (3.27%) aligned concordantly >1 times 5.98% overall alignment rate Processed 59135532 sequences in total Successfully deleted the temporary files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 59135532 Final Cytosine Methylation Report ================================= Total number of C's analysed: 134629299 Total methylated C's in CpG context: 2723348 Total methylated C's in CHG context: 377023 Total methylated C's in CHH context: 2856680 Total methylated C's in Unknown context: 106202 Total unmethylated C's in CpG context: 14351500 Total unmethylated C's in CHG context: 24522642 Total unmethylated C's in CHH context: 89798106 Total unmethylated C's in Unknown context: 627784 C methylated in CpG context: 15.9% C methylated in CHG context: 1.5% C methylated in CHH context: 3.1% C methylated in Unknown context (CN or CHN): 14.5% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF07-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF07-EM01-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/EF07-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM01-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: 236542126 Final Cytosine Methylation Report ================================= Total number of C's analysed: 538311693 Total methylated C's in CpG context: 10902218 Total methylated C's in CHG context: 1510834 Total methylated C's in CHH context: 11438727 Total methylated C's in Unknown context: 424447 Total unmethylated C's in CpG context: 57349452 Total unmethylated C's in CHG context: 98086035 Total unmethylated C's in CHH context: 359024427 Total unmethylated C's in Unknown context: 2507832 C methylated in CpG context: 16.0% C methylated in CHG context: 1.5% C methylated in CHH context: 3.1% C methylated in Unknown context (CN or CHN): 14.5% Deleting temporary report files... Bismark completed in 0d 10h 41m 11s ==================== Bismark run complete ====================