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/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 35705637) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 86060 and offset 4 (sequences written out: 35705636) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 35705637) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 35705636) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 86060 and offset 4 (sequences written out: 35705636) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF02-EM02-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/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 35705637) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF02-EM02-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/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 35705636) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF02-EM02-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/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 35705637) Using the subset file >EF02-EM02-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/EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (35705636 sequences in total) Writing a C -> T converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF02-EM02-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 EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (35705636 sequences in total) Writing a C -> T converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF02-EM02-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 EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (35705637 sequences in total) Writing a C -> T converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF02-EM02-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 EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (35705637 sequences in total) Writing a C -> T converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF02-EM02-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 EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF02-EM02-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 EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (35705637 sequences in total) Input files are EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-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 EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (35705636 sequences in total) Input files are EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF02-EM02-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:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TTTTATATTTATAAAAAAAATTTATTTTTATATATAAATTTTATTTTTTTTTTTTTTAATTTTTTTATTAAAATATTAATTTTATTAAATAATTTTTTAATATTTTTAAAAAAATAATTAATAATAAAAATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 ACAAATAATAACAATAAAAACTAATAAAATTAATTTTATTAATTTTTATTATTAATTATTTTTTTAAAAATATTAAAAAATTATTTAATAAAATTAATATTTTAATAAAAAAATTAAAAAAAAAAAAAATAAAAT FFFFFFFFFFFFFFFFFFFFFFF:,FFFF,FFFFF:FFFFFFF:FF:FF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27190:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 AATTTATGTAAAGTTATTTAAGAATGTAATGTAATGGAAGAGTAAAAATAATAGTAATTGGTTGTAGATTTTTTTTTTTTGTTTAGGTATATTAAGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27190:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 ACAAAAAAAAAAAATCTACAACCAATTACTATTATTTTTACTCTTCCATTACATTACATTCTTAAATAACTTTACATAAATTTATAAAAAAATATAC FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFF:FFFFFFFF:FFFF,FFF:FFFFFF:FFFFFFF:FFFFFF::FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF02-EM02-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)) Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (35705636 sequences in total) Input files are EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF02-EM02-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 EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (35705637 sequences in total) Input files are EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-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 EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-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:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 99 NC_035784.1_GA_converted 91080332 0 7M2I9M5I6M1I105M = 91080361 166 CTCTATACCTACAAAAAAAATCTATCTCTATACATAAATTTTATCTCTCTCTTCTCTAACTTTTTTATTAAAATACCAACTCTACCAAATAATTTTTCAACATTTTTAAAAAAATAACCAACAATAAAAACTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, AS:i:-69 XN:i:0 XM:i:5 XO:i:3 XG:i:8 NM:i:13 MD:Z:0T1T6T1T11C103 YS:i:-52 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 147 NC_035784.1_GA_converted 91080361 0 113M1I15M3D6M = 91080332 -166 ATTTTATCTCTCTCTTCTCTAACTTTTTTATTAAAATACCAACTCTACCAAATAATTTTTCAACATTTTTAAAAAAATAACCAACAATAAAAACTAATAAAACTAATCTCATTAATTTTTATTATTATTATTTAT F:FFFFFFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF,FF:FF:FFFFFFF:FFFFF,FFFF,:FFFFFFFFFFFFFFFFFFFFFFF AS:i:-52 XN:i:0 XM:i:5 XO:i:2 XG:i:4 NM:i:9 MD:Z:115C1C2A3A3^CAA4T1 YS:i:-69 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF02-EM02-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:GW210315000:4:1101:27190:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 AATTTATATAAAATTACTTAAAAATATAATATAATAAAAAAATAAAAATAATAATAATTAATTATAAATTTTTTTTTTTTATTTAAATATATTAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27190:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 ATAAAAAAAAAAAATTTATAATTAATTATTATTATTTTTATTTTTTTATTATATTATATTTTTAAGTAATTTTATATAAATTTATAAAAGAATGTAT FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFF:FFFFFFFF:FFFF,FFF:FFFFFF:FFFFFFF:FFFFFF::FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF02-EM02-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:GW210315000:4:1101:27624:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TGAAATTTTAGTATTTTATTTTAAGTTTGTTGTTGTAATAAGATTTATTTTTTAATTTGTATTGTAATTTTATTATTTGAATTTTGTTATTGTATTTGTTGTTAAATTATTT FFFFFFFFFF:FF:FFFFFFF:FFFFFFFFF,FF:FFF:FF,:FFFFFFFFF,FFFFF,:FFF,,FF,FFFFFFFFF,FF,FFFFFFFF:F:FFFFF,,FFFFFF:,FFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27624:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 AAATACAATAACAAAATTCCAATAATAAAATTCCAATACAAATTAAAAAATAAATCTTATTACAACAACAAACTTAAAATAAAATACTAAAATTTCAATTAAAACATACACA F,F,FFFF,F:FFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFF,FFF::FFFF,FF:FFFFF:FFFF::FFFFFF:FF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF02-EM02-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:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TTGGAATTATTGTGAAATTTTGGTGATTGGAAATGGTTTTGGTTTTTTTTTTTTTTTTGTTTTGAAAAAAATGTTGATAAATATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 CATTTTTTTCAAAACAAAAAAAAAAAAAAAACCAAAACCATTTCCAATCACCAAAATTTCACAATAATTCCAATTTTAAAATTTTAAA FF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF02-EM02-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:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 CTCTATACCTACAAAAAAAATCTATCTCTATACATAAATTTTATCTCTCTCTTCTCTAACTTTTTTATTAAAATACCAACTCTACCAAATAATTTTTCAACATTTTTAAAAAAATAACCAACAATAAAAACTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 ATAAATAATAATAATAAAAATTAATGAGATTAGTTTTATTAGTTTTTATTGTTGGTTATTTTTTTAAAAATGTTGAAAAATTATTTGGTAGAGTTGGTATTTTAATAAAAAAGTTAGAGAAGAGAGAGATAAAAT FFFFFFFFFFFFFFFFFFFFFFF:,FFFF,FFFFF:FFFFFFF:FF:FF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-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:GW210315000:4:1101:27190:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 AATTTATATAAAATTACTTAAAAATATAATATAATAAAAAAATAAAAATAATAATAATTAATTATAAATTTTTTTTTTTTATTTAAATATATTAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27190:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 ATAAAAAAAAAAAATTTATAATTAATTATTATTATTTTTATTTTTTTATTATATTATATTTTTAAGTAATTTTATATAAATTTATAAAAGAATGTAT FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFF:FFFFFFFF:FFFF,FFF:FFFFFF:FFFFFFF:FFFFFF::FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF02-EM02-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:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TTTTATATTTATAAAAAAAATTTATTTTTATATATAAATTTTATTTTTTTTTTTTTTAATTTTTTTATTAAAATATTAATTTTATTAAATAATTTTTTAATATTTTTAAAAAAATAATTAATAATAAAAATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 ACAAATAATAACAATAAAAACTAATAAAATTAATTTTATTAATTTTTATTATTAATTATTTTTTTAAAAATATTAAAAAATTATTTAATAAAATTAATATTTTAATAAAAAAATTAAAAAAAAAAAAAATAAAAT FFFFFFFFFFFFFFFFFFFFFFF:,FFFF,FFFFF:FFFFFFF:FF:FF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27190:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 AATTTATGTAAAGTTATTTAAGAATGTAATGTAATGGAAGAGTAAAAATAATAGTAATTGGTTGTAGATTTTTTTTTTTTGTTTAGGTATATTAAGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27190:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 ACAAAAAAAAAAAATCTACAACCAATTACTATTATTTTTACTCTTCCATTACATTACATTCTTAAATAACTTTACATAAATTTATAAAAAAATATAC FFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFF:FFFFFFFF:FFFF,FFF:FFFFFF:FFFFFFF:FFFFFF::FFFF YT:Z:UP >>> Writing bisulfite mapping results to EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TTAAAATTATTATAAAATTTTAATAATTAAAAATAATTTTAATTTTTTTTTTTTTTTTATTTTAAAAAAAATATTAATAAATATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TATTTTTTTTAAAATAAAAAAAAAAAAAAAATTAAAATTATTTTTAATTATTAAAATTTTATAATAATTTTAATTTTAAAATTTTGAG FF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF02-EM02-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:GW210315000:4:1101:27624:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TAAAATTTTAATATTTTATTTTAAATTTATTATTATAATAAAATTTATTTTTTAATTTATATTATAATTTTATTATTTAAATTTTATTATTATATTTACTATTAAATTATTT FFFFFFFFFF:FF:FFFFFFF:FFFFFFFFF,FF:FFF:FF,:FFFFFFFFF,FFFFF,:FFF,,FF,FFFFFFFFF,FF,FFFFFFFF:F:FFFFF,,FFFFFF:,FFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27624:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 AAATATAATAATAAAATTTTAATAATAAAATTTTAATATAAATTAAAAAATAAATTTTATTATAATAATAAATTTAAAATAAAATATTAAAATTTTAATTAAAATATATATA F,F,FFFF,F:FFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFF,FFF::FFFF,FF:FFFFF:FFFF::FFFFFF:FF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF02-EM02-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)) Reading in the sequence files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TTAAAATTATTATAAAATTTTAATAATTAAAAATAATTTTAATTTTTTTTTTTTTTTTATTTTAAAAAAAATATTAATAAATATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TATTTTTTTTAAAATAAAAAAAAAAAAAAAATTAAAATTATTTTTAATTATTAAAATTTTATAATAATTTTAATTTTAAAATTTTGAG FF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-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:GW210315000:4:1101:27624:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TAAAATTTTAATATTTTATTTTAAATTTATTATTATAATAAAATTTATTTTTTAATTTATATTATAATTTTATTATTTAAATTTTATTATTATATTTACTATTAAATTATTT FFFFFFFFFF:FF:FFFFFFF:FFFFFFFFF,FF:FFF:FF,:FFFFFFFFF,FFFFF,:FFF,,FF,FFFFFFFFF,FF,FFFFFFFF:F:FFFFF,,FFFFFF:,FFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27624:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 AAATATAATAATAAAATTTTAATAATAAAATTTTAATATAAATTAAAAAATAAATTTTATTATAATAATAAATTTAAAATAAAATATTAAAATTTTAATTAAAATATATATA F,F,FFFF,F:FFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFF,FFF::FFFF,FF:FFFFF:FFFF::FFFFFF:FF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF02-EM02-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:GW210315000:4:1101:27624:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TGAAATTTTAGTATTTTATTTTAAGTTTGTTGTTGTAATAAGATTTATTTTTTAATTTGTATTGTAATTTTATTATTTGAATTTTGTTATTGTATTTGTTGTTAAATTATTT FFFFFFFFFF:FF:FFFFFFF:FFFFFFFFF,FF:FFF:FF,:FFFFFFFFF,FFFFF,:FFF,,FF,FFFFFFFFF,FF,FFFFFFFF:F:FFFFF,,FFFFFF:,FFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27624:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 AAATACAATAACAAAATTCCAATAATAAAATTCCAATACAAATTAAAAAATAAATCTTATTACAACAACAAACTTAAAATAAAATACTAAAATTTCAATTAAAACATACACA F,F,FFFF,F:FFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFF,FFF::FFFF,FF:FFFFF:FFFF::FFFFFF:FF,FF YT:Z:UP >>> Writing bisulfite mapping results to EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TTGGAATTATTGTGAAATTTTGGTGATTGGAAATGGTTTTGGTTTTTTTTTTTTTTTTGTTTTGAAAAAAATGTTGATAAATATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 CATTTTTTTCAAAACAAAAAAAAAAAAAAAACCAAAACCATTTCCAATCACCAAAATTTCACAATAATTCCAATTTTAAAATTTTAAA FF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP >>> Writing bisulfite mapping results to EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1125:12147:26005_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17178 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1132:18502:12054_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17149 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1158:7907:2816_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1437:19208:17816_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1545:9118:10457_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:29107:32205_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1353:15528:34554_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1616:13376:24001_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17178 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:28339:32910_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2108:26286:2362_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17127 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2130:7084:27070_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17136 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2226:23122:2268_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17109 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2244:30843:27915_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2254:9815:14544_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2443:1669:10207_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2454:14751:31485_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17152 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2546:22083:10895_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17177 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2138:11288:10582_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 14000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2155:12915:14340_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1108:22516:13651_1:N:0:CTCCACTG+ACGCCCCT NC_007175.2 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1166:25283:21042_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1177:8278:4711_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17114 Processed 9000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1176:5132:4930_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17114 Processed 16000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1245:14380:24048_1:N:0:ATCCACTG+ACGCACCT NC_035781.1 2 Processed 18000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1421:19063:32189_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17175 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1371:1850:32189_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17131 Processed 22000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1432:17978:14841_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17127 Processed 13000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1566:26648:3803_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17178 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1629:28745:6339_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17114 Processed 24000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2131:8142:5885_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1216:25988:28494_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17181 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2270:2139:19789_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17180 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2270:2058:19836_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17180 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2420:23845:11631_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2317:2202:5588_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17177 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2420:23827:11631_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2566:29767:14935_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2603:9742:18552_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17179 Processed 34000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 19000000 sequence pairs so far 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 32085308 (89.86%) aligned concordantly 0 times 1620891 (4.54%) aligned concordantly exactly 1 time 1999438 (5.60%) aligned concordantly >1 times 10.14% overall alignment rate 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 31083673 (87.06%) aligned concordantly 0 times 2081961 (5.83%) aligned concordantly exactly 1 time 2540003 (7.11%) aligned concordantly >1 times 12.94% overall alignment rate 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 32054362 (89.77%) aligned concordantly 0 times 1643514 (4.60%) aligned concordantly exactly 1 time 2007761 (5.62%) aligned concordantly >1 times 10.23% overall alignment rate 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 31043588 (86.94%) aligned concordantly 0 times 2109980 (5.91%) aligned concordantly exactly 1 time 2552069 (7.15%) aligned concordantly >1 times 13.06% overall alignment rate Processed 35705637 sequences in total Successfully deleted the temporary files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 35705637 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224047058 Total methylated C's in CpG context: 5121131 Total methylated C's in CHG context: 766167 Total methylated C's in CHH context: 3786492 Total methylated C's in Unknown context: 194037 Total unmethylated C's in CpG context: 27695547 Total unmethylated C's in CHG context: 45747500 Total unmethylated C's in CHH context: 140930221 Total unmethylated C's in Unknown context: 1195641 C methylated in CpG context: 15.6% C methylated in CHG context: 1.6% C methylated in CHH context: 2.6% C methylated in Unknown context (CN or CHN): 14.0% Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2564:28854:27383_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2602:8477:17300_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17179 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2575:9851:25379_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17193 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2641:9706:14888_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17176 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2642:6054:31516_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17176 Processed 35000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 35000000 sequence pairs so far 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 31078892 (87.04%) aligned concordantly 0 times 2084718 (5.84%) aligned concordantly exactly 1 time 2542027 (7.12%) aligned concordantly >1 times 12.96% overall alignment rate 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 32056020 (89.78%) aligned concordantly 0 times 1642905 (4.60%) aligned concordantly exactly 1 time 2006712 (5.62%) aligned concordantly >1 times 10.22% overall alignment rate 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 32087984 (89.87%) aligned concordantly 0 times 1619029 (4.53%) aligned concordantly exactly 1 time 1998624 (5.60%) aligned concordantly >1 times 10.13% overall alignment rate 35705637 reads; of these: 35705637 (100.00%) were paired; of these: 31043901 (86.94%) aligned concordantly 0 times 2110237 (5.91%) aligned concordantly exactly 1 time 2551499 (7.15%) aligned concordantly >1 times 13.06% overall alignment rate Processed 35705637 sequences in total Successfully deleted the temporary files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 35705637 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224101827 Total methylated C's in CpG context: 5118763 Total methylated C's in CHG context: 766399 Total methylated C's in CHH context: 3799851 Total methylated C's in Unknown context: 194868 Total unmethylated C's in CpG context: 27727235 Total unmethylated C's in CHG context: 45754040 Total unmethylated C's in CHH context: 140935539 Total unmethylated C's in Unknown context: 1194102 C methylated in CpG context: 15.6% C methylated in CHG context: 1.6% C methylated in CHH context: 2.6% C methylated in Unknown context (CN or CHN): 14.0% Processed 22000000 sequence pairs so far 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 32058430 (89.79%) aligned concordantly 0 times 1643354 (4.60%) aligned concordantly exactly 1 time 2003852 (5.61%) aligned concordantly >1 times 10.21% overall alignment rate 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 32087854 (89.87%) aligned concordantly 0 times 1619577 (4.54%) aligned concordantly exactly 1 time 1998205 (5.60%) aligned concordantly >1 times 10.13% overall alignment rate 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 31044652 (86.95%) aligned concordantly 0 times 2111098 (5.91%) aligned concordantly exactly 1 time 2549886 (7.14%) aligned concordantly >1 times 13.05% overall alignment rate 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 31080560 (87.05%) aligned concordantly 0 times 2082816 (5.83%) aligned concordantly exactly 1 time 2542260 (7.12%) aligned concordantly >1 times 12.95% overall alignment rate Processed 35705636 sequences in total Successfully deleted the temporary files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 35705636 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224123897 Total methylated C's in CpG context: 5117451 Total methylated C's in CHG context: 766445 Total methylated C's in CHH context: 3801934 Total methylated C's in Unknown context: 195837 Total unmethylated C's in CpG context: 27702706 Total unmethylated C's in CHG context: 45761122 Total unmethylated C's in CHH context: 140974239 Total unmethylated C's in Unknown context: 1196125 C methylated in CpG context: 15.6% C methylated in CHG context: 1.6% C methylated in CHH context: 2.6% C methylated in Unknown context (CN or CHN): 14.1% Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1566:26829:20619_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17178 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2270:2003:19805_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17180 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2374:25021:14199_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17176 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2457:28194:24455_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2471:20428:18834_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17181 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2577:28682:26115_1:N:0:ATCCACTG+ACGCACCT NC_035781.1 2 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 32086510 (89.86%) aligned concordantly 0 times 1620446 (4.54%) aligned concordantly exactly 1 time 1998680 (5.60%) aligned concordantly >1 times 10.14% overall alignment rate 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 31045422 (86.95%) aligned concordantly 0 times 2111217 (5.91%) aligned concordantly exactly 1 time 2548997 (7.14%) aligned concordantly >1 times 13.05% overall alignment rate 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 32056711 (89.78%) aligned concordantly 0 times 1642140 (4.60%) aligned concordantly exactly 1 time 2006785 (5.62%) aligned concordantly >1 times 10.22% overall alignment rate 35705636 reads; of these: 35705636 (100.00%) were paired; of these: 31083415 (87.05%) aligned concordantly 0 times 2081944 (5.83%) aligned concordantly exactly 1 time 2540277 (7.11%) aligned concordantly >1 times 12.95% overall alignment rate Processed 35705636 sequences in total Successfully deleted the temporary files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 35705636 Final Cytosine Methylation Report ================================= Total number of C's analysed: 224141872 Total methylated C's in CpG context: 5119228 Total methylated C's in CHG context: 764288 Total methylated C's in CHH context: 3787955 Total methylated C's in Unknown context: 194076 Total unmethylated C's in CpG context: 27715339 Total unmethylated C's in CHG context: 45762844 Total unmethylated C's in CHH context: 140992218 Total unmethylated C's in Unknown context: 1192185 C methylated in CpG context: 15.6% C methylated in CHG context: 1.6% C methylated in CHH context: 2.6% C methylated in Unknown context (CN or CHN): 14.0% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF02-EM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF02-EM02-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/EF02-EM02-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> EF02-EM02-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: 142822546 Final Cytosine Methylation Report ================================= Total number of C's analysed: 896414654 Total methylated C's in CpG context: 20476573 Total methylated C's in CHG context: 3063299 Total methylated C's in CHH context: 15176232 Total methylated C's in Unknown context: 778818 Total unmethylated C's in CpG context: 110840827 Total unmethylated C's in CHG context: 183025506 Total unmethylated C's in CHH context: 563832217 Total unmethylated C's in Unknown context: 4778053 C methylated in CpG context: 15.6% C methylated in CHG context: 1.6% C methylated in CHH context: 2.6% C methylated in Unknown context (CN or CHN): 14.0% Deleting temporary report files... Bismark completed in 0d 6h 41m 35s ==================== Bismark run complete ====================