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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 39012927) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 39012926) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz for PID: 99765 and offset 4 (sequences written out: 39012926) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 39012926) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 39012927) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF04-EM04-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/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz for PID: 99765 and offset 4 (sequences written out: 39012926) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF04-EM04-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/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 39012926) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF04-EM04-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/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 39012926) Using the subset file >EF04-EM04-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/EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (39012926 sequences in total) Writing a C -> T converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF04-EM04-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 EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (39012926 sequences in total) Writing a C -> T converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF04-EM04-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 EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (39012926 sequences in total) Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (39012927 sequences in total) Writing a C -> T converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF04-EM04-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 EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF04-EM04-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 EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF04-EM04-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 EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (39012927 sequences in total) Input files are EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-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 EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (39012926 sequences in total) Input files are EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF04-EM04-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:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TTGATTAATATTAAATTTTTATAAAATATTATATT F,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAATTTAATATTAATCAAATCAAAAAAACAAAA ,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30101:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TATGTTATTAAATTTTTGATAATAAGTGGAAATTGTTTAAATTGATATTTATGTAAAGGAGTGTTAATATTTGGTAATTATTGAG FFFFFFFFFFF:FF,FFFFF::FFFFFFFF:F,:FFFFFF:FFFFFFFFFFFFFFF:FFFFFFFF:F:FFFFF:,FF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30101:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 ATATTAACACTCCTTTACATAAATATCAATTTAAACAATTTCCACTTATTATCAAAAATTTAATAACATAAATCAAAAAAACAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF04-EM04-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)) Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (39012926 sequences in total) Input files are EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF04-EM04-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:GW210315000:4:1101:29288:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TTAATTATAATATAATTATTATTAATAAATTTAAAATAGATAATAATTATAATTTAATTTAAATTATATTATTATTAAATAATAATAATATTTATATATATTTAATAATTTAATTTTATTTTTAATATTTATTTA FFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFFFF:FFFFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29288:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 ATATTAAATTAAATAAATATTAAAAATAAAATTAAATTATTAAATATATATAAATATTATTATTATTTAATAATAATATAATTTAAATTAAATTATAATTATTATCTATTTTAAATTTATTAATAATAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFF:FFF,FFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF04-EM04-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:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CTAATCAATATTAAATTTCCACAAAACACTACACC F,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 GGAAATTTAATATTGATTAGATTGGAAGAGTAGGG ,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM04-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:GW210315000:4:1101:30101:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TACATTATTAAATTTTTAATAATAAATAAAAATTATTTAAATTAATATTTATATAAAAAAATATTAATATTTAATAATTATTAAA FFFFFFFFFFF:FF,FFFFF::FFFFFFFF:F,:FFFFFF:FFFFFFFFFFFFFFF:FFFFFFFF:F:FFFFF:,FF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30101:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 ATATTAATATTTTTTTATATAAATATTAATTTAAATAATTTTTATTTATTATTAAAAATTTAATAATGTAGATTGGAAGAGTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF04-EM04-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)) Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (39012926 sequences in total) Input files are EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-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 EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-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:GW210315000:4:1101:29288:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CTAACCACAACATAACTATTACTAATAAATTCAAAACAAACAATAACTACAACTCAATTTAAATTATACTATTACTAAACAACAATAACACCTATACACATTTAATAATCCAATTCTACTTCCAATATTCACTTA FFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFFFF:FFFFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29288:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 GTGTTGAATTAAGTGAATATTGGAAGTAGAATTGGATTATTAAATGTGTATAGGTGTTATTGTTGTTTAGTAATAGTATAATTTAAATTGAGTTGTAGTTATTGTTTGTTTTGAATTTATTAGTAATAGTTATGT FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFF:FFF,FFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF04-EM04-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:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TATTAGTTTTGGATAAGAAGATTTTTTATTTTTTAATGTTTTAATTTTATATATAAGTTTTTAGAATGATTTAAATTTTTTTTTTTTTTTTGTATTTTTTTGTTTTTTTTTTATTAAATTTTTTTTAGGTATTGT FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAACATTAAAAAATAAAAAAAAATAATATACAAAACAAATAAAACAAATTAAAAAAAAAAAAAAAAAAA FFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM04-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:GW210315000:4:1101:29288:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CTAACCACAACATAACTATTACTAATAAATTCAAAACAAACAATAACTACAACTCAATTTAAATTATACTATTACTAAACAACAATAACACCTATACACATTTAATAATCCAATTCTACTTCCAATATTCACTTA FFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFFFF:FFFFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29288:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 GTGTTGAATTAAGTGAATATTGGAAGTAGAATTGGATTATTAAATGTGTATAGGTGTTATTGTTGTTTAGTAATAGTATAATTTAAATTGAGTTGTAGTTATTGTTTGTTTTGAATTTATTAGTAATAGTTATGT FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFF:FFF,FFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF04-EM04-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:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CTAATCAATATTAAATTTCCACAAAACACTACACC F,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 GGAAATTTAATATTGATTAGATTGGAAGAGTAGGG ,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-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:GW210315000:4:1101:30101:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TACATTATTAAATTTTTAATAATAAATAAAAATTATTTAAATTAATATTTATATAAAAAAATATTAATATTTAATAATTATTAAA FFFFFFFFFFF:FF,FFFFF::FFFFFFFF:F,:FFFFFF:FFFFFFFFFFFFFFF:FFFFFFFF:F:FFFFF:,FF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30101:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 ATATTAATATTTTTTTATATAAATATTAATTTAAATAATTTTTATTTATTATTAAAAATTTAATAATGTAGATTGGAAGAGTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF04-EM04-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:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CATTAATTTTAAATAAAAAAATTTTTTATTTTTTAATATTTTAATTTTATATATAAATTTTTAAAATAATTTAAATTTTTTTTTTTTTTTTATATTTTTTTATTTTTTTTTTATTAAATTTTTTTTAAATATTAC FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAATATTAAAAAATAAAAAAAAATAATATATAAAATAAATGAAATAAATTAAAAAAAGAAAGGAAGAAG FFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM04-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:GW210315000:4:1101:29288:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TTAATTATAATATAATTATTATTAATAAATTTAAAATAGATAATAATTATAATTTAATTTAAATTATATTATTATTAAATAATAATAATATTTATATATATTTAATAATTTAATTTTATTTTTAATATTTATTTA FFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFFFF:FFFFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29288:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 ATATTAAATTAAATAAATATTAAAAATAAAATTAAATTATTAAATATATATAAATATTATTATTATTTAATAATAATATAATTTAAATTAAATTATAATTATTATCTATTTTAAATTTATTAATAATAATTATAT FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFF:FFF,FFFFFFFFFF,F YT:Z:UP >>> Writing bisulfite mapping results to EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30101:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TATGTTATTAAATTTTTGATAATAAGTGGAAATTGTTTAAATTGATATTTATGTAAAGGAGTGTTAATATTTGGTAATTATTGAG FFFFFFFFFFF:FF,FFFFF::FFFFFFFF:F,:FFFFFF:FFFFFFFFFFFFFFF:FFFFFFFF:F:FFFFF:,FF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30101:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 ATATTAACACTCCTTTACATAAATATCAATTTAAACAATTTCCACTTATTATCAAAAATTTAATAACATAAATCAAAAAAACAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TTGATTAATATTAAATTTTTATAAAATATTATATT F,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAATTTAATATTAATCAAATCAAAAAAACAAAA ,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP >>> Writing bisulfite mapping results to EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Reading in the sequence files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CATTAATTTTAAATAAAAAAATTTTTTATTTTTTAATATTTTAATTTTATATATAAATTTTTAAAATAATTTAAATTTTTTTTTTTTTTTTATATTTTTTTATTTTTTTTTTATTAAATTTTTTTTAAATATTAC FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAATATTAAAAAATAAAAAAAAATAATATATAAAATAAATGAAATAAATTAAAAAAAGAAAGGAAGAAG FFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-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:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TATTAGTTTTGGATAAGAAGATTTTTTATTTTTTAATGTTTTAATTTTATATATAAGTTTTTAGAATGATTTAAATTTTTTTTTTTTTTTTGTATTTTTTTGTTTTTTTTTTATTAAATTTTTTTTAGGTATTGT FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAACATTAAAAAATAAAAAAAAATAATATACAAAACAAATAAAACAAATTAAAAAAAAAAAAAAAAAAA FFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP >>> Writing bisulfite mapping results to EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.2.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 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1258:4408:29199_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1277:2112:7153_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17202 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1345:8648:21605_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17161 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 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1540:20754:9659_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17162 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1537:30870:34632_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1648:24451:32753_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17194 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2122:15863:13745_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17169 Processed 9000000 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:GW210315000:4:2164:12798:4272_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17152 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 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 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2349:5972:22514_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17193 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2323:6786:16219_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17189 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2443:16486:11600_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17176 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2443:14615:13870_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17176 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2617:14199:34820_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2617:14326:34820_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2619:17553:11537_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1168:24840:9283_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17194 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1172:25852:5431_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17183 Processed 20000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1157:1931:23281_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1168:24614:8422_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17194 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1303:32796:19147_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17146 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1319:15700:4413_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17190 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1369:14714:36025_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17199 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1506:6253:17394_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17176 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 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:2:1552:3712:22576_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1645:2266:16845_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1645:2311:19366_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2104:12418:1329_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17176 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2113:8278:5337_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17188 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2112:8938:26991_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17188 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2122:24704:7858_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17190 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2132:16622:25363_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2113:8223:5400_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17188 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2253:18014:19445_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17146 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2325:21423:34491_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2325:21323:29496_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2325:21441:29512_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2377:18530:6464_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17162 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2570:17933:21684_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17199 Processed 37000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2576:16052:27477_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 38000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 37000000 sequence pairs so far 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37316667 (95.65%) aligned concordantly 0 times 796622 (2.04%) aligned concordantly exactly 1 time 899637 (2.31%) aligned concordantly >1 times 4.35% overall alignment rate 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37359281 (95.76%) aligned concordantly 0 times 785113 (2.01%) aligned concordantly exactly 1 time 868532 (2.23%) aligned concordantly >1 times 4.24% overall alignment rate Processed 39000000 sequence pairs so far 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37315542 (95.65%) aligned concordantly 0 times 792952 (2.03%) aligned concordantly exactly 1 time 904432 (2.32%) aligned concordantly >1 times 4.35% overall alignment rate 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37359795 (95.76%) aligned concordantly 0 times 781368 (2.00%) aligned concordantly exactly 1 time 871763 (2.23%) aligned concordantly >1 times 4.24% overall alignment rate Processed 39012926 sequences in total Successfully deleted the temporary files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 39012926 Final Cytosine Methylation Report ================================= Total number of C's analysed: 69425813 Total methylated C's in CpG context: 1610839 Total methylated C's in CHG context: 511212 Total methylated C's in CHH context: 2375499 Total methylated C's in Unknown context: 116042 Total unmethylated C's in CpG context: 7723321 Total unmethylated C's in CHG context: 12538924 Total unmethylated C's in CHH context: 44666018 Total unmethylated C's in Unknown context: 526443 C methylated in CpG context: 17.3% C methylated in CHG context: 3.9% C methylated in CHH context: 5.0% C methylated in Unknown context (CN or CHN): 18.1% 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37358046 (95.76%) aligned concordantly 0 times 785288 (2.01%) aligned concordantly exactly 1 time 869592 (2.23%) aligned concordantly >1 times 4.24% overall alignment rate Processed 39000000 sequence pairs so far 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37316770 (95.65%) aligned concordantly 0 times 792807 (2.03%) aligned concordantly exactly 1 time 903349 (2.32%) aligned concordantly >1 times 4.35% overall alignment rate 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37318103 (95.66%) aligned concordantly 0 times 796621 (2.04%) aligned concordantly exactly 1 time 898202 (2.30%) aligned concordantly >1 times 4.34% overall alignment rate 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37357299 (95.76%) aligned concordantly 0 times 781011 (2.00%) aligned concordantly exactly 1 time 874616 (2.24%) aligned concordantly >1 times 4.24% overall alignment rate Processed 39012926 sequences in total Successfully deleted the temporary files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 39012926 Final Cytosine Methylation Report ================================= Total number of C's analysed: 69476141 Total methylated C's in CpG context: 1614055 Total methylated C's in CHG context: 510037 Total methylated C's in CHH context: 2380106 Total methylated C's in Unknown context: 115624 Total unmethylated C's in CpG context: 7722434 Total unmethylated C's in CHG context: 12547726 Total unmethylated C's in CHH context: 44701783 Total unmethylated C's in Unknown context: 526221 C methylated in CpG context: 17.3% C methylated in CHG context: 3.9% C methylated in CHH context: 5.1% C methylated in Unknown context (CN or CHN): 18.0% Now waiting for all child processes to complete Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37317322 (95.65%) aligned concordantly 0 times 792975 (2.03%) aligned concordantly exactly 1 time 902629 (2.31%) aligned concordantly >1 times 4.35% overall alignment rate 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37360266 (95.76%) aligned concordantly 0 times 778925 (2.00%) aligned concordantly exactly 1 time 873735 (2.24%) aligned concordantly >1 times 4.24% overall alignment rate Processed 39000000 sequence pairs so far 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37315949 (95.65%) aligned concordantly 0 times 797459 (2.04%) aligned concordantly exactly 1 time 899518 (2.31%) aligned concordantly >1 times 4.35% overall alignment rate 39012926 reads; of these: 39012926 (100.00%) were paired; of these: 37359405 (95.76%) aligned concordantly 0 times 783908 (2.01%) aligned concordantly exactly 1 time 869613 (2.23%) aligned concordantly >1 times 4.24% overall alignment rate Processed 39012926 sequences in total Successfully deleted the temporary files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 39012926 Final Cytosine Methylation Report ================================= Total number of C's analysed: 69390871 Total methylated C's in CpG context: 1607747 Total methylated C's in CHG context: 509115 Total methylated C's in CHH context: 2379779 Total methylated C's in Unknown context: 115245 Total unmethylated C's in CpG context: 7714907 Total unmethylated C's in CHG context: 12543548 Total unmethylated C's in CHH context: 44635775 Total unmethylated C's in Unknown context: 525289 C methylated in CpG context: 17.2% C methylated in CHG context: 3.9% C methylated in CHH context: 5.1% C methylated in Unknown context (CN or CHN): 18.0% 39012927 reads; of these: 39012927 (100.00%) were paired; of these: 37359946 (95.76%) aligned concordantly 0 times 783461 (2.01%) aligned concordantly exactly 1 time 869520 (2.23%) aligned concordantly >1 times 4.24% overall alignment rate 39012927 reads; of these: 39012927 (100.00%) were paired; of these: 37317330 (95.65%) aligned concordantly 0 times 795479 (2.04%) aligned concordantly exactly 1 time 900118 (2.31%) aligned concordantly >1 times 4.35% overall alignment rate 39012927 reads; of these: 39012927 (100.00%) were paired; of these: 37314349 (95.65%) aligned concordantly 0 times 793937 (2.04%) aligned concordantly exactly 1 time 904641 (2.32%) aligned concordantly >1 times 4.35% overall alignment rate Processed 39000000 sequence pairs so far 39012927 reads; of these: 39012927 (100.00%) were paired; of these: 37361168 (95.77%) aligned concordantly 0 times 778638 (2.00%) aligned concordantly exactly 1 time 873121 (2.24%) aligned concordantly >1 times 4.23% overall alignment rate Processed 39012927 sequences in total Successfully deleted the temporary files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 39012927 Final Cytosine Methylation Report ================================= Total number of C's analysed: 69409105 Total methylated C's in CpG context: 1612473 Total methylated C's in CHG context: 509250 Total methylated C's in CHH context: 2380476 Total methylated C's in Unknown context: 115176 Total unmethylated C's in CpG context: 7716264 Total unmethylated C's in CHG context: 12541635 Total unmethylated C's in CHH context: 44649007 Total unmethylated C's in Unknown context: 525866 C methylated in CpG context: 17.3% C methylated in CHG context: 3.9% C methylated in CHH context: 5.1% C methylated in Unknown context (CN or CHN): 18.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF04-EM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << Merging from file >> EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF04-EM04-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/EF04-EM04-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt << Merging from file >> EF04-EM04-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: 156051705 Final Cytosine Methylation Report ================================= Total number of C's analysed: 277701930 Total methylated C's in CpG context: 6445114 Total methylated C's in CHG context: 2039614 Total methylated C's in CHH context: 9515860 Total methylated C's in Unknown context: 462087 Total unmethylated C's in CpG context: 30876926 Total unmethylated C's in CHG context: 50171833 Total unmethylated C's in CHH context: 178652583 Total unmethylated C's in Unknown context: 2103819 C methylated in CpG context: 17.3% C methylated in CHG context: 3.9% C methylated in CHH context: 5.1% C methylated in Unknown context (CN or CHN): 18.0% Deleting temporary report files... Bismark completed in 0d 6h 59m 32s ==================== Bismark run complete ====================