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/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Output will be written into the directory: /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/ Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Running Bismark Parallel version. Number of parallel instances to be spawned: 4 Current working directory is: /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz for PID: 10778 and offset 4 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 1 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to EF01-EM01-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/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz for PID: 10778 and offset 4 (sequences written out: 30638514) Using the subset file >EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz< as new in-file 2 (instead of >/gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to EF01-EM01-Zygote_R1_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 EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (30638514 sequences in total) Writing a C -> T converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (30638514 sequences in total) Writing a C -> T converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (30638514 sequences in total) Writing a C -> T converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (30638514 sequences in total) Writing a C -> T converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (30638514 sequences in total) Input files are EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (30638514 sequences in total) Input files are EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (30638514 sequences in total) Input files are EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30373:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TGTTGGGATATTATGTTAGTGAGGATGGGTATTTTGGTTGGATGTTGTAGAAATGGATATTATTTTGTGAGTTATTTGGTGGGTGTGTTTTGTTTATTTATGTTTTTGAATTTGTGGAGGATGGGT FFFFFFFFFFF:FFFFFFFFFFFFFF::FF,:F:FFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFF:FFFFFFFF,FFFF:FFFFFFFFFFFFFF:FFFF:FFFFFFF:FFFFFFFF::F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30373:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 ATTCAAAAACATAAATAAACAAAACACACCCACCAAATAACTCACAAAATAATATCCATTTCTACAACATCCAACCAAAATACCCATCCTCACTAACATAATATCCCAACACCACACCACTAACAT F,F:FFFFFFF:FFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFF:FF,FFFFF:,FFFFFFFF:FFFF,F,:FFF:,:FFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF,:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TTAATAATTATTTTTTTTTTTTTATAATTAATATATAATATATTTTTTTTTTTTTATTTTTAATAATATTAGAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 AAATAAAAAAAAAAAAATATATTATATATTAATTATAAAAAAAAAAAAATAATTATTAAAAAAAAAATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30915:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 AAAAGAGAGGAAAGAGGGAGAAAAGAGGTAGAAAGAGAAGAGAAGATAGGTAGAGAGAGAAAATGAGAAAGAAAGGATGTAGAGAGAGGAAGTAGAGAAAGAAAAGTAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30915:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TACTTCCTCTCTCTACATCCTTTCTTTCTCATTTTCTCTCTCTACCTATCTTCTCTTCTCTTTCTACCTCTTTTCTCCCTCTTTCCTCTCTTTTTTCTTTCTTCTAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFF:FFFFFF:FFFFF:FFFFFF:FFFF:FF,FF,F:::F:FF:FF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30373:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TATTAAAATATTATATTAATAAAAATAAATATTTTAATTAAATATTATAAAAATAAATATTATTTTATAAATTATTTAATAAATATATTTTATTTATTTATATTTTTAAATTTATAAAAAATAAAC FFFFFFFFFFF:FFFFFFFFFFFFFF::FF,:F:FFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFF:FFFFFFFF,FFFF:FFFFFFFFFFFFFF:FFFF:FFFFFFF:FFFFFFFF::F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30373:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 ATTTAAAAATATAAATAAATAAAATATATTTATTAAATAATTTATAAAATAATATTTATTTTTATAATATTTAATTAAAATATTTATTTTTATTAATATAATATTTTAATATTATATTATTAGTAT F,F:FFFFFFF:FFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFF:FF,FFFFF:,FFFFFFFF:FFFF,F,:FFF:,:FFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF,:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TTAATAATCATTTTTTTCTTTTTATAACTAACATATAATATACTTTTTTCCTCTTATTTCTAACAACATTAAAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 AAATAAGAGGAAAAAAGTATATTATATGTTAGTTATAAAAAGAAAAAAATGATTATTAAAGAAAAAGTGTTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30915:1047_1:N:0:TAATACAG+GTGAATAT/1 99 NC_035788.1_GA_converted 98972998 2 27M2I17M1I62M = 98973002 109 AAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAATAAATAAAAAAAAAAAATAAAAAAAAAAAAATATAAAAAAAAAAAATAAAAAAAAAAAAACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFF AS:i:-49 XS:i:-50 XN:i:0 XM:i:5 XO:i:2 XG:i:3 NM:i:8 MD:Z:1T72A1A12A13A2 YS:i:-52 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:30915:1047_2:N:0:TAATACAG+GTGAATAT/2 147 NC_035788.1_GA_converted 98973002 2 61M1I30M3I14M = 98972998 -109 AACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAATAAATAAAAAAAAAAAATAAAAAAAAAAAAATATAAAAAAAAAAAATA FFFFFFFFFFFFFF:FF:FF:F:::F,FF,FF:FFFF:FFFFFF:FFFFF:FFFFFF:FFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-52 XS:i:-58 XN:i:0 XM:i:5 XO:i:2 XG:i:4 NM:i:9 MD:Z:2A0A52T7A12A27 YS:i:-49 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30373:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TATTAAAATATTATATTAATAAAAATAAATATTTTAATTAAATATTATAAAAATAAATATTATTTTATAAATTATTTAATAAATATATTTTATTTATTTATATTTTTAAATTTATAAAAAATAAAC FFFFFFFFFFF:FFFFFFFFFFFFFF::FF,:F:FFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFF:FFFFFFFF,FFFF:FFFFFFFFFFFFFF:FFFF:FFFFFFF:FFFFFFFF::F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30373:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 ATTTAAAAATATAAATAAATAAAATATATTTATTAAATAATTTATAAAATAATATTTATTTTTATAATATTTAATTAAAATATTTATTTTTATTAATATAATATTTTAATATTATATTATTAGTAT F,F:FFFFFFF:FFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFF:FF,FFFFF:,FFFFFFFF:FFFF,F,:FFF:,:FFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF,:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TTAATAATCATTTTTTTCTTTTTATAACTAACATATAATATACTTTTTTCCTCTTATTTCTAACAACATTAAAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 AAATAAGAGGAAAAAAGTATATTATATGTTAGTTATAAAAAGAAAAAAATGATTATTAAAGAAAAAGTGTTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30915:1047_1:N:0:TAATACAG+GTGAATAT/1 83 NC_035782.1_CT_converted 32124084 2 32M1I28M2I17M1I28M = 32123885 -304 TTGTTTTTTTTTTTTTATTTTTTTTTTTTATATTTTTTTTTTTTTATTTTTTTTTTTTATTTATTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTT FFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-57 XN:i:0 XM:i:5 XO:i:3 XG:i:4 NM:i:9 MD:Z:2T13T16A36A12A21 YS:i:-50 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:30915:1047_2:N:0:TAATACAG+GTGAATAT/2 163 NC_035782.1_CT_converted 32123885 2 26M1D83M = 32124084 304 TATTTTTTTTTTTTATATTTTTTTTTTTTTATTTTTTTTTTTTATTTATTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFF:FFFFFF:FFFFF:FFFFFF:FFFF:FF,FF,F:::F:FF:FF:FFFFFFFFFFFFFF AS:i:-50 XS:i:-54 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:1T14T9^A17T3T17T39T0T2 YS:i:-57 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30915:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 AAAAGAGAGGAAAGAGGGAGAAAAGAGGTAGAAAGAGAAGAGAAGATAGGTAGAGAGAGAAAATGAGAAAGAAAGGATGTAGAGAGAGGAAGTAGAGAAAGAAAAGTAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30915:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TACTTCCTCTCTCTACATCCTTTCTTTCTCATTTTCTCTCTCTACCTATCTTCTCTTCTCTTTCTACCTCTTTTCTCCCTCTTTCCTCTCTTTTTTCTTTCTTCTAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFF:FFFFFF:FFFFF:FFFFFF:FFFF:FF,FF,F:::F:FF:FF:FFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TTAATAATTATTTTTTTTTTTTTATAATTAATATATAATATATTTTTTTTTTTTTATTTTTAATAATATTAGAA FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 AAATAAAAAAAAAAAAATATATTATATATTAATTATAAAAAAAAAAAAATAATTATTAAAAAAAAAATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP >>> Writing bisulfite mapping results to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30373:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 TGTTGGGATATTATGTTAGTGAGGATGGGTATTTTGGTTGGATGTTGTAGAAATGGATATTATTTTGTGAGTTATTTGGTGGGTGTGTTTTGTTTATTTATGTTTTTGAATTTGTGGAGGATGGGT FFFFFFFFFFF:FFFFFFFFFFFFFF::FF,:F:FFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFF:FFFFFFFF,FFFF:FFFFFFFFFFFFFF:FFFF:FFFFFFF:FFFFFFFF::F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30373:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 ATTCAAAAACATAAATAAACAAAACACACCCACCAAATAACTCACAAAATAATATCCATTTCTACAACATCCAACCAAAATACCCATCCTCACTAACATAATATCCCAACACCACACCACTAACAT F,F:FFFFFFF:FFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFF:FF,FFFFF:,FFFFFFFF:FFFF,F,:FFF:,:FFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF,:FFF YT:Z:UP >>> Writing bisulfite mapping results to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Reading in the sequence files EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Reading in the sequence files EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (30638514 sequences in total) Input files are EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/kdurkin1/kathleen-coral/project/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31186:1047_1:N:0:TAATACAG+GTGAATAT/1 99 NC_035784.1_CT_converted 86609271 40 37M = 86609256 -52 GGATAATTTTTATAAATAGTAGGGAAGATATTGTGAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:32A4 YS:i:-6 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:31186:1047_2:N:0:TAATACAG+GTGAATAT/2 147 NC_035784.1_CT_converted 86609256 40 37M = 86609271 52 TTTGTATAGTTGATTGGATAATTTTTATAAATAGTAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0G36 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31186:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 AAATAATTTTTATAAATAATAAAAAAAATATTATAAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31186:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TTATTATTTATAAAAATTATTTAATTAATTGTATAGA FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31186:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 AAATAATTTTTATAAATAATAAAAAAAATATTATAAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31186:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TTATTATTTATAAAAATTATTTAATTAATTGTATAGA FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:31186:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 GGATAATTTTTATAAATAGTAGGGAAGATATTGTGAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:31186:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 CTACTATTTATAAAAATTATCCAATCAACTATACAAA FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1430:25382:30420_1:N:0:TAATACAG+GTGAATAT NC_035780.1 3 Processed 3000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1473:18295:22874_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17168 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1335:15383:33395_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 5000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1601:28447:2691_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1473:19533:21198_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17168 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1473:19108:23657_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17168 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1515:30535:19805_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2169:10963:6543_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2119:16324:35180_1:N:0:TAATACAG+GTGAATAT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2131:25997:35963_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2252:3170:20071_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 7000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2318:15266:18443_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2274:27082:12571_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2571:15908:32863_1:N:0:TAATACAG+GTGTATAT NC_007175.2 2 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2332:8567:4993_1:N:0:TAATACAG+GGGAATAT NC_007175.2 2 Processed 10000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2431:21287:3630_1:N:0:TAATACAG+GTGAATAT NC_035780.1 3 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2431:21513:3709_1:N:0:TAATACAG+GTGAATAT NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2474:15275:13573_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17168 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2510:1714:17519_1:N:0:TAATACAG+GTGAATAT NC_035781.1 2 Processed 12000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2668:27724:8328_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1407:27118:22435_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1407:29080:26334_1:N:0:TAATACAG+GGGAATAT NC_007175.2 2 Processed 14000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1171:14326:25801_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1171:16260:25175_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Processed 18000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1202:22083:16282_1:N:0:TAATACAG+GTGAATAT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1202:22643:19601_1:N:0:TAATACAG+GTGAATAT NC_035780.1 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1513:2582:29669_1:N:0:TAATACAG+GTGAATAT NC_035780.1 65668305 Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1258:13874:16939_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 17000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1361:22381:21089_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17175 Processed 15000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1472:26277:34788_1:N:0:TAATACAG+GTGAATAT NC_007175.2 3 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1578:7961:2910_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1578:5095:20306_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1628:10022:9893_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 16000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 17000000 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:2:2145:21441:4085_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 18000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1513:2220:35180_1:N:0:TAATACAG+GTGAATAT NC_035780.1 65668305 Processed 22000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2355:31060:21621_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2139:6135:10300_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 27000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2406:18945:23030_1:N:0:TAATACAG+GGGAATAT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2163:3296:34788_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17121 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2226:23104:6496_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17116 Processed 28000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2238:14398:37012_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2239:11017:21574_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:5330:19022_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:5204:19398_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Processed 24000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2522:10845:9565_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17118 Processed 28000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27287639 (89.06%) aligned concordantly 0 times 1632387 (5.33%) aligned concordantly exactly 1 time 1718488 (5.61%) aligned concordantly >1 times 10.94% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27429829 (89.53%) aligned concordantly 0 times 1552844 (5.07%) aligned concordantly exactly 1 time 1655841 (5.40%) aligned concordantly >1 times 10.47% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27273341 (89.02%) aligned concordantly 0 times 1633823 (5.33%) aligned concordantly exactly 1 time 1731350 (5.65%) aligned concordantly >1 times 10.98% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27446053 (89.58%) aligned concordantly 0 times 1547542 (5.05%) aligned concordantly exactly 1 time 1644919 (5.37%) aligned concordantly >1 times 10.42% overall alignment rate Processed 30638514 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 30638514 Final Cytosine Methylation Report ================================= Total number of C's analysed: 201126158 Total methylated C's in CpG context: 6492225 Total methylated C's in CHG context: 1853566 Total methylated C's in CHH context: 8724052 Total methylated C's in Unknown context: 245645 Total unmethylated C's in CpG context: 20243164 Total unmethylated C's in CHG context: 38316166 Total unmethylated C's in CHH context: 125496985 Total unmethylated C's in Unknown context: 940109 C methylated in CpG context: 24.3% C methylated in CHG context: 4.6% C methylated in CHH context: 6.5% C methylated in Unknown context (CN or CHN): 20.7% Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2467:12048:1971_1:N:0:TAATACAG+GTGAATAT NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2467:13404:22200_1:N:0:TAATACAG+GTGAATAT NC_035781.1 2 Processed 30000000 sequence pairs so far 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27446924 (89.58%) aligned concordantly 0 times 1546273 (5.05%) aligned concordantly exactly 1 time 1645317 (5.37%) aligned concordantly >1 times 10.42% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27284614 (89.05%) aligned concordantly 0 times 1634033 (5.33%) aligned concordantly exactly 1 time 1719867 (5.61%) aligned concordantly >1 times 10.95% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27430869 (89.53%) aligned concordantly 0 times 1552140 (5.07%) aligned concordantly exactly 1 time 1655505 (5.40%) aligned concordantly >1 times 10.47% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27271006 (89.01%) aligned concordantly 0 times 1635275 (5.34%) aligned concordantly exactly 1 time 1732233 (5.65%) aligned concordantly >1 times 10.99% overall alignment rate Processed 30638514 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 30638514 Final Cytosine Methylation Report ================================= Total number of C's analysed: 201161142 Total methylated C's in CpG context: 6496215 Total methylated C's in CHG context: 1849123 Total methylated C's in CHH context: 8714079 Total methylated C's in Unknown context: 245711 Total unmethylated C's in CpG context: 20233841 Total unmethylated C's in CHG context: 38342091 Total unmethylated C's in CHH context: 125525793 Total unmethylated C's in Unknown context: 940928 C methylated in CpG context: 24.3% C methylated in CHG context: 4.6% C methylated in CHH context: 6.5% C methylated in Unknown context (CN or CHN): 20.7% Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2518:30915:36871_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2522:10773:9439_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17118 Processed 28000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 29000000 sequence pairs so far 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27430453 (89.53%) aligned concordantly 0 times 1553506 (5.07%) aligned concordantly exactly 1 time 1654555 (5.40%) aligned concordantly >1 times 10.47% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27283689 (89.05%) aligned concordantly 0 times 1633833 (5.33%) aligned concordantly exactly 1 time 1720992 (5.62%) aligned concordantly >1 times 10.95% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27445190 (89.58%) aligned concordantly 0 times 1549266 (5.06%) aligned concordantly exactly 1 time 1644058 (5.37%) aligned concordantly >1 times 10.42% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27271875 (89.01%) aligned concordantly 0 times 1633912 (5.33%) aligned concordantly exactly 1 time 1732727 (5.66%) aligned concordantly >1 times 10.99% overall alignment rate Processed 30638514 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 30638514 Final Cytosine Methylation Report ================================= Total number of C's analysed: 201243725 Total methylated C's in CpG context: 6492979 Total methylated C's in CHG context: 1851756 Total methylated C's in CHH context: 8733925 Total methylated C's in Unknown context: 245694 Total unmethylated C's in CpG context: 20259435 Total unmethylated C's in CHG context: 38345775 Total unmethylated C's in CHH context: 125559855 Total unmethylated C's in Unknown context: 939942 C methylated in CpG context: 24.3% C methylated in CHG context: 4.6% C methylated in CHH context: 6.5% C methylated in Unknown context (CN or CHN): 20.7% Processed 30000000 sequence pairs so far 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27270293 (89.01%) aligned concordantly 0 times 1633546 (5.33%) aligned concordantly exactly 1 time 1734675 (5.66%) aligned concordantly >1 times 10.99% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27428733 (89.52%) aligned concordantly 0 times 1553171 (5.07%) aligned concordantly exactly 1 time 1656610 (5.41%) aligned concordantly >1 times 10.48% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27284678 (89.05%) aligned concordantly 0 times 1631429 (5.32%) aligned concordantly exactly 1 time 1722407 (5.62%) aligned concordantly >1 times 10.95% overall alignment rate 30638514 reads; of these: 30638514 (100.00%) were paired; of these: 27440942 (89.56%) aligned concordantly 0 times 1551738 (5.06%) aligned concordantly exactly 1 time 1645834 (5.37%) aligned concordantly >1 times 10.44% overall alignment rate Processed 30638514 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 30638514 Final Cytosine Methylation Report ================================= Total number of C's analysed: 201192564 Total methylated C's in CpG context: 6498874 Total methylated C's in CHG context: 1851352 Total methylated C's in CHH context: 8739866 Total methylated C's in Unknown context: 245430 Total unmethylated C's in CpG context: 20241393 Total unmethylated C's in CHG context: 38324623 Total unmethylated C's in CHH context: 125536456 Total unmethylated C's in Unknown context: 940260 C methylated in CpG context: 24.3% C methylated in CHG context: 4.6% C methylated in CHH context: 6.5% C methylated in Unknown context (CN or CHN): 20.7% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Failed to delete temporary FastQ file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Failed to delete temporary FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Now merging BAM files EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> EF01-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam << [E::hts_open_format] Failed to open file "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam" : No such file or directory samtools view: failed to open "/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam" for reading: No such file or directory Failed to close filehandle Failed to close output filehandle Deleting temporary BAM files... Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam: No such file or directory Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam: No such file or directory Writing report to /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt into >>> /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Failed to read from temporary mapping report '/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/EF01-EM01-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt'