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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz and /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 95868 and offset 4 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz<) Finished subdividing /gscratch/srlab/kdurkin1/kathleen-coral/project/data/trimmed-WGBS-reads/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 3 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM03-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/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 1 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM03-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/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 0 and offset 2 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM03-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/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz for PID: 95868 and offset 4 (sequences written out: 32735426) Using the subset file >CF03-CM03-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/CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz (32735426 sequences in total) Writing a C -> T converted version of the input file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM03-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 CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz (32735426 sequences in total) Writing a C -> T converted version of the input file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM03-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 CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz (32735426 sequences in total) Writing a C -> T converted version of the input file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM03-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 CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz to CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz (32735426 sequences in total) Writing a C -> T converted version of the input file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM03-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 CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz to CF03-CM03-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 CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz (32735426 sequences in total) Input files are CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26341:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TGGAGAGTTAGTGATGTTTTTGAAAATTGAATTATTTGAATATAATGGTGTGATTGTTATGTTTTTTGAATTGTTAGTTTTGT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26341:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 CAAAAAACATAACAATCACACCATTATATTCAAATAATTCAATTTTCAAAAACATCACTAACTCTCCAAATTAACTAACAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26341:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TAAAAAATTAATAATATTTTTAAAAATTAAATTATTTAAATATAATAATATAATTATTATATTTTTTAAATTATTAATTTTAT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26341:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TAAAAAATATAATAATTATATTATTATATTTAAATAATTTAATTTTTAAAAATATTATTAATTTTTTAAATTAATTAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26341:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TAAAAAATTAATAATATTTTTAAAAATTAAATTATTTAAATATAATAATATAATTATTATATTTTTTAAATTATTAATTTTAT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26341:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TAAAAAATATAATAATTATATTATTATATTTAAATAATTTAATTTTTAAAAATATTATTAATTTTTTAAATTAATTAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26341:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TGGAGAGTTAGTGATGTTTTTGAAAATTGAATTATTTGAATATAATGGTGTGATTGTTATGTTTTTTGAATTGTTAGTTTTGT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26341:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 CAAAAAACATAACAATCACACCATTATATTCAAATAATTCAATTTTCAAAAACATCACTAACTCTCCAAATTAACTAACAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz (32735426 sequences in total) Input files are CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25274:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TAAAATATTTTTAAATTAAAAATAAATAAAAAATTATATATTATTTTAAAAAAAATAAAAATAAAATAATAAAAAAATATATTTTAAATTTTAAAATTTTTTTTAAAATTATTAAATTAATTTTAAATAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25274:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 AATTTAATAATTTTAAAAAAAATTTTAAAATTTAAAATATATTTTTTTATTATTTTATTTTTATTTTTTTTAAAATAATATATAATTTTTTATTTATTTTTAATTTAAAAATATTTTATATTATATTTAATTA FFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFFF:FFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25274:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 CAAAACATTCTTAAATTAAAAATAAATAAAAAACCATATACTATCCCAAAAAAAATAAAAACAAAACAATAAAAAAACATATTCCAAATTTTAAAATCTTCTTCAAAACCACTAAACCAATTTCAAACAAACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25274:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 GGTTTAGTGGTTTTGAAGAAGATTTTAAAATTTGGAATATGTTTTTTTATTGTTTTGTTTTTATTTTTTTTGGGATAGTATATGGTTTTTTATTTATTTTTAATTTAAGAATGTTTTGTGTTATGTTTGGTTG FFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFFF:FFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25274:1047_1:N:0:GGACTTGG+CGTCTGCG/1 83 NC_035784.1_CT_converted 37499203 42 78M1D55M = 37499218 149 AGTTTGTTTGAAATTGGTTTAGTGGTTTTGAAGAAGATTTTAAAATTTGGAATATGTTTTTTTATTGTTTTGTTTTTATTTTTTTTGGGATAGTATATGGTTTTTTATTTATTTTTAATTTAAGAATGTTTTG FFFFFFFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:78^T32G22 YS:i:-14 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25274:1047_2:N:0:GGACTTGG+CGTCTGCG/2 163 NC_035784.1_CT_converted 37499218 42 63M1D70M = 37499203 -149 GGTTTAGTGGTTTTGAAGAAGATTTTAAAATTTGGAATATGTTTTTTTATTGTTTTGTTTTTATTTTTTTTGGGATAGTATATGGTTTTTTATTTATTTTTAATTTAAGAATGTTTTGTGTTATGTTTGGTTG FFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFFF:FFFFFFFFFFFF: AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:63^T32G37 YS:i:-14 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25274:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TAAAATATTTTTAAATTAAAAATAAATAAAAAATTATATATTATTTTAAAAAAAATAAAAATAAAATAATAAAAAAATATATTTTAAATTTTAAAATTTTTTTTAAAATTATTAAATTAATTTTAAATAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25274:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 AATTTAATAATTTTAAAAAAAATTTTAAAATTTAAAATATATTTTTTTATTATTTTATTTTTATTTTTTTTAAAATAATATATAATTTTTTATTTATTTTTAATTTAAAAATATTTTATATTATATTTAATTA FFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFFF:FFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz (32735426 sequences in total) Input files are CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25925:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 AAATTAAATAATAATATTTGATAGATAAAATTATATATTAAAATTTTTTTAAATATATAAATAAAAAATTAAATAATAATATTTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TTAATTTTTTATTTATATATTTAAAAAAATTTTAATATATAATTTTATCTATCAAATATTATTATTTAATTTTTTATTTATATATTT FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25925:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 AAACTAAACAACAATACCTAACAAACAAAACTACATATCAAAATTTTCCTAAATACACAAACAAAAAACTAAACAACAATACCTAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TTAGTTTTTTGTTTGTGTATTTAGGAAAATTTTGATATGTAGTTTTGTTTGTTAGGTATTGTTGTTTAGTTTTTTGTTTGTGTATTT FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25925:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 AAACTAAACAACAATACCTAACAAACAAAACTACATATCAAAATTTTCCTAAATACACAAACAAAAAACTAAACAACAATACCTAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TTAGTTTTTTGTTTGTGTATTTAGGAAAATTTTGATATGTAGTTTTGTTTGTTAGGTATTGTTGTTTAGTTTTTTGTTTGTGTATTT FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:25925:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 AAATTAAATAATAATATTTGATAGATAAAATTATATATTAAAATTTTTTTAAATATATAAATAAAAAATTAAATAATAATATTTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TTAATTTTTTATTTATATATTTAAAAAAATTTTAATATATAATTTTATCTATCAAATATTATTATTTAATTTTTTATTTATATATTT FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz (32735426 sequences in total) Input files are CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM03-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 CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26702:1047_1:N:0:GGACTTGG+CGTCTGCG/1 99 NC_035781.1_CT_converted 51173057 0 9M7I47M1D72M = 51173094 173 TATGTGATGTGTGATTATAAGGATTTTGTATGTAGTGTAATTTTTTAAAAGAGTAGAGGTATAGTATAATGTTATATAAGATGTAAAGGTTTTTAATTATTTTTTATGTTAGGTAGGTTATTAATGTTTTTAATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFF:FFFFFF:FFFFFFFFF AS:i:-70 XN:i:0 XM:i:6 XO:i:2 XG:i:8 NM:i:14 MD:Z:22T23A9^T5T10A37A5T11 YS:i:-50 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26702:1047_2:N:0:GGACTTGG+CGTCTGCG/2 147 NC_035781.1_CT_converted 51173094 0 19M1D116M = 51173057 -173 TTAAAAGAGTAGAGGTATAGTATAATGTTATATAAGATGTAAAGGTTTTTAATTATTTTTTATGTTAGGTAGGTTATTAATGTTTTTAATGGTTAGTATTTTTTTGTTTATTTTTTGATGAGAATTTATGTTTGA FFFFFFFF:FFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:-50 XN:i:0 XM:i:7 XO:i:1 XG:i:1 NM:i:8 MD:Z:9A9^T5T10A37A5T25A27A1 YS:i:-70 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26702:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TATATAATATATAATTATAAAAATTTTATATATAATATAATTTTTTAAAAAAATAAAAATATAATATAATATTATATAAAATATAAAAATTTTTAATTATTTTTTATATTAAATAAATTATTAATATTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFF:FFFFFF:FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26702:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TTAAATATAAATTTTTATTAAAAAATAAATAAAAAAATATTAATTATTAAAAATATTAATAATTTATTTAATATAAAAAATAATTAAAAATTTTTATATTTTATATAATATTATATTATATTTTTATTTTTTTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF:FFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_G_to_A.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26702:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TATATAATATATAATTATAAAAATTTTATATATAATATAATTTTTTAAAAAAATAAAAATATAATATAATATTATATAAAATATAAAAATTTTTAATTATTTTTTATATTAAATAAATTATTAATATTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFF:FFFFFF:FFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26702:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 TTAAATATAAATTTTTATTAAAAAATAAATAAAAAAATATTAATTATTAAAAATATTAATAATTTATTTAATATAAAAAATAATTAAAAATTTTTATATTTTATATAATATTATATTATATTTTTATTTTTTTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF:FFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_C_to_T.fastq.gz and CF03-CM03-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:GW210315000:4:1101:26702:1047_1:N:0:GGACTTGG+CGTCTGCG/1 83 NC_035780.1_GA_converted 16201778 14 135M = 16201734 -179 CATTAAAAACATTAATAACCTACCTAACATAAAAAATAATTAAAAACCTTTACATCTTATATAACATTATACTATACCTCTACTCTTTTAAAAAATTACACTACATACAAAATCCTTATAATCACACATCACATA FFFFFFFFF:FFFFFF:FFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-30 XS:i:-72 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:17T9T58A18C13C15 YS:i:-18 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26702:1047_2:N:0:GGACTTGG+CGTCTGCG/2 163 NC_035780.1_GA_converted 16201734 14 135M = 16201778 179 TCAAACATAAATTCTCATCAAAAAATAAACAAAAAAATACTAACCATTAAAAACATTAATAACCTACCTAACATAAAAAATAATTAAAAACCTTTACATCTTATATAACATTATACTATACCTCTACTCTTTTAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFF:FFFFFFFF AS:i:-18 XS:i:-44 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:61T9T58A4 YS:i:-30 YT:Z:CP >>> Writing bisulfite mapping results to CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1175:28754:36417_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1233:10547:36135_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1661:30110:26177_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17177 Processed 3000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2112:5773:10551_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17150 Processed 3000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1415:4860:36558_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Processed 5000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1525:30282:1579_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2502:32624:29121_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 65668306 Processed 7000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1647:28682:32158_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17177 Processed 8000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2634:24162:31501_1:N:0:GGACTTGG+CGTCTGCG NC_035781.1 2 Processed 9000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1574:6379:27289_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17194 Processed 11000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1524:28429:36855_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1540:9805:22138_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1235:20952:27696_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 2 Processed 8000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1309:30472:19914_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1307:23728:19194_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 1 Processed 19000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1550:16251:8500_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17176 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1566:11324:30060_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17184 Processed 23000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2510:10257:3630_1:N:0:AGACTTGG+CGTCTGCG NC_007175.2 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2270:13250:12132_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2533:4878:19022_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 65668306 Processed 31000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2630:9453:1141_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Processed 32000000 sequence pairs so far 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29115820 (88.94%) aligned concordantly 0 times 1705020 (5.21%) aligned concordantly exactly 1 time 1914586 (5.85%) aligned concordantly >1 times 11.06% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29866340 (91.24%) aligned concordantly 0 times 1347114 (4.12%) aligned concordantly exactly 1 time 1521972 (4.65%) aligned concordantly >1 times 8.76% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29123982 (88.97%) aligned concordantly 0 times 1700223 (5.19%) aligned concordantly exactly 1 time 1911221 (5.84%) aligned concordantly >1 times 11.03% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29869669 (91.25%) aligned concordantly 0 times 1345078 (4.11%) aligned concordantly exactly 1 time 1520679 (4.65%) aligned concordantly >1 times 8.75% overall alignment rate Processed 32735426 sequences in total Successfully deleted the temporary files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 32735426 Final Cytosine Methylation Report ================================= Total number of C's analysed: 179870008 Total methylated C's in CpG context: 4888227 Total methylated C's in CHG context: 919376 Total methylated C's in CHH context: 5191607 Total methylated C's in Unknown context: 169458 Total unmethylated C's in CpG context: 18426110 Total unmethylated C's in CHG context: 33849313 Total unmethylated C's in CHH context: 116595375 Total unmethylated C's in Unknown context: 856634 C methylated in CpG context: 21.0% C methylated in CHG context: 2.6% C methylated in CHH context: 4.3% C methylated in Unknown context (CN or CHN): 16.5% Processed 26000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2621:9561:26694_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Processed 32000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29865358 (91.23%) aligned concordantly 0 times 1346211 (4.11%) aligned concordantly exactly 1 time 1523857 (4.66%) aligned concordantly >1 times 8.77% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29125361 (88.97%) aligned concordantly 0 times 1699968 (5.19%) aligned concordantly exactly 1 time 1910097 (5.83%) aligned concordantly >1 times 11.03% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29126293 (88.97%) aligned concordantly 0 times 1701420 (5.20%) aligned concordantly exactly 1 time 1907713 (5.83%) aligned concordantly >1 times 11.03% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29872526 (91.25%) aligned concordantly 0 times 1344184 (4.11%) aligned concordantly exactly 1 time 1518716 (4.64%) aligned concordantly >1 times 8.75% overall alignment rate Processed 32735426 sequences in total Successfully deleted the temporary files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 32735426 Final Cytosine Methylation Report ================================= Total number of C's analysed: 179741712 Total methylated C's in CpG context: 4888935 Total methylated C's in CHG context: 919960 Total methylated C's in CHH context: 5210420 Total methylated C's in Unknown context: 168436 Total unmethylated C's in CpG context: 18413181 Total unmethylated C's in CHG context: 33829167 Total unmethylated C's in CHH context: 116480049 Total unmethylated C's in Unknown context: 854774 C methylated in CpG context: 21.0% C methylated in CHG context: 2.6% C methylated in CHH context: 4.3% C methylated in Unknown context (CN or CHN): 16.5% 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29123380 (88.97%) aligned concordantly 0 times 1702133 (5.20%) aligned concordantly exactly 1 time 1909913 (5.83%) aligned concordantly >1 times 11.03% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29121252 (88.96%) aligned concordantly 0 times 1702759 (5.20%) aligned concordantly exactly 1 time 1911415 (5.84%) aligned concordantly >1 times 11.04% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29865216 (91.23%) aligned concordantly 0 times 1345324 (4.11%) aligned concordantly exactly 1 time 1524886 (4.66%) aligned concordantly >1 times 8.77% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29870924 (91.25%) aligned concordantly 0 times 1345271 (4.11%) aligned concordantly exactly 1 time 1519231 (4.64%) aligned concordantly >1 times 8.75% overall alignment rate Processed 32735426 sequences in total Successfully deleted the temporary files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz, CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz, CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 32735426 Final Cytosine Methylation Report ================================= Total number of C's analysed: 179827555 Total methylated C's in CpG context: 4880985 Total methylated C's in CHG context: 919477 Total methylated C's in CHH context: 5198539 Total methylated C's in Unknown context: 169055 Total unmethylated C's in CpG context: 18421713 Total unmethylated C's in CHG context: 33837462 Total unmethylated C's in CHH context: 116569379 Total unmethylated C's in Unknown context: 857760 C methylated in CpG context: 20.9% C methylated in CHG context: 2.6% C methylated in CHH context: 4.3% C methylated in Unknown context (CN or CHN): 16.5% Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2308:23240:22326_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2310:30933:13636_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 2 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2414:11216:18662_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29129653 (88.99%) aligned concordantly 0 times 1699280 (5.19%) aligned concordantly exactly 1 time 1906493 (5.82%) aligned concordantly >1 times 11.01% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29125675 (88.97%) aligned concordantly 0 times 1701352 (5.20%) aligned concordantly exactly 1 time 1908399 (5.83%) aligned concordantly >1 times 11.03% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29871477 (91.25%) aligned concordantly 0 times 1344834 (4.11%) aligned concordantly exactly 1 time 1519115 (4.64%) aligned concordantly >1 times 8.75% overall alignment rate 32735426 reads; of these: 32735426 (100.00%) were paired; of these: 29864929 (91.23%) aligned concordantly 0 times 1347470 (4.12%) aligned concordantly exactly 1 time 1523027 (4.65%) aligned concordantly >1 times 8.77% overall alignment rate Processed 32735426 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 32735426 Final Cytosine Methylation Report ================================= Total number of C's analysed: 179741417 Total methylated C's in CpG context: 4888140 Total methylated C's in CHG context: 920375 Total methylated C's in CHH context: 5215071 Total methylated C's in Unknown context: 168610 Total unmethylated C's in CpG context: 18398776 Total unmethylated C's in CHG context: 33821776 Total unmethylated C's in CHH context: 116497279 Total unmethylated C's in Unknown context: 859310 C methylated in CpG context: 21.0% C methylated in CHG context: 2.6% C methylated in CHH context: 4.3% C methylated in Unknown context (CN or CHN): 16.4% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Failed to delete temporary FastQ file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Failed to delete temporary FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz: No such file or directory Now merging BAM files CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam into >>> CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam <<< Merging from file >> CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF03-CM03-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/CF03-CM03-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/CF03-CM03-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 >> CF03-CM03-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/CF03-CM03-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/CF03-CM03-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 >> CF03-CM03-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/CF03-CM03-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/CF03-CM03-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 Deleting temporary BAM files... Failed to delete temporary BAM file /gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM03-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/CF03-CM03-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/CF03-CM03-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/CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt Now merging temporary reports CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_PE_report.txt <<< Merging from file >> CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt'