Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 16042685) Using the subset file >CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 18662 and offset 2 (sequences written out: 16042685) Using the subset file >CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 18662 and offset 2 (sequences written out: 16042685) Using the subset file >CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 16042685) Using the subset file >CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (16042685 sequences in total) Writing a C -> T converted version of the input file CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (16042685 sequences in total) Writing a C -> T converted version of the input file CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (16042685 sequences in total) Input files are CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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 CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (16042685 sequences in total) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30879:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 GNATTAAATTTTAATATATAGTAATTTTTAATTTTATTAAAATAATTATAATTTATTTAATAATAATATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30879:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 TATATTATTATTAAATAAATTATAATTATTTTAATAAAATTAAAAATTACTATATATTAAAATTTAATAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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)) Input files are CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30879:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 ANACTAAACTCCAACATATAATAACCCTTAATTTTATTAAAATAACCACAATTTATTTAACAACAACACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30879:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 TGTGTTGTTGTTAAATAAATTGTGGTTATTTTAATAAAATTAAGGGTTATTATATGTTGGAGTTTAGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25491:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 ANATTATATTAATATAAAAAAAAATAAAATATTAATTATATTATTAATTAATTTAATTTTATAAAAAAATATAAAATTTAAATTAATAAATTTTATTTATAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25491:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 CCTATAAATAAAATTTATTAATTTAAATTTTATATTTTTTTATAAAATTAAATTAATTAATAATATAATTAATATTTTATTTTTTTTTATATTAATATAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30879:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 ANACTAAACTCCAACATATAATAACCCTTAATTTTATTAAAATAACCACAATTTATTTAACAACAACACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30879:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 TGTGTTGTTGTTAAATAAATTGTGGTTATTTTAATAAAATTAAGGGTTATTATATGTTGGAGTTTAGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25491:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 ANACCATACTAACACAAAAAAAAACAAAATACCAATCATACCACCAACTAACTTAACTCCACAAAAAAACATAAAATTCAAATCAACAAATTTCATCCACAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25491:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 TTTGTGGATGAAATTTGTTGATTTGAATTTTATGTTTTTTTGTGGAGTTAAGTTAGTTGGTGGTATGATTGGTATTTTGTTTTTTTTTGTGTTAGTATGGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30879:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 GNATTAAATTTTAATATATAGTAATTTTTAATTTTATTAAAATAATTATAATTTATTTAATAATAATATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30879:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 TATATTATTATTAAATAAATTATAATTATTTTAATAAAATTAAAAATTACTATATATTAAAATTTAATAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25491:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 ANACCATACTAACACAAAAAAAAACAAAATACCAATCATACCACCAACTAACTTAACTCCACAAAAAAACATAAAATTCAAATCAACAAATTTCATCCACAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25491:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 TTTGTGGATGAAATTTGTTGATTTGAATTTTATGTTTTTTTGTGGAGTTAAGTTAGTTGGTGGTATGATTGGTATTTTGTTTTTTTTTGTGTTAGTATGGTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25491:1047_1:N:0:TTATAACC+TCGATATC/1 77 * 0 0 * * 0 0 ANATTATATTAATATAAAAAAAAATAAAATATTAATTATATTATTAATTAATTTAATTTTATAAAAAAATATAAAATTTAAATTAATAAATTTTATTTATAGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25491:1047_2:N:0:TTATAACC+TCGATATC/2 141 * 0 0 * * 0 0 CCTATAAATAAAATTTATTAATTTAAATTTTATATTTTTTTATAAAATTAAATTAATTAATAATATAATTAATATTTTATTTTTTTTTATATTAATATAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1235:7202:14121_1:N:0:TTATAACC+TCGATATC NC_007175.2 17178 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1235:8965:13917_1:N:0:TTATAACC+TCGATATC NC_007175.2 17178 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1365:12572:4570_1:N:0:TTATAACC+TCGATATC NC_035780.1 2 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1469:23077:5008_1:N:0:TTATAACC+TCGATATC NC_007175.2 17108 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2234:2311:34679_1:N:0:TTATAACC+TCGATATC NC_035780.1 1 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far 16042685 reads; of these: 16042685 (100.00%) were paired; of these: 14899727 (92.88%) aligned concordantly 0 times 529302 (3.30%) aligned concordantly exactly 1 time 613656 (3.83%) aligned concordantly >1 times 7.12% overall alignment rate 16042685 reads; of these: 16042685 (100.00%) were paired; of these: 15047684 (93.80%) aligned concordantly 0 times 457705 (2.85%) aligned concordantly exactly 1 time 537296 (3.35%) aligned concordantly >1 times 6.20% overall alignment rate 16042685 reads; of these: 16042685 (100.00%) were paired; of these: 1604268514893507 reads; of these: ( 92.84 %16042685) aligned concordantly 0 times ( 534419 (100.003.33%%) were paired; of these:) aligned concordantly exactly 1 time 15051496614759 ( (93.823.83%%) aligned concordantly 0 times) aligned concordantly >1 times 7.16454868% ( overall alignment rate2.84 %) aligned concordantly exactly 1 time 536321 (3.34%) aligned concordantly >1 times 6.18% overall alignment rate Processed 16042685 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 64170740. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 64170740. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 64170740. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 64170740. Processed 16000000 sequence pairs so far Successfully deleted the temporary files CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 16042685 Final Cytosine Methylation Report ================================= Total number of C's analysed: 59471675 Total methylated C's in CpG context: 1332973 Total methylated C's in CHG context: 280420 Total methylated C's in CHH context: 1562523 Total methylated C's in Unknown context: 84418 Total unmethylated C's in CpG context: 6094816 Total unmethylated C's in CHG context: 10722143 Total unmethylated C's in CHH context: 39478800 Total unmethylated C's in Unknown context: 412202 C methylated in CpG context: 17.9% C methylated in CHG context: 2.5% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 17.0% Now waiting for all child processes to complete 16042685 reads; of these: 16042685 (100.00%) were paired; of these: 14900725 (92.88%) aligned concordantly 0 times 529720 (3.30%) aligned concordantly exactly 1 time 612240 (3.82%) aligned concordantly >1 times 7.12% overall alignment rate 16042685 reads; of these: 16042685 (100.00%) were paired; of these: 14896542 (92.86%) aligned concordantly 0 times 532002 (3.32%) aligned concordantly exactly 1 time 614141 (3.83%) aligned concordantly >1 times 7.14% overall alignment rate 16042685 reads; of these: 16042685 (100.00%) were paired; of these: 15047885 (93.80%) aligned concordantly 0 times 458567 (2.86%) aligned concordantly exactly 1 time 536233 (3.34%) aligned concordantly >1 times 6.20% overall alignment rate 16042685 reads; of these: 16042685 (100.00%) were paired; of these: 15051431 (93.82%) aligned concordantly 0 times 455933 (2.84%) aligned concordantly exactly 1 time 535321 (3.34%) aligned concordantly >1 times 6.18% overall alignment rate Processed 16042685 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 64170740. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 64170740. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 64170740. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 64170740. Successfully deleted the temporary files CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 16042685 Final Cytosine Methylation Report ================================= Total number of C's analysed: 59443763 Total methylated C's in CpG context: 1335117 Total methylated C's in CHG context: 281640 Total methylated C's in CHH context: 1555366 Total methylated C's in Unknown context: 84581 Total unmethylated C's in CpG context: 6088917 Total unmethylated C's in CHG context: 10718103 Total unmethylated C's in CHH context: 39464620 Total unmethylated C's in Unknown context: 411209 C methylated in CpG context: 18.0% C methylated in CHG context: 2.6% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 17.1% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 32085370 Final Cytosine Methylation Report ================================= Total number of C's analysed: 118915438 Total methylated C's in CpG context: 2668090 Total methylated C's in CHG context: 562060 Total methylated C's in CHH context: 3117889 Total methylated C's in Unknown context: 168999 Total unmethylated C's in CpG context: 12183733 Total unmethylated C's in CHG context: 21440246 Total unmethylated C's in CHH context: 78943420 Total unmethylated C's in Unknown context: 823411 C methylated in CpG context: 18.0% C methylated in CHG context: 2.6% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 17.0% Deleting temporary report files... Bismark completed in 0d 0h 57m 22s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 46610 and offset 2 (sequences written out: 67079578) Using the subset file >CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 67079578) Using the subset file >CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 46610 and offset 2 (sequences written out: 67079578) Using the subset file >CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 67079578) Using the subset file >CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (67079578 sequences in total) Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (67079578 sequences in total) Writing a C -> T converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (67079578 sequences in total) Created C -> T as well as G -> A converted versions of the FastQ file CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (67079578 sequences in total) Input files are CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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)) Input files are CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANTATAAAAATATAAAATAAAATATATTATATATTGTAAATTTATAATTAAAAATTATAAAATTTAAATTTTTAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 ATAAAAATTTAAATTTTATAATTTTTAATTATAAATTTACAATATATAATATATTTTATTTTATATTTTTATATT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTTTTTATTATAAAAATATTATTTTTAATAAATAATTTAAAATAATTTATTAAAATATAATAATTTTTATTATAAAAAAAATTATATTTTTAATAATTTAAAATTTATTAATATAATATTATAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTAATAATATTTATTATTAAATTATTTTATTTTATAATTTATAATATTATATTAATAAATTTTAAATTATTAAAAATATAATTTTTTTTATAATAAAAATTATTATATTTTAATAAATTATTTTAAAATATTTATTAAAAATAATAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 99 NC_035786.1_GA_converted 38378351 11 75M = 38378351 75 ANTACAAAAATACAAAATAAAATACATCATATATCATAAATTTATAATTAAAAATTATAAAATTTAAATCTTTAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-13 XS:i:-25 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1A49T0C22 YS:i:-12 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 147 NC_035786.1_GA_converted 38378351 11 75M = 38378351 -75 AATACAAAAATACAAAATAAAATACATCATATATCATAAATTTATAATTAAAAATTATAAAATTTAAATCTTTAC FF:FFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:51T0C22 YS:i:-13 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTCCTCACTATAAAAATACTATCTCCAACAAACAATCCAAAACAATTTACCAAAATACAATAATTCCTATTATAAAAAAAATTATACTCTCAATAATCCAAAATTTATCAACATAACACCACAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTGGTGATATTTATTGTTGAATTGTTTTGTTTTATAGTTTGTGGTGTTATGTTGATAAATTTTGGATTATTGAGAGTATAATTTTTTTTATAATAGGAATTATTGTATTTTGGTAAATTGTTTTGGAGTGTTTGTTGGAGATAGTAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 83 NC_035789.1_CT_converted 2210749 12 75M = 2210749 -75 GTAAAGATTTAAATTTTATAATTTTTAATTATAAATTTATGATATATGATGTATTTTATTTTGTATTTTTGTANT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-1 XS:i:-7 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:73T1 YS:i:0 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 163 NC_035789.1_CT_converted 2210749 12 75M = 2210749 75 GTAAAGATTTAAATTTTATAATTTTTAATTATAAATTTATGATATATGATGTATTTTATTTTGTATTTTTGTATT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFF:FF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:-1 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTCCTCACTATAAAAATACTATCTCCAACAAACAATCCAAAACAATTTACCAAAATACAATAATTCCTATTATAAAAAAAATTATACTCTCAATAATCCAAAATTTATCAACATAACACCACAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTGGTGATATTTATTGTTGAATTGTTTTGTTTTATAGTTTGTGGTGTTATGTTGATAAATTTTGGATTATTGAGAGTATAATTTTTTTTATAATAGGAATTATTGTATTTTGGTAAATTGTTTTGGAGTGTTTGTTGGAGATAGTAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27534:1047_1:N:0:GCACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANTATAAAAATATAAAATAAAATATATTATATATTGTAAATTTATAATTAAAAATTATAAAATTTAAATTTTTAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27534:1047_2:N:0:GCACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 ATAAAAATTTAAATTTTATAATTTTTAATTATAAATTTACAATATATAATATATTTTATTTTATATTTTTATATT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFF:FF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26612:1047_1:N:0:ACACGGAC+TGCGAGAC/1 77 * 0 0 * * 0 0 ANATTAATTTTTATAATTAATAAATTTTTTTATTATAAAAATATTATTTTTAATAAATAATTTAAAATAATTTATTAAAATATAATAATTTTTATTATAAAAAAAATTATATTTTTAATAATTTAAAATTTATTAATATAATATTATAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26612:1047_2:N:0:ACACGGAC+TGCGAGAC/2 141 * 0 0 * * 0 0 TTTTTAATAATATTTATTATTAAATTATTTTATTTTATAATTTATAATATTATATTAATAAATTTTAAATTATTAAAAATATAATTTTTTTTATAATAAAAATTATTATATTTTAATAAATTATTTTAAAATATTTATTAAAAATAATAT :F:FFF:FFFFF:FFFFFFFFFFF:FFFFFF::FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF,F:FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFF:F:FFF:FFFFFF:FFF:,:F:FFFFFF:F:FFFF:,F YT:Z:UP >>> Writing bisulfite mapping results to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1116:7292:4977_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1116:7274:6198_1:N:0:GCACGGAC+TGCGAGAC 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:GW210315000:4:1129:11107:29371_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:10809:29700_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1129:11225:30138_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1137:29396:17989_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1151:28076:7216_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1163:11921:2566_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1175:18032:33004_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1228:12671:16611_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1263:25852:3427_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1321:3558:21402_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1326:17589:19805_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1321:3676:21856_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1341:14109:27336_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1344:28772:19946_1:N:0:ACACGGAC+TGCGAGAC NC_035780.1 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1355:21197:17503_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1420:3685:25911_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1420:4282:26694_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:11577:15217_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1543:16016:18114_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1560:23222:24236_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1560:21414:24017_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:9227:11083_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:8070:12524_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1610:9634:21120_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1610:9986:27336_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1669:18548:7780_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2158:31277:36558_1:N:0:GCACGGAC+TGCGAGAC NC_035781.1 3 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2213:20980:17754_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2213:20844:17707_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2272:29975:21465_1:N:0:GCACAGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2305:17002:1063_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:23330:19006_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:23393:21684_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2318:19515:14184_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2320:3459:18756_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 17164 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2328:11686:35603_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2354:17047:24533_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2377:2917:14622_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2420:1271:31939_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2424:22697:27931_1:N:0:GCACGGAC+TGCGAGAC NC_035781.1 3 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2512:23764:30405_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2531:25247:4319_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2530:27326:19100_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2661:3323:5462_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2666:5267:22889_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1108:9109:27258_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1142:13765:17190_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1133:15157:17973_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1154:6903:22310_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1237:18719:33191_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1248:28266:11804_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1270:2248:7263_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1268:19931:31438_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1355:19171:25488_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1374:14977:14465_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1374:16269:22373_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1375:17806:25285_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1433:5909:29168_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1638:24975:35728_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2107:10926:23202_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2213:10493:35822_1:N:0:ACACGGAC+TGCGAGAC NC_035780.1 2 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2253:30951:8782_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 2 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:23963:29904_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:24080:29982_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2426:26359:31798_1:N:0:GCACGGAC+TGCGAGAC NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2447:12726:28729_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2448:13367:2534_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2603:1118:5807_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2572:18593:20447_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2632:10068:28260_1:N:0:GCACGGAC+TGCGAGAC NC_035780.1 2 Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 55619611 (82.92%) aligned concordantly 0 times 5123328 (7.64%) aligned concordantly exactly 1 time 6336639 (9.45%) aligned concordantly >1 times 17.08% overall alignment rate 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 55607480 (82.90%) aligned concordantly 0 times 5124775 (7.64%) aligned concordantly exactly 1 time 6347323 (9.46%) aligned concordantly >1 times 17.10% overall alignment rate 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 54969532 (81.95%) aligned concordantly 0 times 5380042 (8.02%) aligned concordantly exactly 1 time 6730004 (10.03%) aligned concordantly >1 times 18.05% overall alignment rate 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 54962504 (81.94%) aligned concordantly 0 times 5386048 (8.03%) aligned concordantly exactly 1 time 6731026 (10.03%) aligned concordantly >1 times 18.06% overall alignment rate Processed 67079578 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 268318312. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 268318312. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 268318312. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 268318312. Successfully deleted the temporary files CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 67079578 Final Cytosine Methylation Report ================================= Total number of C's analysed: 885602665 Total methylated C's in CpG context: 24578832 Total methylated C's in CHG context: 4200973 Total methylated C's in CHH context: 17445133 Total methylated C's in Unknown context: 1053696 Total unmethylated C's in CpG context: 111964437 Total unmethylated C's in CHG context: 190314102 Total unmethylated C's in CHH context: 537099188 Total unmethylated C's in Unknown context: 4260323 C methylated in CpG context: 18.0% C methylated in CHG context: 2.2% C methylated in CHH context: 3.1% C methylated in unknown context (CN or CHN): 19.8% Now waiting for all child processes to complete Processed 67000000 sequence pairs so far 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 55609552 (82.90%) aligned concordantly 0 times 5125479 (7.64%) aligned concordantly exactly 1 time 6344547 (9.46%) aligned concordantly >1 times 17.10% overall alignment rate 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 54966794 (81.94%) aligned concordantly 0 times 5383926 (8.03%) aligned concordantly exactly 1 time 6728858 (10.03%) aligned concordantly >1 times 18.06% overall alignment rate 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 55617576 (82.91%) aligned concordantly 0 times 5126168 (7.64%) aligned concordantly exactly 1 time 6335834 (9.45%) aligned concordantly >1 times 17.09% overall alignment rate 67079578 reads; of these: 67079578 (100.00%) were paired; of these: 54964799 (81.94%) aligned concordantly 0 times 5384299 (8.03%) aligned concordantly exactly 1 time 6730480 (10.03%) aligned concordantly >1 times 18.06% overall alignment rate Processed 67079578 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 268318312. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 268318312. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 268318312. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 268318312. Successfully deleted the temporary files CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 67079578 Final Cytosine Methylation Report ================================= Total number of C's analysed: 885652965 Total methylated C's in CpG context: 24571553 Total methylated C's in CHG context: 4194058 Total methylated C's in CHH context: 17480029 Total methylated C's in Unknown context: 1052754 Total unmethylated C's in CpG context: 111966072 Total unmethylated C's in CHG context: 190319975 Total unmethylated C's in CHH context: 537121278 Total unmethylated C's in Unknown context: 4260915 C methylated in CpG context: 18.0% C methylated in CHG context: 2.2% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 19.8% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF01-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF01-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF01-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 134159156 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1771255630 Total methylated C's in CpG context: 49150385 Total methylated C's in CHG context: 8395031 Total methylated C's in CHH context: 34925162 Total methylated C's in Unknown context: 2106450 Total unmethylated C's in CpG context: 223930509 Total unmethylated C's in CHG context: 380634077 Total unmethylated C's in CHH context: 1074220466 Total unmethylated C's in Unknown context: 8521238 C methylated in CpG context: 18.0% C methylated in CHG context: 2.2% C methylated in CHH context: 3.1% C methylated in unknown context (CN or CHN): 19.8% Deleting temporary report files... Bismark completed in 0d 5h 16m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 3907 and offset 2 (sequences written out: 103973790) Using the subset file >CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 103973790) Using the subset file >CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 3907 and offset 2 (sequences written out: 103973790) Using the subset file >CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 103973790) Using the subset file >CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (103973790 sequences in total) Writing a C -> T converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (103973790 sequences in total) Writing a C -> T converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (103973790 sequences in total) Input files are CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25672:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TNGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTGATTTTATGTTATTTTTTTTGGGATTGTTAATAGATGGAAGAGTATATGTTTGAATTTTATTTATTTGGATTTATTTTGTATTTTGTTATTAGTATGAAAAAAGGGGGGGGGGGGG F#FFFFFFFFF:FFFFFFFF,FFFFF,FF,FF,FFFF:,FFF,FFF:F,FFFFF,,:F:FFFFFFFF,F::FFF,F,::FFF::F,FFF,,,FF,FFF:,:,FFF,:FF::,,FFF,F,::F:,F,,:,:,FFFF,,,,:,,FF,FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25672:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAATA F:,,,,:FFFF::::FFF:FFFFFFFFFFFFF:,F:,FF:::,:F,,,,:,,,F,:,,,:::,,,:,:FF,F,F:FF:::F:,::,F,,,:,FFFF:::,:::,:FF,F,,F:F:FFF::F:,,,,,,,,,,:FFF:FFFFFFFF::,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25672:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 CNATTATTATTATTATTATTATTATTATTATTATAATTTTATATTATTTTTTTTAAAATTATTAATAAATAAAAAAACACACATCTAAACTCCATTCACTTAAACTCATCTCATATTCCATCATCAACATAAAAAAAAAAAAAAAAAAAA F#FFFFFFFFF:FFFFFFFF,FFFFF,FF,FF,FFFF:,FFF,FFF:F,FFFFF,,:F:FFFFFFFF,F::FFF,F,::FFF::F,FFF,,,FF,FFF:,:,FFF,:FF::,,FFF,F,::F:,F,,:,:,FFFF,,,,:,,FF,FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25672:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AGGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAATA F:,,,,:FFFF::::FFF:FFFFFFFFFFFFF:,F:,FF:::,:F,,,,:,,,F,:,,,:::,,,:,:FF,F,F:FF:::F:,::,F,,,:,FFFF:::,:::,:FF,F,,F:F:FFF::F:,,,,,,,,,,:FFF:FFFFFFFF::,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25672:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 CNATTATTATTATTATTATTATTATTATTATTATAATTTTATATTATTTTTTTTAAAATTATTAATAAATAAAAAAACACACATCTAAACTCCATTCACTTAAACTCATCTCATATTCCATCATCAACATAAAAAAAAAAAAAAAAAAAA F#FFFFFFFFF:FFFFFFFF,FFFFF,FF,FF,FFFF:,FFF,FFF:F,FFFFF,,:F:FFFFFFFF,F::FFF,F,::FFF::F,FFF,,,FF,FFF:,:,FFF,:FF::,,FFF,F,::F:,F,,:,:,FFFF,,,,:,,FF,FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25672:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AGGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAATA F:,,,,:FFFF::::FFF:FFFFFFFFFFFFF:,F:,FF:::,:F,,,,:,,,F,:,,,:::,,,:,:FF,F,F:FF:::F:,::,F,,,:,FFFF:::,:::,:FF,F,,F:F:FFF::F:,,,,,,,,,,:FFF:FFFFFFFF::,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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)) Created C -> T as well as G -> A converted versions of the FastQ file CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (103973790 sequences in total) Input files are CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25672:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 TNGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTGATTTTATGTTATTTTTTTTGGGATTGTTAATAGATGGAAGAGTATATGTTTGAATTTTATTTATTTGGATTTATTTTGTATTTTGTTATTAGTATGAAAAAAGGGGGGGGGGGGG F#FFFFFFFFF:FFFFFFFF,FFFFF,FF,FF,FFFF:,FFF,FFF:F,FFFFF,,:F:FFFFFFFF,F::FFF,F,::FFF::F,FFF,,,FF,FFF:,:,FFF,:FF::,,FFF,F,::F:,F,,:,:,FFFF,,,,:,,FF,FFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25672:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAATA F:,,,,:FFFF::::FFF:FFFFFFFFFFFFF:,F:,FF:::,:F,,,,:,,,F,:,,,:::,,,:,:FF,F,F:FF:::F:,::,F,,,:,FFFF:::,:::,:FF,F,,F:F:FFF::F:,,,,,,,,,,:FFF:FFFFFFFF::,,, YT:Z:UP >>> Writing bisulfite mapping results to CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ANTTGGTATATGGGAATGTTAGTTATTATTATATTTGGTGAGTAGTTAGGTGTGGTGATGTGGTGTTTTTGATGATTTTGAAAATATTAGTTATGTTGGATAGGGTGTGTGTGTTGAAGGTTTTAGTTTGTTTTTGTTTGTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AAACAAACAAAAACAAACTAAAACCTTCAACACACACACCCTATCCAACATAACTAATATTTTCAAAATCATCAAAAACACCACATCACCACACCTAACTACTCACCAAATATAATAATAACTAACATTCCCATATACCAACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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)) Reading in the sequence files CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ANCTAATATATAAAAATATTAATTATTATTATATTTAATAAATAATTAAATATAATAATATAATATTTTTAATAATTTTAAAAATATTAATTATATCAAATAAAATATATATATTAAAAACTTTAATTTATTTTTATTTATTC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 GAATAAATAAAAATAAATTAAAGTTTTTAATATATATATTTTATTTGATATAATTAATATTTTTAAAATTATTAAAAATATTATATTATTATATTTAATTATTTATTAAATATAATAATAATTAATATTTTTATATATTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ANCTAATATATAAAAATATTAATTATTATTATATTTAATAAATAATTAAATATAATAATATAATATTTTTAATAATTTTAAAAATATTAATTATATCAAATAAAATATATATATTAAAAACTTTAATTTATTTTTATTTATTC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 GAATAAATAAAAATAAATTAAAGTTTTTAATATATATATTTTATTTGATATAATTAATATTTTTAAAATTATTAAAAATATTATATTATTATATTTAATTATTTATTAAATATAATAATAATTAATATTTTTATATATTAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25726:1047_1:N:0:TTGGACTC+CTGCTTCC/1 77 * 0 0 * * 0 0 ANTTGGTATATGGGAATGTTAGTTATTATTATATTTGGTGAGTAGTTAGGTGTGGTGATGTGGTGTTTTTGATGATTTTGAAAATATTAGTTATGTTGGATAGGGTGTGTGTGTTGAAGGTTTTAGTTTGTTTTTGTTTGTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25726:1047_2:N:0:TTGGACTC+CTGCTTCC/2 141 * 0 0 * * 0 0 AAACAAACAAAAACAAACTAAAACCTTCAACACACACACCCTATCCAACATAACTAATATTTTCAAAATCATCAAAAACACCACATCACCACACCTAACTACTCACCAAATATAATAATAACTAACATTCCCATATACCAACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1339:23357:2738_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1517:14009:33865_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 65668301 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1517:13494:32847_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 65668301 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1517:14018:33974_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 65668301 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1527:11180:11960_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1548:25563:5243_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1548:20735:5525_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1548:32009:18474_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1550:4472:35383_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1677:20103:13260_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17173 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2203:22191:20071_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17126 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2364:29451:22592_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17154 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2365:6949:4726_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2367:17589:10974_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17179 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2664:30544:6918_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17146 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1214:6054:31986_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17096 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1229:13557:36338_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1248:27208:31234_1:N:0:TTGGACTC+CTGATTCC NC_007175.2 17163 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1276:9986:36542_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17179 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1330:6017:16861_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1331:2166:20431_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 3 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1432:32045:1908_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17161 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1439:5367:20870_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17096 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1449:5475:23876_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17172 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1515:25654:11224_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:19569:11303_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:19506:14857_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1627:3188:2879_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1648:28483:31657_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2115:9625:20917_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2115:9588:20979_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2171:14389:20400_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17163 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2243:30400:33004_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2251:8793:5071_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 2 Processed 79000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2337:16378:5901_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17174 Processed 84000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2432:4734:32487_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 65668290 Processed 89000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2464:29188:15687_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 2 Processed 92000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 94000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2528:2148:21809_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17173 Processed 95000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2561:26847:2143_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 2 Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2578:14534:33426_1:N:0:TTGGACTC+CTGCTTCC NC_007175.2 17161 Processed 99000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 100000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2634:27597:21324_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 3 Processed 101000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 102000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2660:26883:1423_1:N:0:TTGGACTC+CTGCTTCC NC_035780.1 3 Processed 103000000 sequence pairs so far Processed 103000000 sequence pairs so far 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 97770873 (94.03%) aligned concordantly 0 times 2771521 (2.67%) aligned concordantly exactly 1 time 3431396 (3.30%) aligned concordantly >1 times 5.97% overall alignment rate 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 95019105 (91.39%) aligned concordantly 0 times 4072671 (3.92%) aligned concordantly exactly 1 time 4882014 (4.70%) aligned concordantly >1 times 8.61% overall alignment rate 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 95033502 (91.40%) aligned concordantly 0 times 4065982 (3.91%) aligned concordantly exactly 1 time 4874306 (4.69%) aligned concordantly >1 times 8.60% overall alignment rate 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 97777900 (94.04%) aligned concordantly 0 times 2768270 (2.66%) aligned concordantly exactly 1 time 3427620 (3.30%) aligned concordantly >1 times 5.96% overall alignment rate Processed 103973790 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 415895160. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 415895160. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 415895160. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 415895160. Successfully deleted the temporary files CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 103973790 Final Cytosine Methylation Report ================================= Total number of C's analysed: 335910587 Total methylated C's in CpG context: 7997866 Total methylated C's in CHG context: 3118162 Total methylated C's in CHH context: 17969162 Total methylated C's in Unknown context: 543408 Total unmethylated C's in CpG context: 30924223 Total unmethylated C's in CHG context: 56896761 Total unmethylated C's in CHH context: 219004413 Total unmethylated C's in Unknown context: 2369251 C methylated in CpG context: 20.5% C methylated in CHG context: 5.2% C methylated in CHH context: 7.6% C methylated in unknown context (CN or CHN): 18.7% 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 97766829 (94.03%) aligned concordantly 0 times 2773474 (2.67%) aligned concordantly exactly 1 time 3433487 (3.30%) aligned concordantly >1 times 5.97% overall alignment rate 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 97775494 (94.04%) aligned concordantly 0 times 2768469 (2.66%) aligned concordantly exactly 1 time 3429827 (3.30%) aligned concordantly >1 times 5.96% overall alignment rate 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 95032346 (91.40%) aligned concordantly 0 times 4066622 (3.91%) aligned concordantly exactly 1 time 4874822 (4.69%) aligned concordantly >1 times 8.60% overall alignment rate 103973790 reads; of these: 103973790 (100.00%) were paired; of these: 95014057 (91.38%) aligned concordantly 0 times 4073411 (3.92%) aligned concordantly exactly 1 time 4886322 (4.70%) aligned concordantly >1 times 8.62% overall alignment rate Processed 103973790 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 415895160. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 415895160. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 415895160. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 415895160. Successfully deleted the temporary files CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 103973790 Final Cytosine Methylation Report ================================= Total number of C's analysed: 335840882 Total methylated C's in CpG context: 7994202 Total methylated C's in CHG context: 3120171 Total methylated C's in CHH context: 17996549 Total methylated C's in Unknown context: 544356 Total unmethylated C's in CpG context: 30938949 Total unmethylated C's in CHG context: 56863127 Total unmethylated C's in CHH context: 218927884 Total unmethylated C's in Unknown context: 2373035 C methylated in CpG context: 20.5% C methylated in CHG context: 5.2% C methylated in CHH context: 7.6% C methylated in unknown context (CN or CHN): 18.7% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF02-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF02-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF02-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 207947580 Final Cytosine Methylation Report ================================= Total number of C's analysed: 671751469 Total methylated C's in CpG context: 15992068 Total methylated C's in CHG context: 6238333 Total methylated C's in CHH context: 35965711 Total methylated C's in Unknown context: 1087764 Total unmethylated C's in CpG context: 61863172 Total unmethylated C's in CHG context: 113759888 Total unmethylated C's in CHH context: 437932297 Total unmethylated C's in Unknown context: 4742286 C methylated in CpG context: 20.5% C methylated in CHG context: 5.2% C methylated in CHH context: 7.6% C methylated in unknown context (CN or CHN): 18.7% Deleting temporary report files... Bismark completed in 0d 5h 58m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 65952634) Using the subset file >CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 31190 and offset 2 (sequences written out: 65952633) Using the subset file >CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 65952634) Using the subset file >CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.1.gz to CF03-CM03-Zygote_R1_001.fastp-trim.20220827.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.20220827.fq.gz.temp.1.gz to CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 31190 and offset 2 (sequences written out: 65952633) Using the subset file >CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz to CF03-CM03-Zygote_R1_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz to CF03-CM03-Zygote_R1_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz (65952633 sequences in total) Writing a C -> T converted version of the input file CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz to CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.1.gz (65952634 sequences in total) Writing a C -> T converted version of the input file CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.1.gz to CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (65952633 sequences in total) Input files are CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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 ANATATATAAATAAAAAATTAAATAATAATATTTGATAGATAAAATTATATATTAAAATTTTTTTAAATATATAAATAAAAAATTAAATAATAATATTTGAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 ATCAAATATTATTATTTAATTTTTTATTTATATATTTAAAAAAATTTTAATATATAATTTTATCTATCAAATATTATTATTTAATTTTTTATTTATATATTT FFFFFF::FFFFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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 ANATACACAAACAAAAAACTAAACAACAATACCTAACAAACAAAACTACATATCAAAATTTTCCTAAATACACAAACAAAAAACTAAACAACAATACCTAAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 GTTAGGTATTGTTGTTTAGTTTTTTGTTTGTGTATTTAGGAAAATTTTGATATGTAGTTTTGTTTGTTAGGTATTGTTGTTTAGTTTTTTGTTTGTGTATTT FFFFFF::FFFFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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 ANATACACAAACAAAAAACTAAACAACAATACCTAACAAACAAAACTACATATCAAAATTTTCCTAAATACACAAACAAAAAACTAAACAACAATACCTAAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 GTTAGGTATTGTTGTTTAGTTTTTTGTTTGTGTATTTAGGAAAATTTTGATATGTAGTTTTGTTTGTTAGGTATTGTTGTTTAGTTTTTTGTTTGTGTATTT FFFFFF::FFFFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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 ANATATATAAATAAAAAATTAAATAATAATATTTGATAGATAAAATTATATATTAAAATTTTTTTAAATATATAAATAAAAAATTAAATAATAATATTTGAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25925:1047_2:N:0:GGACTTGG+CGTCTGCG/2 141 * 0 0 * * 0 0 ATCAAATATTATTATTTAATTTTTTATTTATATATTTAAAAAAATTTTAATATATAATTTTATCTATCAAATATTATTATTTAATTTTTTATTTATATATTT FFFFFF::FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (65952634 sequences in total) Input files are CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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)) Reading in the sequence files CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25274:1047_1:N:0:GGACTTGG+CGTCTGCG/1 77 * 0 0 * * 0 0 TNATTAAATATAATATAAAATATTTTTAAATTAAAAATAAATAAAAAATTATATATTATTTTAAAAAAAATAAAAATAAAATAATAAAAAAATATATTTTAAATTTTAAAATTTTTTTTAAAATTATTAAATTAATTTTAAATAAATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: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 AATTTATTTAAAATTAATTTAATAATTTTAAAAAAAATTTTAAAATTTAAAATATATTTTTTTATTATTTTATTTTTATTTTTTTTAAAATAATATATAATTTTTTATTTATTTTTAATTTAAAAATATTTTATATTATATTTAATTA FFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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 CNACCAAACATAACACAAAACATTCTTAAATTAAAAATAAATAAAAAACCATATACTATCCCAAAAAAAATAAAAACAAAACAATAAAAAAACATATTCCAAATTTTAAAATCTTCTTCAAAACCACTAAACCAATTTCAAACAAACT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: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 AGTTTGTTTGAAATTGGTTTAGTGGTTTTGAAGAAGATTTTAAAATTTGGAATATGTTTTTTTATTGTTTTGTTTTTATTTTTTTTGGGATAGTATATGGTTTTTTATTTATTTTTAATTTAAGAATGTTTTGTGTTATGTTTGGTTG FFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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 78M1D70M = 37499203 -149 AGTTTGTTTGAAATTGGTTTAGTGGTTTTGAAGAAGATTTTAAAATTTGGAATATGTTTTTTTATTGTTTTGTTTTTATTTTTTTTGGGATAGTATATGGTTTTTTATTTATTTTTAATTTAAGAATGTTTTGTGTTATGTTTGGTNG FFFFFFFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-15 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:78^T32G35T1 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 37499203 42 78M1D70M = 37499203 149 AGTTTGTTTGAAATTGGTTTAGTGGTTTTGAAGAAGATTTTAAAATTTGGAATATGTTTTTTTATTGTTTTGTTTTTATTTTTTTTGGGATAGTATATGGTTTTTTATTTATTTTTAATTTAAGAATGTTTTGTGTTATGTTTGGTTG FFFFFFFFFFFFFFFFFF: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:78^T32G37 YS:i:-15 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.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 TNATTAAATATAATATAAAATATTTTTAAATTAAAAATAAATAAAAAATTATATATTATTTTAAAAAAAATAAAAATAAAATAATAAAAAAATATATTTTAAATTTTAAAATTTTTTTTAAAATTATTAAATTAATTTTAAATAAATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: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 AATTTATTTAAAATTAATTTAATAATTTTAAAAAAAATTTTAAAATTTAAAATATATTTTTTTATTATTTTATTTTTATTTTTTTTAAAATAATATATAATTTTTTATTTATTTTTAATTTAAAAATATTTTATATTATATTTAATTA FFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1214:3649:21026_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17106 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1214:3459:22388_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17106 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 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 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1524:28429:36855_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 2 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 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 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 17162 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1661:30110:26177_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17162 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1668:22408:3004_1:N:0:GGACTTGG+CGTCTGCG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2112:5773:10551_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17135 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 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 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1146:24650:4883_1:N:0:GGACTTGG+CGTCTGCG NC_007175.2 17163 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 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 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 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 2 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 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 45000000 sequence pairs so far Processed 45000000 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 17161 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 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 2 Processed 55000000 sequence pairs so far 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 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 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 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 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 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 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 64000000 sequence pairs so far Processed 64000000 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 65000000 sequence pairs so far Processed 65000000 sequence pairs so far 65952633 reads; of these: 65952633 (100.00%) were paired; of these: 56766970 (86.07%) aligned concordantly 0 times 4243426 (6.43%) aligned concordantly exactly 1 time 4942237 (7.49%) aligned concordantly >1 times 13.93% overall alignment rate 65952633 reads; of these: 65952633 (100.00%) were paired; of these: 56776531 (86.09%) aligned concordantly 0 times 4241797 (6.43%) aligned concordantly exactly 1 time 4934305 (7.48%) aligned concordantly >1 times 13.91% overall alignment rate 65952633 reads; of these: 65952633 (100.00%) were paired; of these: 58691768 (88.99%) aligned concordantly 0 times 3337224 (5.06%) aligned concordantly exactly 1 time 3923641 (5.95%) aligned concordantly >1 times 11.01% overall alignment rate 65952633 reads; of these: 65952633 (100.00%) were paired; of these: 58700584 (89.00%) aligned concordantly 0 times 3337434 (5.06%) aligned concordantly exactly 1 time 3914615 (5.94%) aligned concordantly >1 times 11.00% overall alignment rate Processed 65952633 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 263810532. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 263810532. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 263810532. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 263810532. Successfully deleted the temporary files CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 65952633 Final Cytosine Methylation Report ================================= Total number of C's analysed: 456817648 Total methylated C's in CpG context: 12261779 Total methylated C's in CHG context: 2808784 Total methylated C's in CHH context: 15052218 Total methylated C's in Unknown context: 683758 Total unmethylated C's in CpG context: 47232777 Total unmethylated C's in CHG context: 88089526 Total unmethylated C's in CHH context: 291372564 Total unmethylated C's in Unknown context: 2705686 C methylated in CpG context: 20.6% C methylated in CHG context: 3.1% C methylated in CHH context: 4.9% C methylated in unknown context (CN or CHN): 20.2% Now waiting for all child processes to complete 65952634 reads; of these: 65952634 (100.00%65952634) were paired; of these: reads; of these: 5870060065952634 ( (89.00%) aligned concordantly 0 times 3336566 (100.005.06%%) were paired; of these:) aligned concordantly exactly 1 time 586870073915468 ( (88.985.94%%) aligned concordantly 0 times) aligned concordantly >1 times 11.003338606% ( overall alignment rate5.06 %) aligned concordantly exactly 1 time 3927021 (5.95%) aligned concordantly >1 times 11.02% overall alignment rate 65952634 reads; of these: 65952634 (100.00%) were paired; of these: 56769576 (86.08%) aligned concordantly 0 times 4241127 (6.43%) aligned concordantly exactly 1 time 4941931 (7.49%) aligned concordantly >1 times 13.92% overall alignment rate 65952634 reads; of these: 65952634 (100.00%) were paired; of these: 56776785 (86.09%) aligned concordantly 0 times 4243560 (6.43%) aligned concordantly exactly 1 time 4932289 (7.48%) aligned concordantly >1 times 13.91% overall alignment rate Processed 65952634 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 263810536. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 263810536. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 263810536. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 263810536. Successfully deleted the temporary files CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 65952634 Final Cytosine Methylation Report ================================= Total number of C's analysed: 456793199 Total methylated C's in CpG context: 12264114 Total methylated C's in CHG context: 2808385 Total methylated C's in CHH context: 15067309 Total methylated C's in Unknown context: 680612 Total unmethylated C's in CpG context: 47230818 Total unmethylated C's in CHG context: 88052566 Total unmethylated C's in CHH context: 291370007 Total unmethylated C's in Unknown context: 2713562 C methylated in CpG context: 20.6% C methylated in CHG context: 3.1% C methylated in CHH context: 4.9% C methylated in unknown context (CN or CHN): 20.1% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF03-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF03-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF03-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 131905267 Final Cytosine Methylation Report ================================= Total number of C's analysed: 913610847 Total methylated C's in CpG context: 24525893 Total methylated C's in CHG context: 5617169 Total methylated C's in CHH context: 30119527 Total methylated C's in Unknown context: 1364370 Total unmethylated C's in CpG context: 94463595 Total unmethylated C's in CHG context: 176142092 Total unmethylated C's in CHH context: 582742571 Total unmethylated C's in Unknown context: 5419248 C methylated in CpG context: 20.6% C methylated in CHG context: 3.1% C methylated in CHH context: 4.9% C methylated in unknown context (CN or CHN): 20.1% Deleting temporary report files... Bismark completed in 0d 4h 21m 59s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 12182 and offset 2 (sequences written out: 61305430) Using the subset file >CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 61305430) Using the subset file >CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 12182 and offset 2 (sequences written out: 61305430) Using the subset file >CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 61305430) Using the subset file >CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM04-Larvae_R1_001.fastp-trim.20220827.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-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (61305430 sequences in total) Writing a C -> T converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (61305430 sequences in total) Writing a C -> T converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (61305430 sequences in total) Input files are CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (61305430 sequences in total) Input files are CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ANTAAAAAAATTTATTTAAATTATATATATTTTTATTAAAAAAAATTAAATATAATAAAAAATTATTTATTTTTTTTTTAAAATTAAAAAAATTATTTTTTATAAAAATTTTATTTATTTATAAAAATTATTAAAATTTTTTAAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 ATCTACAATACCTACAATTATAACAATAAATCTATATTAACAACAAAAAAAAACAATAACACCACTTAACACTACTTATACACTATATTCTTAAAATACAAAATATCTATTCAATAATATAATAATTATAAACTCAATACTTTATACTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TNTTTTAATAAATTTTAAAATAATATTAAAAATTATTATAAATAAAAATTAATTAAATAATTTTTTTTTTAATTTTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AAAAAATTAAAAAAAAAATTATTTAATTAATTTTTATTTATAATAATTTTTAATATTATTTTAAAATTTATTAAAAAA FFFFF:FFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ANCAAAAAAACTCACTTAAACTATACATATTTTTACTAAAAAAAACTAAATACAATAAAAAACCATTTACTCCCTTTTTAAAATCAAAAAAACCATTTTTTATAAAAACTTTATCCATTTATAAAAATTACCAAAATTTTTCAAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 GTTTATAATATTTATAATTATAATAATAAATTTATATTAATAATAAAAAAAAATAATAATATTATTTAATATTATTTATATATTATATTTTTAAAATATAAAATATTTATTTAATAATATAATAATTATAAATTTAATATTTTATATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 99 NC_035782.1_GA_converted 26572244 0 4M1I7M3I63M = 26572237 -81 CNCTTCAACAAACCCCAAAATAACATCAAAAATCATTATAAACAAAAACCAACTAAATAATTCTCCTTCCAATTCCCC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-41 XS:i:-41 XN:i:0 XM:i:4 XO:i:2 XG:i:4 NM:i:8 MD:Z:0A0A1A4C65 YS:i:-42 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 147 NC_035782.1_GA_converted 26572237 0 6M1D4M1D4M1D64M = 26572244 81 CCCTTCAACAAACCCCAAAATAACATCAAAAATCATTATAAACAAAAACCAACTAAATAATTCTCCTTCCAATTCCCC FFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFF:FFFFF AS:i:-42 XS:i:-42 XN:i:0 XM:i:3 XO:i:3 XG:i:3 NM:i:6 MD:Z:0A3A1^A4^C4^A0A63 YS:i:-41 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ANCAAAAAAACTCACTTAAACTATACATATTTTTACTAAAAAAAACTAAATACAATAAAAAACCATTTACTCCCTTTTTAAAATCAAAAAAACCATTTTTTATAAAAACTTTATCCATTTATAAAAATTACCAAAATTTTTCAAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 GTTTATAATATTTATAATTATAATAATAAATTTATATTAATAATAAAAAAAAATAATAATATTATTTAATATTATTTATATATTATATTTTTAAAATATAAAATATTTATTTAATAATATAATAATTATAAATTTAATATTTTATATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 CNCTTCAACAAACCCCAAAATAACATCAAAAATCATTATAAACAAAAACCAACTAAATAATTCTCCTTCCAATTCCCC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 GGGGAATTGGAAGGAGAATTATTTAGTTGGTTTTTGTTTATAATGATTTTTGATGTTATTTTGGGGTTTGTTGAAGGG FFFFF:FFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26214:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 ANTAAAAAAATTTATTTAAATTATATATATTTTTATTAAAAAAAATTAAATATAATAAAAAATTATTTATTTTTTTTTTAAAATTAAAAAAATTATTTTTTATAAAAATTTTATTTATTTATAAAAATTATTAAAATTTTTTAAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26214:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 ATCTACAATACCTACAATTATAACAATAAATCTATATTAACAACAAAAAAAAACAATAACACCACTTAACACTACTTATACACTATATTCTTAAAATACAAAATATCTATTCAATAATATAATAATTATAAACTCAATACTTTATACTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27281:1047_1:N:0:TACCGAGG+AGTTCAGG/1 77 * 0 0 * * 0 0 TNTTTTAATAAATTTTAAAATAATATTAAAAATTATTATAAATAAAAATTAATTAAATAATTTTTTTTTTAATTTTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27281:1047_2:N:0:TACCGAGG+AGTTCAGG/2 141 * 0 0 * * 0 0 AAAAAATTAAAAAAAAAATTATTTAATTAATTTTTATTTATAATAATTTTTAATATTATTTTAAAATTTATTAAAAAA FFFFF:FFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Reading in the sequence files CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1128:3161:31735_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1239:18593:3098_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1318:29432:19961_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1339:17219:24925_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1425:28013:23829_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1443:5846:29027_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1512:4887:31093_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1624:11171:28510_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1624:12970:29089_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1653:12075:4742_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2328:25762:33865_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2328:25843:34601_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2556:19578:22498_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2656:30020:11365_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1134:20365:1282_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1146:24985:27226_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1175:3830:2425_1:N:0:TACCGAGG+AGTTCAGG NC_007175.2 17112 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1216:28655:21778_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1216:29649:21934_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1365:13494:20259_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1471:27028:28291_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1471:27932:12383_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:19831:5400_1:N:0:TACCGAGG+AGTTCAGG NC_007175.2 17160 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:19732:5321_1:N:0:TACCGAGG+AGTTCAGG NC_007175.2 17160 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1644:8567:1517_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1644:8811:14184_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2236:4689:24048_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2441:20057:3129_1:N:0:TACCGAGG+AGTTCAGG NC_035781.1 2 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2559:26901:27946_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2678:20464:25128_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 61305430 reads; of these: 61305430 (100.00%) were paired; of these: 48027517 (78.34%) aligned concordantly 0 times 5889931 (9.61%) aligned concordantly exactly 1 time 7387982 (12.05%) aligned concordantly >1 times 21.66% overall alignment rate 61305430 reads; of these: 61305430 (100.00%) were paired; of these: 48036870 (78.36%) aligned concordantly 0 times 5900826 (9.63%) aligned concordantly exactly 1 time 7367734 (12.02%) aligned concordantly >1 times 21.64% overall alignment rate 61305430 reads; of these: 61305430 (100.00%) were paired; of these: 46772424 (76.29%) aligned concordantly 0 times 6436906 (10.50%) aligned concordantly exactly 1 time 8096100 (13.21%) aligned concordantly >1 times 23.71% overall alignment rate 61305430 reads; of these: 61305430 (100.00%) were paired; of these: 46780528 (76.31%) aligned concordantly 0 times 6437843 (10.50%) aligned concordantly exactly 1 time 8087059 (13.19%) aligned concordantly >1 times 23.69% overall alignment rate Processed 61305430 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 245221720. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 245221720. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 245221720. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 245221720. Successfully deleted the temporary files CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 61305430 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1119077253 Total methylated C's in CpG context: 30929201 Total methylated C's in CHG context: 4066976 Total methylated C's in CHH context: 14829059 Total methylated C's in Unknown context: 875082 Total unmethylated C's in CpG context: 135055512 Total unmethylated C's in CHG context: 235004642 Total unmethylated C's in CHH context: 699191863 Total unmethylated C's in Unknown context: 4575730 C methylated in CpG context: 18.6% C methylated in CHG context: 1.7% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 16.1% Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2678:15863:34695_1:N:0:TACCGAGG+AGTTCAGG NC_035780.1 2 61305430 reads; of these: 61305430 (100.00%) were paired; of these: 48021845 (78.33%) aligned concordantly 0 times 5891651 (9.61%) aligned concordantly exactly 1 time 7391934 (12.06%) aligned concordantly >1 times 21.67% overall alignment rate 61305430 reads; of these: 61305430 (100.00%) were paired; of these: 48029169 (78.34%) aligned concordantly 0 times 5905944 (9.63%) aligned concordantly exactly 1 time 7370317 (12.02%) aligned concordantly >1 times 21.66% overall alignment rate 61305430 reads; of these: 61305430 (100.00%) were paired; of these: 4678197861305430 ( reads; of these:76.31 % ) aligned concordantly 0 times61305430 ( 6437513 (10.50%) aligned concordantly exactly 1 time 100.008085939% () were paired; of these:13.19 % ) aligned concordantly >1 times46790922 (23.6976.32%% overall alignment rate) aligned concordantly 0 times 6436515 (10.50%) aligned concordantly exactly 1 time 8077993 (13.18%) aligned concordantly >1 times 23.68% overall alignment rate Processed 61305430 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 245221720. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 245221720. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 245221720. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 245221720. Successfully deleted the temporary files CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 61305430 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1118925792 Total methylated C's in CpG context: 30936834 Total methylated C's in CHG context: 4065311 Total methylated C's in CHH context: 14847745 Total methylated C's in Unknown context: 876137 Total unmethylated C's in CpG context: 135074110 Total unmethylated C's in CHG context: 234928359 Total unmethylated C's in CHH context: 699073433 Total unmethylated C's in Unknown context: 4571941 C methylated in CpG context: 18.6% C methylated in CHG context: 1.7% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 16.1% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF03-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF03-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF03-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 122610860 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2238003045 Total methylated C's in CpG context: 61866035 Total methylated C's in CHG context: 8132287 Total methylated C's in CHH context: 29676804 Total methylated C's in Unknown context: 1751219 Total unmethylated C's in CpG context: 270129622 Total unmethylated C's in CHG context: 469933001 Total unmethylated C's in CHH context: 1398265296 Total unmethylated C's in Unknown context: 9147671 C methylated in CpG context: 18.6% C methylated in CHG context: 1.7% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 16.1% Deleting temporary report files... Bismark completed in 0d 6h 6m 9s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 47019 and offset 2 (sequences written out: 57319681) Using the subset file >CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 57319682) Using the subset file >CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 47019 and offset 2 (sequences written out: 57319681) Using the subset file >CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 57319682) Using the subset file >CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM05-Larvae_R1_001.fastp-trim.20220827.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-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (57319682 sequences in total) Writing a C -> T converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (57319681 sequences in total) Writing a C -> T converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (57319682 sequences in total) Input files are CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (57319681 sequences in total) Input files are CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 ANAGTATTAATTTATAAGAAATATTAAAATATTATTATATATTAAATTATTAATTTAAATTTTAATTTTATTATTATAATATTATTAATTTTATTAAAAATTATATTTTATATTTTTTTTAAAATT F#F:FFFFFFFFFFFFFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 AATTTTAAAAAAAATATAAAATATAATTTTTAATAAAATTAATAATATTATAATAATAAAATTAAAATTTAAATTAATAATTTAATATATAATAATATTTTAATATTTCTTATAAATTAATACTAT ,FFFFFFFFFFFFF:FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 GNTTTGTTTTTTTGATTTTAATATATAATTTTATTATTTTAATTAAATATTTAATTATTATAAATATATAAATATATATAAAATAAATAAAAAAAAATATTATTAAATTAAAATGGTG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 CACCATTTTAATTTAATAATATTTTTTTTTATTTATTTTATATATATTTATATATTTATAATAATTAAATATTTAATTAAAATAATAAAATTATATATTAAAATCAAAAAAACAAAAC FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 99 NC_035786.1_GA_converted 56962922 0 5M1I2M1D3M2I100M2D5M = 56962922 118 ANCCTACTCTTCCAATCTCAATATACAACCTCACCATTTTAATTAAACATTTAATTACTATAAACATATAAATATACACAAAACAAATAAAAAAAAATACTACCAAATTAAAATAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-63 XN:i:0 XM:i:5 XO:i:4 XG:i:6 NM:i:11 MD:Z:1T5^C4T6A91^CC0C2A1 YS:i:-68 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 147 NC_035786.1_GA_converted 56962922 0 5M1I2M1D3M2I100M2D5M = 56962922 -118 ACCCTACTCTTCCAATCTCAATATACAACCTCACCATTTTAATTAAACATTTAATTACTATAAACATATAAATATACACAAAACAAATAAAAAAAAATACTACCAAATTAAAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:-68 XN:i:0 XM:i:5 XO:i:4 XG:i:6 NM:i:11 MD:Z:1T5^C4T6A91^CC0C2A1 YS:i:-63 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 ANAACACCAATCCATAAAAAATATCAAAACACCACTACACATTAAATCATTAATCCAAATCTTAATCCCATCACCACAACATTACCAACCTTACTAAAAACTATACCCTACATCCCCCCCAAAACC F#F:FFFFFFFFFFFFFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 GGTTTTGGGGGGGATGTAGGGTATAGTTTTTAGTAAGGTTGGTAATGTTGTGGTGATGGGATTAAGATTTGGATTAATGATTTAATGTGTAGTGGTGTTTTGATATTTTTTATGGATTGGTGTTAT ,FFFFFFFFFFFFF:FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 ANCCTACTCTTCCAATCTCAATATACAACCTCACCATTTTAATTAAACATTTAATTACTATAAACATATAAATATACACAAAACAAATAAAAAAAAATACTACCAAATTAAAATAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 TATTATTTTAATTTGGTAGTATTTTTTTTTATTTGTTTTGTGTATATTTATATGTTTATAGTAATTAAATGTTTAATTAAAATGGTGAGGTTGTATATTGAGATTGGAAGAGTAGGGT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 ANAACACCAATCCATAAAAAATATCAAAACACCACTACACATTAAATCATTAATCCAAATCTTAATCCCATCACCACAACATTACCAACCTTACTAAAAACTATACCCTACATCCCCCCCAAAACC F#F:FFFFFFFFFFFFFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 GGTTTTGGGGGGGATGTAGGGTATAGTTTTTAGTAAGGTTGGTAATGTTGTGGTGATGGGATTAAGATTTGGATTAATGATTTAATGTGTAGTGGTGTTTTGATATTTTTTATGGATTGGTGTTAT ,FFFFFFFFFFFFF:FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25310:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 ANAGTATTAATTTATAAGAAATATTAAAATATTATTATATATTAAATTATTAATTTAAATTTTAATTTTATTATTATAATATTATTAATTTTATTAAAAATTATATTTTATATTTTTTTTAAAATT F#F:FFFFFFFFFFFFFFF:F,FFFFFFFF:F:FFFFFFFF:FFFF::FF:FFFF:FFFFFFF:FFFFFF::FFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25310:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 AATTTTAAAAAAAATATAAAATATAATTTTTAATAAAATTAATAATATTATAATAATAAAATTAAAATTTAAATTAATAATTTAATATATAATAATATTTTAATATTTCTTATAAATTAATACTAT ,FFFFFFFFFFFFF:FFFFFFF:FF:FFF:FF::FFFFFF,FFFFFF:F,FFFFFFFF:FFFFFFF,FFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:FF,:FFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25346:1047_1:N:0:CGGCGTGA+ACAGGCGC/1 77 * 0 0 * * 0 0 GNTTTGTTTTTTTGATTTTAATATATAATTTTATTATTTTAATTAAATATTTAATTATTATAAATATATAAATATATATAAAATAAATAAAAAAAAATATTATTAAATTAAAATGGTG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25346:1047_2:N:0:CGGCGTGA+ACAGGCGC/2 141 * 0 0 * * 0 0 CACCATTTTAATTTAATAATATTTTTTTTTATTTATTTTATATATATTTATATATTTATAATAATTAAATATTTAATTAAAATAATAAAATTATATATTAAAATCAAAAAAACAAAAC FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Reading in the sequence files CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1232:13268:30890_1:N:0:CGGCGTGA+ACAGGCGC NC_007175.2 17173 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1273:20518:32957_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 3 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1277:12264:5384_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1469:10086:28573_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1475:26160:16172_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 3 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2628:29839:20885_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2649:23692:34100_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 1 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1114:1190:3145_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1140:31747:9189_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1152:18114:25347_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1204:23411:25567_1:N:0:CGGCGTGA+ACAGGCGC NC_007175.2 17173 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1222:6198:33833_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1318:10619:13495_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1373:9588:17534_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1373:10077:4601_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1460:22923:3208_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1460:22761:3490_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1460:22535:3630_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1575:8124:10958_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 3 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1677:16034:16830_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2128:23131:18537_1:N:0:CGGCGTGA+ACAGGCGC NC_007175.2 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2128:21124:18724_1:N:0:CGGCGTGA+ACAGGCGC NC_007175.2 3 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2221:11894:3490_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2232:12382:33865_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 65668291 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2319:5945:27070_1:N:0:CGGCGTGA+ACAGGCGC NC_035781.1 2 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2469:13675:4758_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2545:14434:34194_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far 57319682 reads; of these: 57319682 (100.00%) were paired; of these: 48280630 (84.23%) aligned concordantly 0 times 4162022 (7.26%) aligned concordantly exactly 1 time 4877030 (8.51%) aligned concordantly >1 times 15.77% overall alignment rate 57319682 reads; of these: 57319682 (100.00%) were paired; of these: 47963559 (83.68%) aligned concordantly 0 times 4312664 (7.52%) aligned concordantly exactly 1 time 5043459 (8.80%) aligned concordantly >1 times 16.32% overall alignment rate 57319682 reads; of these: 57319682 (100.00%) were paired; of these: 47958228 (83.67%) aligned concordantly 0 times 4300178 (7.50%) aligned concordantly exactly 1 time 5061276 (8.83%) aligned concordantly >1 times 16.33% overall alignment rate 57319682 reads; of these: 57319682 (100.00%) were paired; of these: 48291317 (84.25%) aligned concordantly 0 times 4169192 (7.27%) aligned concordantly exactly 1 time 4859173 (8.48%) aligned concordantly >1 times 15.75% overall alignment rate Processed 57319682 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 229278728. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 229278728. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 229278728. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 229278728. Successfully deleted the temporary files CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 57319682 Final Cytosine Methylation Report ================================= Total number of C's analysed: 776196110 Total methylated C's in CpG context: 22788936 Total methylated C's in CHG context: 5780084 Total methylated C's in CHH context: 21066767 Total methylated C's in Unknown context: 1220205 Total unmethylated C's in CpG context: 94661247 Total unmethylated C's in CHG context: 163022291 Total unmethylated C's in CHH context: 468876785 Total unmethylated C's in Unknown context: 4091399 C methylated in CpG context: 19.4% C methylated in CHG context: 3.4% C methylated in CHH context: 4.3% C methylated in unknown context (CN or CHN): 23.0% Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2677:16188:19257_1:N:0:CGGCGTGA+ACAGGCGC NC_035780.1 2 57319681 reads; of these: 57319681 (100.00%) were paired; of these: 47959505 (83.67%) aligned concordantly 0 times 4310396 (7.52%) aligned concordantly exactly 1 time 5049780 (8.81%) aligned concordantly >1 times 16.33% overall alignment rate 57319681 reads; of these: 57319681 (100.00%) were paired; of these: 48291451 (84.25%) aligned concordantly 0 times 4168825 (7.27%) aligned concordantly exactly 1 time 57319681 reads; of these:4859405 ( 8.4857319681% () aligned concordantly >1 times 15.75% overall alignment rate100.00 %) were paired; of these: 47952408 (83.66%) aligned concordantly 0 times 4301331 (7.50%) aligned concordantly exactly 1 time 5065942 (8.84%) aligned concordantly >1 times 16.34% overall alignment rate 57319681 reads; of these: 57319681 (100.00%) were paired; of these: 48276048 (84.22%) aligned concordantly 0 times 4164576 (7.27%) aligned concordantly exactly 1 time 4879057 (8.51%) aligned concordantly >1 times 15.78% overall alignment rate Processed 57319681 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 229278724. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 229278724. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 229278724. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 229278724. Successfully deleted the temporary files CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 57319681 Final Cytosine Methylation Report ================================= Total number of C's analysed: 776269156 Total methylated C's in CpG context: 22771842 Total methylated C's in CHG context: 5777055 Total methylated C's in CHH context: 21099189 Total methylated C's in Unknown context: 1218733 Total unmethylated C's in CpG context: 94668006 Total unmethylated C's in CHG context: 163057006 Total unmethylated C's in CHH context: 468896058 Total unmethylated C's in Unknown context: 4091392 C methylated in CpG context: 19.4% C methylated in CHG context: 3.4% C methylated in CHH context: 4.3% C methylated in unknown context (CN or CHN): 23.0% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF03-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF03-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF03-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 114639363 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1552465266 Total methylated C's in CpG context: 45560778 Total methylated C's in CHG context: 11557139 Total methylated C's in CHH context: 42165956 Total methylated C's in Unknown context: 2438938 Total unmethylated C's in CpG context: 189329253 Total unmethylated C's in CHG context: 326079297 Total unmethylated C's in CHH context: 937772843 Total unmethylated C's in Unknown context: 8182791 C methylated in CpG context: 19.4% C methylated in CHG context: 3.4% C methylated in CHH context: 4.3% C methylated in unknown context (CN or CHN): 23.0% Deleting temporary report files... Bismark completed in 0d 4h 45m 56s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 38233 and offset 2 (sequences written out: 64738402) Using the subset file >CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 64738403) Using the subset file >CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 64738403) Using the subset file >CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 38233 and offset 2 (sequences written out: 64738402) Using the subset file >CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (64738403 sequences in total) Writing a C -> T converted version of the input file CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (64738402 sequences in total) Writing a C -> T converted version of the input file CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (64738403 sequences in total) Input files are CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26539:1047_1:N:0:ACTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 TNTGTAGAAGTGGGGTTATGTTTTTTAAGTTTGTAGTAGTTAATTAAAAATATTTTTATTTGTAAATAGATTGTTTTATATTTGTTTGAAAAAAGGAATGTTATTTTTTTATAGATGTTATG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26539:1047_2:N:0:ACTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 CATAACATCTATAAAAAAATAACATTCCTTTTTTCAAACAAATATAAAACAATCTATTTACAAATAAAAATATTTTTAATTAACTACTACAAACTTAAAAAACATAACCCCACTTCTACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (64738402 sequences in total) Input files are CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29414:1047_1:N:0:GCTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 TNTTATTAATAAAATAAATTAATATTTTATTAAAATTAAATAAAATTAAATTATTTTAATATTAAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29414:1047_2:N:0:GCTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 TATTTAATATTAAAATAATTTAATTTTATTTAATTTTAATAAAATATTAATTTATTTTATTAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26539:1047_1:N:0:ACTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 TNTATAAAAATAAAATTATATTTTTTAAATTTATAATAATTAATTAAAAATATTTTTATTTATAAATAAATTATTTTATATTTATTTAAAAAAAAAAATATTATTTTTTTATAAATATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26539:1047_2:N:0:ACTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 TATAATATTTATAAAAAAATAATATTTTTTTTTTTAAATAAATATAAAATAATTTATTTATAAATAAAAATATTTTTAATTAATTATTATAAATTTAAAAAATATAATTTTATTTTTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29414:1047_1:N:0:GCTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 CNCCACCAACAAAATAAACCAACATTTTATTAAAATCAAACAAAATTAAATTACCCTAATACCAAACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29414:1047_2:N:0:GCTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 TGTTTGGTATTAGGGTAATTTAATTTTGTTTGATTTTAATAAAATGTTGGTTTATTTTGTTGGTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26539:1047_1:N:0:ACTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 TNTATAAAAATAAAATTATATTTTTTAAATTTATAATAATTAATTAAAAATATTTTTATTTATAAATAAATTATTTTATATTTATTTAAAAAAAAAAATATTATTTTTTTATAAATATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26539:1047_2:N:0:ACTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 TATAATATTTATAAAAAAATAATATTTTTTTTTTTAAATAAATATAAAATAATTTATTTATAAATAAAAATATTTTTAATTAATTATTATAAATTTAAAAAATATAATTTTATTTTTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29414:1047_1:N:0:GCTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 CNCCACCAACAAAATAAACCAACATTTTATTAAAATCAAACAAAATTAAATTACCCTAATACCAAACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29414:1047_2:N:0:GCTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 TGTTTGGTATTAGGGTAATTTAATTTTGTTTGATTTTAATAAAATGTTGGTTTATTTTGTTGGTGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26539:1047_1:N:0:ACTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 TNTGTAGAAGTGGGGTTATGTTTTTTAAGTTTGTAGTAGTTAATTAAAAATATTTTTATTTGTAAATAGATTGTTTTATATTTGTTTGAAAAAAGGAATGTTATTTTTTTATAGATGTTATG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26539:1047_2:N:0:ACTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 CATAACATCTATAAAAAAATAACATTCCTTTTTTCAAACAAATATAAAACAATCTATTTACAAATAAAAATATTTTTAATTAACTACTACAAACTTAAAAAACATAACCCCACTTCTACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29414:1047_1:N:0:GCTTGTCA+GTATGTTC/1 77 * 0 0 * * 0 0 TNTTATTAATAAAATAAATTAATATTTTATTAAAATTAAATAAAATTAAATTATTTTAATATTAAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29414:1047_2:N:0:GCTTGTCA+GTATGTTC/2 141 * 0 0 * * 0 0 TATTTAATATTAAAATAATTTAATTTTATTTAATTTTAATAAAATATTAATTTATTTTATTAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP >>> Writing bisulfite mapping results to CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Reading in the sequence files CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1135:4806:18176_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1175:3965:33098_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1377:30309:17253_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1538:17806:16892_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1538:14507:19633_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 3 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1666:8386:20087_1:N:0:GCTTGTCA+GGATGTTC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1666:7853:21449_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2145:12454:1110_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2224:24623:24471_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2224:22788:21950_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2270:4128:19006_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2424:30445:10848_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2511:13241:29121_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2555:13485:16047_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 17151 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2651:18539:14058_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1120:22589:2848_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1164:1334:24752_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 1 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1229:1696:3333_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1252:2971:36010_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 17158 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1253:22987:20134_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1263:28094:36871_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1266:17427:33583_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1263:28058:36965_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1333:20600:32315_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1403:9435:21997_1:N:0:GCTTGTCA+GGATGTTC NC_035780.1 2 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1454:20419:21449_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1661:13015:3709_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2212:5150:17989_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2212:5195:17942_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2223:32615:20149_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2232:26069:5118_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2253:23918:8469_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2401:28700:31688_1:N:0:ACTTGTCA+GGATGTTC NC_035780.1 3 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2418:10827:32831_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 17104 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2454:18466:15562_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2554:19623:21825_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2656:25581:17300_1:N:0:GCTTGTCA+GTATGTTC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2673:3251:2018_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 2 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2664:32172:14309_1:N:0:GCTTGTCA+GTATGTTC NC_007175.2 17158 64738402 reads; of these: 64738402 (100.00%) were paired; of these: 55603911 (85.89%) aligned concordantly 0 times 4298349 (6.64%) aligned concordantly exactly 1 time 4836142 (7.47%) aligned concordantly >1 times 14.11% overall alignment rate 64738402 reads; of these: 64738402 (100.00%) were paired; of these: 57868297 (89.39%) aligned concordantly 0 times 3212524 (4.96%) aligned concordantly exactly 1 time 3657581 (5.65%) aligned concordantly >1 times 10.61% overall alignment rate 64738402 reads; of these: 64738402 (100.00%) were paired; of these: 55635186 (85.94%) aligned concordantly 0 times 4278116 (6.61%) aligned concordantly exactly 1 time 4825100 (7.45%) aligned concordantly >1 times 14.06% overall alignment rate 64738402 reads; of these: 64738402 (100.00%) were paired; of these: 57895556 (89.43%) aligned concordantly 0 times 3195857 (4.94%) aligned concordantly exactly 1 time 3646989 (5.63%) aligned concordantly >1 times 10.57% overall alignment rate Processed 64738402 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 258953608. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 258953608. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 258953608. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 258953608. Successfully deleted the temporary files CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 64738402 Final Cytosine Methylation Report ================================= Total number of C's analysed: 526280876 Total methylated C's in CpG context: 13421242 Total methylated C's in CHG context: 2959679 Total methylated C's in CHH context: 14280739 Total methylated C's in Unknown context: 759862 Total unmethylated C's in CpG context: 56601054 Total unmethylated C's in CHG context: 102712649 Total unmethylated C's in CHH context: 336305513 Total unmethylated C's in Unknown context: 3014363 C methylated in CpG context: 19.2% C methylated in CHG context: 2.8% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 20.1% Now waiting for all child processes to complete 64738403 reads; of these: 64738403 (100.00%) were paired; of these: 55604151 (85.89%) aligned concordantly 0 times 4298916 (6.64%) aligned concordantly exactly 1 time 4835336 (7.47%) aligned concordantly >1 times 14.11% overall alignment rate 64738403 reads; of these: 64738403 (100.00%) were paired; of these: 57892808 (89.43%) aligned concordantly 0 times 3195109 (4.94%) aligned concordantly exactly 1 time 3650486 (5.64%) aligned concordantly >1 times 10.57% overall alignment rate 64738403 reads; of these: 64738403 (100.00%) were paired; of these: 55637308 (85.94%) aligned concordantly 0 times 4276748 (6.61%) aligned concordantly exactly 1 time 4824347 (7.45%) aligned concordantly >1 times 14.06% overall alignment rate 64738403 reads; of these: 64738403 (100.00%) were paired; of these: 57870922 (89.39%) aligned concordantly 0 times 3209065 (4.96%) aligned concordantly exactly 1 time 3658416 (5.65%) aligned concordantly >1 times 10.61% overall alignment rate Processed 64738403 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 258953612. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 258953612. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 258953612. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 258953612. Successfully deleted the temporary files CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 64738403 Final Cytosine Methylation Report ================================= Total number of C's analysed: 526039895 Total methylated C's in CpG context: 13415114 Total methylated C's in CHG context: 2959443 Total methylated C's in CHH context: 14273951 Total methylated C's in Unknown context: 757370 Total unmethylated C's in CpG context: 56591317 Total unmethylated C's in CHG context: 102667175 Total unmethylated C's in CHH context: 336132895 Total unmethylated C's in Unknown context: 3016623 C methylated in CpG context: 19.2% C methylated in CHG context: 2.8% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 20.1% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF04-CM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF04-CM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF04-CM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 129476805 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1052320771 Total methylated C's in CpG context: 26836356 Total methylated C's in CHG context: 5919122 Total methylated C's in CHH context: 28554690 Total methylated C's in Unknown context: 1517232 Total unmethylated C's in CpG context: 113192371 Total unmethylated C's in CHG context: 205379824 Total unmethylated C's in CHH context: 672438408 Total unmethylated C's in Unknown context: 6030986 C methylated in CpG context: 19.2% C methylated in CHG context: 2.8% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 20.1% Deleting temporary report files... Bismark completed in 0d 4h 31m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 22279 and offset 2 (sequences written out: 82487090) Using the subset file >CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 82487091) Using the subset file >CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 82487091) Using the subset file >CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 22279 and offset 2 (sequences written out: 82487090) Using the subset file >CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (82487090 sequences in total) Writing a C -> T converted version of the input file CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (82487091 sequences in total) Writing a C -> T converted version of the input file CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (82487090 sequences in total) Input files are CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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 CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (82487091 sequences in total) Input files are CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26720:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 77 * 0 0 * * 0 0 GNTTTTAATAATAATTTTAAAAAATATAAATATTAATATTATATTTAATTTATAAAATTATAAAATTTAATTATTTTTATTTTAAATAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26720:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 141 * 0 0 * * 0 0 AAATTATTTAAAATAAAAATAATTAAATTTTATAATTTTATAAATTAAATATAATATTAATATTTATATTTTTTAAAATTATTATTAAAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26051:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 77 * 0 0 * * 0 0 ANTTTAAATTTAATTATATATATTTTATTTTTAATATTAAATAATTATAATTAATTATTAAAAAATAAAAATATTATAATAAATTATATTTTTAATTTTTAATTTAATAATAAATTTTTTATATATATTAAATAATAAAAAAAATATATA F#F:FFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFF:FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FF:FFF,FFFFFF,,FFFFFFF:FFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFF:FFFF,FFFF,FFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26051:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 141 * 0 0 * * 0 0 TTATATTTAATTTTTATTAAAAATTTAATTAATTTTTTATTTTTTTAATAAAATTTTATTATAAATTTTTTTTATTATTTAATATATATAAAAAATTTATTATTAAATTAAAAATTAAAAATATAATTTATTATAATATTTTTATTTTTT :FFFFFFF:FFFFFFFF:FFFFF,FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,F,FFFFFFFFFFFF,FFF:,FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26720:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 77 * 0 0 * * 0 0 ANCTTCAATAATAACTTCAAAAAATACAAACACTAACACTACATTCAACCTACAAAACTATAAAATCTAATCACCTCCATCCCAAACAACCC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26720:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 141 * 0 0 * * 0 0 GGGTTGTTTGGGATGGAGGTGATTAGATTTTATAGTTTTGTAGGTTGAATGTAGTGTTAGTGTTTGTATTTTTTGAAGTTATTATTGAAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26051:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 99 NC_035780.1_GA_converted 5568298 17 150M = 5568357 209 ANTTTAAATTTAACCACATACACCTTATTTCCAATATTAAACAATTATAATCAACTATTAAAAAACAAAAATACCATAATAAATTATACTTTCAATTTTCAATTCAATAATAAACTCTTTACATATACCAAACAATAAAAAAAATATACA F#F:FFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFF:FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FF:FFF,FFFFFF,,FFFFFFF:FFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFF:FFFF,FFFF,FFFF AS:i:-13 XS:i:-42 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C11A131T4 YS:i:-6 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26051:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 147 NC_035780.1_GA_converted 5568357 17 150M = 5568298 -209 AAAAAACAAAAATACCATAATAAATTATACTTTCAATTTTCAATTCAATAATAAACTCTTTACATATACCAAACAATAAAAAAAATTTACAATAAAATTCTATTAAAAAAACAAAAAATTAATTAAATTTTTAATAAAAATCAAACACAA FFFFFFFFFFFFF,:FFF,FFFFFFFFFFFF,F,FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF,FFFFF:FFFFFFFF:FFFFFFF: AS:i:-6 XS:i:-29 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:106T43 YS:i:-13 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26720:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 77 * 0 0 * * 0 0 ANCTTCAATAATAACTTCAAAAAATACAAACACTAACACTACATTCAACCTACAAAACTATAAAATCTAATCACCTCCATCCCAAACAACCC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26720:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 141 * 0 0 * * 0 0 GGGTTGTTTGGGATGGAGGTGATTAGATTTTATAGTTTTGTAGGTTGAATGTAGTGTTAGTGTTTGTATTTTTTGAAGTTATTATTGAAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26051:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 77 * 0 0 * * 0 0 ANTTTAAATTTAACCACATACACCTTATTTCCAATATTAAACAATTATAATCAACTATTAAAAAACAAAAATACCATAATAAATTATACTTTCAATTTTCAATTCAATAATAAACTCTTTACATATACCAAACAATAAAAAAAATATACA F#F:FFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFF:FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FF:FFF,FFFFFF,,FFFFFFF:FFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFF:FFFF,FFFF,FFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26051:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 141 * 0 0 * * 0 0 TTGTGTTTGATTTTTATTAAAAATTTAATTAATTTTTTGTTTTTTTAATAGAATTTTATTGTAAATTTTTTTTATTGTTTGGTATATGTAAAGAGTTTATTATTGAATTGAAAATTGAAAGTATAATTTATTATGGTATTTTTGTTTTTT :FFFFFFF:FFFFFFFF:FFFFF,FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,F,FFFFFFFFFFFF,FFF:,FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26720:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 77 * 0 0 * * 0 0 GNTTTTAATAATAATTTTAAAAAATATAAATATTAATATTATATTTAATTTATAAAATTATAAAATTTAATTATTTTTATTTTAAATAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26720:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 141 * 0 0 * * 0 0 AAATTATTTAAAATAAAAATAATTAAATTTTATAATTTTATAAATTAAATATAATATTAATATTTATATTTTTTAAAATTATTATTAAAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26051:1047_1:N:0:ACTAAGAT+CCGCGGTT/1 77 * 0 0 * * 0 0 ANTTTAAATTTAATTATATATATTTTATTTTTAATATTAAATAATTATAATTAATTATTAAAAAATAAAAATATTATAATAAATTATATTTTTAATTTTTAATTTAATAATAAATTTTTTATATATATTAAATAATAAAAAAAATATATA F#F:FFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFF:FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FF:FFF,FFFFFF,,FFFFFFF:FFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFF:FFFF,FFFF,FFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26051:1047_2:N:0:ACTAAGAT+CCGCGGTT/2 141 * 0 0 * * 0 0 TTATATTTAATTTTTATTAAAAATTTAATTAATTTTTTATTTTTTTAATAAAATTTTATTATAAATTTTTTTTATTATTTAATATATATAAAAAATTTATTATTAAATTAAAAATTAAAAATATAATTTATTATAATATTTTTATTTTTT :FFFFFFF:FFFFFFFF:FFFFF,FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,F,FFFFFFFFFFFF,FFF:,FFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1125:28185:2581_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 3 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1145:13286:32456_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1166:13259:1532_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1171:17852:7357_1:N:0:ACTAAGAT+CCGCGGTT NC_007175.2 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1336:28456:10285_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1404:27968:35399_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:18792:20823_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1520:16893:23860_1:N:0:ACTAAGAT+CCGCGGTT NC_007175.2 17163 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1606:27651:29684_1:N:0:ACTAAGAT+CCGCGGTT NC_035781.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1667:27037:26334_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2120:8088:27774_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2204:2899:22921_1:N:0:ACTAAGAT+ACGCGGTT NC_035780.1 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2222:3278:5572_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2244:16450:11224_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2271:6804:24173_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2329:20500:4993_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2329:20356:4993_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2341:5936:5259_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2341:6985:9925_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2520:18159:14904_1:N:0:ACTAAGAT+CCGCGTTT NC_007175.2 17163 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2558:7853:17190_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2558:5412:17315_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2634:12038:24064_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2637:27516:4523_1:N:0:ACTCAGAT+CCGCGGTT NC_035781.1 2 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1111:7175:18145_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1129:15980:18834_1:N:0:ACTAAGAT+CCACGGTT NC_035780.1 3 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1219:29649:34147_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1219:31439:12821_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1235:23936:31234_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1236:21621:18771_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1236:22173:9987_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1236:22652:11757_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1262:12689:20682_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1277:15872:32800_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1314:6894:18067_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1319:13060:19914_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1320:14398:9298_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1453:2202:36996_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1467:27642:7216_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1467:26458:13777_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1474:19976:33395_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1474:18756:33442_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1477:24035:7106_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1532:26467:9784_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1545:25681:10895_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1545:20528:15499_1:N:0:ACTAAGAT+GCGCGGTT NC_035780.1 65668292 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1575:30951:24345_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1576:29469:25379_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1625:25690:9502_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1640:23222:25207_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 3 Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2109:27181:27398_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2121:15004:17613_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2121:15058:17957_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2206:6804:25833_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2215:30038:30749_1:N:0:ACTAAGAT+CCGCGGTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2227:20925:35603_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 3 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2230:20980:23171_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2251:16721:4930_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2258:9127:35180_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2259:9344:2707_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2271:25174:14685_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2321:20971:33771_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2365:2817:14199_1:N:0:ACTAAGAT+CCGCGGTT NC_035781.1 2 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2419:15646:23641_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2436:24985:18709_1:N:0:ACTAAGAT+CCGCGGTT NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2437:9381:26882_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2438:9742:1485_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2438:9869:2895_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2456:20112:31688_1:N:0:ACTAAGAT+CCGCGGTT NC_035783.1 59691729 Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2457:4942:19914_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2470:32832:34710_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2513:17110:16438_1:N:0:ACTAAGAT+CCACGGTT NC_035780.1 2 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2514:16143:1297_1:N:0:ACTAAGAT+CCACGGTT NC_035780.1 2 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2531:29658:15248_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2544:21187:26256_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 76000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2556:16740:4272_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2610:14606:26287_1:N:0:ACTAAGAT+GCGCGGTT NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2613:18403:15139_1:N:0:ACTAAGAT+TCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2613:18421:15139_1:N:0:ACTAAGAT+TCGCGGTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2613:18656:33082_1:N:0:ACTAAGAT+TCGCGGTT NC_035780.1 2 Processed 79000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2627:16459:24205_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 80000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2662:15872:12226_1:N:0:ACTAAGAT+CCGCGGTT NC_035780.1 2 Processed 82000000 sequence pairs so far Processed 82000000 sequence pairs so far 82487090 reads; of these: 82487090 (100.00%) were paired; of these: 67112316 (81.36%) aligned concordantly 0 times 6711792 (8.14%) aligned concordantly exactly 1 time 8662982 (10.50%) aligned concordantly >1 times 18.64% overall alignment rate 82487090 reads; of these: 82487090 (100.00%) were paired; of these: 68779607 (83.38%) aligned concordantly 0 times 6021971 (7.30%) aligned concordantly exactly 1 time 7685512 (9.32%) aligned concordantly >1 times 16.62% overall alignment rate 82487090 reads; of these: 82487090 (100.00%) were paired; of these: 67124702 (81.38%) aligned concordantly 0 times 6729972 (8.16%) aligned concordantly exactly 1 time 8632416 (10.47%) aligned concordantly >1 times 18.62% overall alignment rate 82487090 reads; of these: 82487090 (100.00%) were paired; of these: 68773486 (83.37%) aligned concordantly 0 times 5997988 (7.27%) aligned concordantly exactly 1 time 7715616 (9.35%) aligned concordantly >1 times 16.63% overall alignment rate Processed 82487090 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 329948360. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 329948360. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 329948360. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 329948360. Successfully deleted the temporary files CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 82487090 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1168664526 Total methylated C's in CpG context: 30827374 Total methylated C's in CHG context: 4159155 Total methylated C's in CHH context: 17171639 Total methylated C's in Unknown context: 1139945 Total unmethylated C's in CpG context: 146498286 Total unmethylated C's in CHG context: 249045248 Total unmethylated C's in CHH context: 720962824 Total unmethylated C's in Unknown context: 5476378 C methylated in CpG context: 17.4% C methylated in CHG context: 1.6% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 17.2% Now waiting for all child processes to complete 82487091 reads; of these: 82487091 (100.00%) were paired; of these: 68778624 (83.38%) aligned concordantly 0 times 6023513 (7.30%) aligned concordantly exactly 1 time 7684954 (9.32%) aligned concordantly >1 times 16.62% overall alignment rate 82487091 reads; of these: 82487091 (100.00%) were paired; of these: 67114548 (81.36%) aligned concordantly 0 times 6713118 (8.14%) aligned concordantly exactly 1 time 8659425 (10.50%) aligned concordantly >1 times 18.64% overall alignment rate 82487091 reads; of these: 82487091 (100.00%) were paired; of these: 67120380 (81.37%) aligned concordantly 0 times 6728480 (8.16%) aligned concordantly exactly 1 time 8638231 (10.47%) aligned concordantly >1 times 18.63% overall alignment rate 82487091 reads; of these: 82487091 (100.00%) were paired; of these: 68776458 (83.38%) aligned concordantly 0 times 5998667 (7.27%) aligned concordantly exactly 1 time 7711966 (9.35%) aligned concordantly >1 times 16.62% overall alignment rate Processed 82487091 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 329948364. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 329948364. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 329948364. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 329948364. Successfully deleted the temporary files CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 82487091 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1168794489 Total methylated C's in CpG context: 30860934 Total methylated C's in CHG context: 4158882 Total methylated C's in CHH context: 17194544 Total methylated C's in Unknown context: 1137823 Total unmethylated C's in CpG context: 146485829 Total unmethylated C's in CHG context: 249080992 Total unmethylated C's in CHH context: 721013308 Total unmethylated C's in Unknown context: 5474859 C methylated in CpG context: 17.4% C methylated in CHG context: 1.6% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 17.2% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF05-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF05-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF05-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 164974181 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2337459015 Total methylated C's in CpG context: 61688308 Total methylated C's in CHG context: 8318037 Total methylated C's in CHH context: 34366183 Total methylated C's in Unknown context: 2277768 Total unmethylated C's in CpG context: 292984115 Total unmethylated C's in CHG context: 498126240 Total unmethylated C's in CHH context: 1441976132 Total unmethylated C's in Unknown context: 10951237 C methylated in CpG context: 17.4% C methylated in CHG context: 1.6% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 17.2% Deleting temporary report files... Bismark completed in 0d 6h 51m 39s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 26842 and offset 2 (sequences written out: 73012246) Using the subset file >CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 73012246) Using the subset file >CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 26842 and offset 2 (sequences written out: 73012246) Using the subset file >CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 73012246) Using the subset file >CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (73012246 sequences in total) Writing a C -> T converted version of the input file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (73012246 sequences in total) Writing a C -> T converted version of the input file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (73012246 sequences in total) Input files are CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26232:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 ANTGTAGATGGAATTGGGATAGATGGATGAATTAAGGAGATAGAGAGATATATATAGATTATGAGAGTTATATGTTTAGGAGGAAA F#FFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26232:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 TTTCCTCCTAAACATATAACTCTCATAATCTATATATATCTCTCTATCTCCTTAATTCATCCATCTATCCCAATTCCATCTACAAT FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (73012246 sequences in total) Input files are CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26232:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 ANTATAAATAAAATTAAAATAAATAAATAAATTAAAAAAATAAAAAAATATATATAAATTATAAAAATTATATATTTAAAAAAAAA F#FFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26232:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 TTTTTTTTTAAATATATAATTTTTATAATTTATATATATTTTTTTATTTTTTTAATTTATTTATTTATTTTAATTTTATTTATAAT FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 99 NC_035786.1_CT_converted 44505755 0 80M1D6M = 44505755 87 TNTTTTTTTTTTAGTATATATATTTATTTTTGAGTAAAGTTAAGTATAGGAAAAAAAGGAAATAGTTGTATTTTATTGAAATTTAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F,FFFFFFF::F,FF:FFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFF AS:i:-21 XS:i:-21 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A0A44G32^T6 YS:i:-26 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 147 NC_035786.1_CT_converted 44505755 0 80M1D6M = 44505755 -87 TTTTTTTTTTTTAGTATATATATTTATTTTTGAGTAAAGTTAAGTATAGGAAAAAAAGGAAATAGTTGTATTTTATTGAAATTTAT FFFFFFFFF:FFFFFFF,FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-26 XS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A0A44G32^T6 YS:i:-21 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26232:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 ANTATAAATAAAATTAAAATAAATAAATAAATTAAAAAAATAAAAAAATATATATAAATTATAAAAATTATATATTTAAAAAAAAA F#FFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26232:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 TTTTTTTTTAAATATATAATTTTTATAATTTATATATATTTTTTTATTTTTTTAATTTATTTATTTATTTTAATTTTATTTATAAT FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 TNTTTTTTTTTCAATACATATATTTATTTTTAAATAAAATTAAATATAAAAAAAAAAAAAAATAATTATATTTTATTAAAATTTAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F,FFFFFFF::F,FF:FFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 GTAAATTTTAATAAAATATAATTATTTTTTTTTTTTTTTATATTTAATTTTATTTAAAAATAAATATATGTATTGAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26232:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 ANTGTAGATGGAATTGGGATAGATGGATGAATTAAGGAGATAGAGAGATATATATAGATTATGAGAGTTATATGTTTAGGAGGAAA F#FFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26232:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 TTTCCTCCTAAACATATAACTCTCATAATCTATATATATCTCTCTATCTCCTTAATTCATCCATCTATCCCAATTCCATCTACAAT FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 77 * 0 0 * * 0 0 TNTTTTTTTTTCAATACATATATTTATTTTTAAATAAAATTAAATATAAAAAAAAAAAAAAATAATTATATTTTATTAAAATTTAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F,FFFFFFF::F,FF:FFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 141 * 0 0 * * 0 0 GTAAATTTTAATAAAATATAATTATTTTTTTTTTTTTTTATATTTAATTTTATTTAAAAATAAATATATGTATTGAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.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)) Reading in the sequence files CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25509:1047_1:N:0:AGTTCAGG+TCTGTTGG/1 83 NC_035780.1_GA_converted 36883175 2 6M1D80M = 36883175 -87 ATAAATTTCAATAAAATACAACTATTTCCTTTTTTTCCTATACTTAACTTTACTCAAAAATAAATATATATACTAAAAAAAAAANA FFFFFFFFFFFFF:F:FFFFFFFFFFFFFF:FFFFFF:FF,F::FFFFFFF,F:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-15 XS:i:-21 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:6^A77T0T1 YS:i:-20 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25509:1047_2:N:0:AGTTCAGG+TCTGTTGG/2 163 NC_035780.1_GA_converted 36883175 2 6M1D80M = 36883175 87 ATAAATTTCAATAAAATACAACTATTTCCTTTTTTTCCTATACTTAACTTTACTCAAAAATAAATATATATACTAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFF:FFFFFFFFF AS:i:-20 XS:i:-20 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:6^A77T0T1 YS:i:-15 YT:Z:CP >>> Writing bisulfite mapping results to CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1150:29695:23109_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1274:16161:6370_1:N:0:AGTTCAGG+TCAGTTGG NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1269:8856:7905_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17111 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1274:16324:6308_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1274:16107:6370_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17161 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1349:28655:12759_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 1 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1428:30418:24862_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1432:32027:19946_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1474:16586:31407_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17157 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1474:17128:33191_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17157 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1469:31738:29277_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 3 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1557:26413:12790_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17097 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1607:22028:2002_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1652:25943:13135_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17166 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1651:19027:29590_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1662:16260:5102_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17165 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2131:22535:24205_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2137:18991:10864_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2159:10239:9893_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2225:24017:34538_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2225:22309:34867_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2225:25129:35524_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2306:14624:4272_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2319:7211:24846_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17100 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2460:2709:5713_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2468:7880:8907_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2468:7048:8312_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2504:18285:5572_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 3 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2633:2003:17801_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2633:3025:18630_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2633:2618:20556_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2639:6686:27477_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17099 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1112:10248:34021_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 2 Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1152:3540:32268_1:N:0:AGTTCAGG+TCTGTTGG NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1152:3459:32440_1:N:0:AGTTCAGG+TCTGTTGG NC_035781.1 2 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1203:17137:8281_1:N:0:AGTTCAGG+TCTGTTGG NC_035781.1 2 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1241:16278:8860_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 1 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1257:20139:9627_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 3 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1270:30192:13041_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1356:23692:24893_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1356:24108:29872_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1410:22715:14465_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1418:8440:33677_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1447:12780:36213_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17166 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1515:26359:28541_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1525:1036:6731_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1574:31521:12587_1:N:0:AGTTCAGG+TCTGTTGG NC_035781.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1649:30409:23907_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2157:31060:13009_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17166 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2201:17246:29543_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2207:16559:7592_1:N:0:AGTTCAGG+GCTGTTGG NC_035780.1 2 Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2344:32054:11569_1:N:0:AGTTCAGG+TCTGTTGG NC_035781.1 2 Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2356:7835:34006_1:N:0:AGTTCAGG+TCTGTTGG NC_035781.1 3 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2375:8377:16282_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2403:20012:27696_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17095 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2415:9073:17989_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2418:27670:1658_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 17156 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2429:30707:24173_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2429:30807:24220_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2446:19153:29465_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2515:8648:35634_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2527:18882:19163_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2545:4634:30311_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 2 Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2620:1958:30217_1:N:0:AGTTCAGG+TCTGTTGG NC_007175.2 1 Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2641:29984:24486_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 3 Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2669:4743:15374_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2668:8666:6417_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2668:8892:6464_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2668:7464:27696_1:N:0:AGTTCAGG+TCTGTTGG NC_035780.1 2 Processed 73000000 sequence pairs so far 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 64642427 (88.54%) aligned concordantly 0 times 3941155 (5.40%) aligned concordantly exactly 1 time 4428664 (6.07%) aligned concordantly >1 times 11.46% overall alignment rate 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 64691439 (88.60%) aligned concordantly 0 times 3907003 (5.35%) aligned concordantly exactly 1 time 4413804 (6.05%) aligned concordantly >1 times 11.40% overall alignment rate 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 63482699 (86.95%) aligned concordantly 0 times 4484016 (6.14%) aligned concordantly exactly 1 time 5045531 (6.91%) aligned concordantly >1 times 13.05% overall alignment rate 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 63426210 (86.87%) aligned concordantly 0 times 4514096 (6.18%) aligned concordantly exactly 1 time 5071940 (6.95%) aligned concordantly >1 times 13.13% overall alignment rate Processed 73012246 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 292048984. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 292048984. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 292048984. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 292048984. Successfully deleted the temporary files CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 73012246 Final Cytosine Methylation Report ================================= Total number of C's analysed: 626530283 Total methylated C's in CpG context: 18604313 Total methylated C's in CHG context: 4432142 Total methylated C's in CHH context: 18979904 Total methylated C's in Unknown context: 928456 Total unmethylated C's in CpG context: 70075838 Total unmethylated C's in CHG context: 127701351 Total unmethylated C's in CHH context: 386736735 Total unmethylated C's in Unknown context: 3466746 C methylated in CpG context: 21.0% C methylated in CHG context: 3.4% C methylated in CHH context: 4.7% C methylated in unknown context (CN or CHN): 21.1% Now waiting for all child processes to complete Processed 73000000 sequence pairs so far 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 64690722 (88.60%) aligned concordantly 0 times 3905238 (5.35%) aligned concordantly exactly 1 time 4416286 (6.05%) aligned concordantly >1 times 11.40% overall alignment rate 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 64638191 (88.53%) aligned concordantly 0 times 3941312 (5.40%) aligned concordantly exactly 1 time 4432743 (6.07%) aligned concordantly >1 times 11.47% overall alignment rate 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 63481999 (86.95%) aligned concordantly 0 times 4482908 (6.14%) aligned concordantly exactly 1 time 5047339 (6.91%) aligned concordantly >1 times 13.05% overall alignment rate 73012246 reads; of these: 73012246 (100.00%) were paired; of these: 63421218 (86.86%) aligned concordantly 0 times 4518289 (6.19%) aligned concordantly exactly 1 time 5072739 (6.95%) aligned concordantly >1 times 13.14% overall alignment rate Processed 73012246 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 292048984. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 292048984. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 292048984. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 292048984. Successfully deleted the temporary files CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 73012246 Final Cytosine Methylation Report ================================= Total number of C's analysed: 626442744 Total methylated C's in CpG context: 18622802 Total methylated C's in CHG context: 4442249 Total methylated C's in CHH context: 18977553 Total methylated C's in Unknown context: 926025 Total unmethylated C's in CpG context: 70054434 Total unmethylated C's in CHG context: 127673503 Total unmethylated C's in CHH context: 386672203 Total unmethylated C's in Unknown context: 3470299 C methylated in CpG context: 21.0% C methylated in CHG context: 3.4% C methylated in CHH context: 4.7% C methylated in unknown context (CN or CHN): 21.1% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF05-CM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF05-CM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF05-CM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 146024492 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1252973027 Total methylated C's in CpG context: 37227115 Total methylated C's in CHG context: 8874391 Total methylated C's in CHH context: 37957457 Total methylated C's in Unknown context: 1854481 Total unmethylated C's in CpG context: 140130272 Total unmethylated C's in CHG context: 255374854 Total unmethylated C's in CHH context: 773408938 Total unmethylated C's in Unknown context: 6937045 C methylated in CpG context: 21.0% C methylated in CHG context: 3.4% C methylated in CHH context: 4.7% C methylated in unknown context (CN or CHN): 21.1% Deleting temporary report files... Bismark completed in 0d 5h 1m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 40222 and offset 2 (sequences written out: 74182512) Using the subset file >CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 74182512) Using the subset file >CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 40222 and offset 2 (sequences written out: 74182512) Using the subset file >CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 74182512) Using the subset file >CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (74182512 sequences in total) Writing a C -> T converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (74182512 sequences in total) Writing a C -> T converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (74182512 sequences in total) Input files are CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TNTTGAATGTTGTATTATATTAAGAGATAATGTGGGTTTTAAGATATAGAAGTAATATATGTTTGGATATTATTTTAGATGAAGTTAAATTATTTTAAATAGAGTGATTGGTATTAAGGTGGGATGTAAATGTTAATAGAAATAATTTTT F#FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATTTCCAACCATATAATAAAAATTCCATAAAATATAATAAAATAAACTATTTTAATCAACTAATACATAATCAACATATTAATATATAAAAATTATTTCTATTAACATTTACATCCCACCTTAATACCAATCACTCTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 CNCTAAATATTATATTATATTAAAAAATAATATAAATTTTAAAATATAAAAATAATATATATTTAAATATTATTTTAAATAAAATTAAATTATTTTAAATAAAATAATTAATATTAAAATAAAATATAAATATTAATAAAAATAATTTTT F#FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATTTTTAATTATATAATAAAAATTTTATAAAATATAATAAAATAAATTATTTTAATTAATTAATATATAATTAATATATTAATATATAAAAATTATTTTTATTAATATTTATATTTTATTTTAATATTAATTATTTTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 CNCTAAATATTATATTATATTAAAAAATAATATAAATTTTAAAATATAAAAATAATATATATTTAAATATTATTTTAAATAAAATTAAATTATTTTAAATAAAATAATTAATATTAAAATAAAATATAAATATTAATAAAAATAATTTTT F#FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATTTTTAATTATATAATAAAAATTTTATAAAATATAATAAAATAAATTATTTTAATTAATTAATATATAATTAATATATTAATATATAAAAATTATTTTTATTAATATTTATATTTTATTTTAATATTAATTATTTTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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)) Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (74182512 sequences in total) Input files are CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27425:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 TNTTGAATGTTGTATTATATTAAGAGATAATGTGGGTTTTAAGATATAGAAGTAATATATGTTTGGATATTATTTTAGATGAAGTTAAATTATTTTAAATAGAGTGATTGGTATTAAGGTGGGATGTAAATGTTAATAGAAATAATTTTT F#FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27425:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 AATTTCCAACCATATAATAAAAATTCCATAAAATATAATAAAATAAACTATTTTAATCAACTAATACATAATCAACATATTAATATATAAAAATTATTTCTATTAACATTTACATCCCACCTTAATACCAATCACTCTATTTAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,F:FFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ANAAGTATAAATTTTATATTAAATTATTATTTTATTAATTAAATTTTTATTATATTTATTTTTTATAATATTAAATATTAGTTAATTATATTTATTTATAATAATTAAATTATTATAATTATAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 ATATAATTATAATAATTTAATTATTATAAATAAATATAATTAACTAATATTTAATATTATAAAAAATAAATATAATAAAAATTTAATTAATAAAATAATAATTTAATATAAAATTTATACTTAT FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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)) Reading in the sequence files CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ANAAACATAAACCTTACACCAAACCACCATTCCACCAACCAAACTTTTACTACATTTATCCTTCATAATATCAAACATTAACTAATCATATTCATCCACAACAACCAAACCACTATAACCACAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 GTGTGGTTATAGTGGTTTGGTTGTTGTGGATGAATATGATTAGTTAATGTTTGATATTATGAAGGATAAATGTAGTAAAAGTTTGGTTGGTGGAATGGTGGTTTGGTGTAAGGTTTATGTTTGT FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ANAAACATAAACCTTACACCAAACCACCATTCCACCAACCAAACTTTTACTACATTTATCCTTCATAATATCAAACATTAACTAATCATATTCATCCACAACAACCAAACCACTATAACCACAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 GTGTGGTTATAGTGGTTTGGTTGTTGTGGATGAATATGATTAGTTAATGTTTGATATTATGAAGGATAAATGTAGTAAAAGTTTGGTTGGTGGAATGGTGGTTTGGTGTAAGGTTTATGTTTGT FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26793:1047_1:N:0:TGGATCGA+TATCGCAC/1 77 * 0 0 * * 0 0 ANAAGTATAAATTTTATATTAAATTATTATTTTATTAATTAAATTTTTATTATATTTATTTTTTATAATATTAAATATTAGTTAATTATATTTATTTATAATAATTAAATTATTATAATTATAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26793:1047_2:N:0:TGGATCGA+TATCGCAC/2 141 * 0 0 * * 0 0 ATATAATTATAATAATTTAATTATTATAAATAAATATAATTAACTAATATTTAATATTATAAAAAATAAATATAATAAAAATTTAATTAATAAAATAATAATTTAATATAAAATTTATACTTAT FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1122:17264:16799_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17158 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1135:19135:29590_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17099 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1135:19162:30013_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17099 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1171:8522:6104_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 1 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1214:26386:26772_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1218:25247:15342_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17100 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1426:1651:21981_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1436:19786:11303_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1473:13178:28197_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1515:31304:32127_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17180 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1527:7970:1642_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2158:29324:19241_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17119 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2202:17535:5838_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2201:26431:5807_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17129 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2202:17544:5885_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2272:30680:20306_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:26539:9565_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17137 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2303:9227:21919_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17122 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2307:26521:9533_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17137 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2308:27263:9972_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17137 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2326:31141:19633_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17174 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2324:10013:9283_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2343:31060:16924_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17126 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2343:28772:19946_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17126 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2526:5918:30530_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2535:31629:18818_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:11062:25191_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 3 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2631:13946:11240_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2635:1434:28526_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2668:10420:36166_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1257:1154:6903_1:N:0:TGGATCGA+TGTCGCAC NC_035789.1 1 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1249:15076:19147_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1270:4119:20901_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1260:26169:34695_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1274:27480:35524_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1329:3332:6605_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1336:29803:30405_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1419:31177:12900_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1572:15582:36652_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17092 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1577:14172:24408_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1631:2311:17957_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1636:7401:3317_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2102:12057:14325_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2130:21377:8547_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 65668296 Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2164:19479:13432_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2162:1678:28166_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2164:19452:13479_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2237:20916:7216_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2237:23556:16861_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2237:25238:23218_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2273:22625:13150_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2273:22083:13463_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2330:2817:33708_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2444:20365:9330_1:N:0:TGGATCGT+TATCGCAC NC_007175.2 17158 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:25762:21057_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 2 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2603:25265:32503_1:N:0:TGGATCGA+TATCGCAC NC_035789.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2615:23023:28714_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 1 Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2646:29794:16892_1:N:0:TGGATCGA+CATCGCAC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2654:8205:8406_1:N:0:TGGATCGA+TATCGCAC NC_007175.2 2 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2645:16712:23641_1:N:0:TGGATCGA+TATCGCAC NC_035780.1 1 Processed 74000000 sequence pairs so far 74182512 reads; of these: 74182512 (100.00%) were paired; of these: 66274652 (89.34%) aligned concordantly 0 times 3695904 (4.98%) aligned concordantly exactly 1 time 4211956 (5.68%) aligned concordantly >1 times 10.66% overall alignment rate 74182512 reads; of these: 74182512 (100.00%) were paired; of these: 64712433 (87.23%) aligned concordantly 0 times 4471043 (6.03%) aligned concordantly exactly 1 time 4999036 (6.74%) aligned concordantly >1 times 12.77% overall alignment rate 74182512 reads; of these: 74182512 (100.00%) were paired; of these: 66279552 (89.35%) aligned concordantly 0 times 3704700 (4.99%) aligned concordantly exactly 1 time 4198260 (5.66%) aligned concordantly >1 times 10.65% overall alignment rate 74182512 reads; of these: 74182512 (100.00%) were paired; of these: 64699376 (87.22%) aligned concordantly 0 times 4466591 (6.02%) aligned concordantly exactly 1 time 5016545 (6.76%) aligned concordantly >1 times 12.78% overall alignment rate Processed 74182512 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 296730048. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 296730048. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 296730048. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 296730048. Successfully deleted the temporary files CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 74182512 Final Cytosine Methylation Report ================================= Total number of C's analysed: 492391766 Total methylated C's in CpG context: 14010895 Total methylated C's in CHG context: 3873941 Total methylated C's in CHH context: 18632501 Total methylated C's in Unknown context: 865945 Total unmethylated C's in CpG context: 50525541 Total unmethylated C's in CHG context: 92706563 Total unmethylated C's in CHH context: 312642325 Total unmethylated C's in Unknown context: 3314139 C methylated in CpG context: 21.7% C methylated in CHG context: 4.0% C methylated in CHH context: 5.6% C methylated in unknown context (CN or CHN): 20.7% Processed 74000000 sequence pairs so far 74182512 reads; of these: 74182512 (100.00%) were paired; of these: 66284123 (89.35%) aligned concordantly 0 times 3701137 (4.99%) aligned concordantly exactly 1 time 4197252 (5.66%) aligned concordantly >1 times 10.65% overall alignment rate 74182512 reads; of these: 74182512 (100.00%) were paired; of these: 66279109 (89.35%) aligned concordantly 0 times 3695086 (4.98%) aligned concordantly exactly 1 time 4208317 (5.67%) aligned concordantly >1 times 10.65% overall alignment rate 74182512 reads; of these: 74182512 (100.00%) were paired; of these: 64717798 (87.2474182512% reads; of these:) aligned concordantly 0 times 741825124467308 ( (6.02%) aligned concordantly exactly 1 time 100.00 %4997406) were paired; of these: ( 6.74 %64706823) aligned concordantly >1 times ( 87.2312.76%%) aligned concordantly 0 times overall alignment rate 4467103 (6.02%) aligned concordantly exactly 1 time 5008586 (6.75%) aligned concordantly >1 times 12.77% overall alignment rate Processed 74182512 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 296730048. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 296730048. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 296730048. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 296730048. Successfully deleted the temporary files CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 74182512 Final Cytosine Methylation Report ================================= Total number of C's analysed: 492237404 Total methylated C's in CpG context: 14026877 Total methylated C's in CHG context: 3873224 Total methylated C's in CHH context: 18612485 Total methylated C's in Unknown context: 864997 Total unmethylated C's in CpG context: 50473242 Total unmethylated C's in CHG context: 92705205 Total unmethylated C's in CHH context: 312546371 Total unmethylated C's in Unknown context: 3307773 C methylated in CpG context: 21.7% C methylated in CHG context: 4.0% C methylated in CHH context: 5.6% 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... Now merging BAM files CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF06-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF06-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF06-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 148365024 Final Cytosine Methylation Report ================================= Total number of C's analysed: 984629170 Total methylated C's in CpG context: 28037772 Total methylated C's in CHG context: 7747165 Total methylated C's in CHH context: 37244986 Total methylated C's in Unknown context: 1730942 Total unmethylated C's in CpG context: 100998783 Total unmethylated C's in CHG context: 185411768 Total unmethylated C's in CHH context: 625188696 Total unmethylated C's in Unknown context: 6621912 C methylated in CpG context: 21.7% C methylated in CHG context: 4.0% C methylated in CHH context: 5.6% C methylated in unknown context (CN or CHN): 20.7% Deleting temporary report files... Bismark completed in 0d 4h 50m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 56564643) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 33626 and offset 2 (sequences written out: 56564643) Using the subset file >CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Using the subset file >CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 33626 and offset 2 (sequences written out: 56564643) Using the subset file >CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 56564643) Using the subset file >CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (56564643 sequences in total) Writing a C -> T converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (56564643 sequences in total) Writing a C -> T converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (56564643 sequences in total) Input files are CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TNTATTAAAATATTAATATAATATAATATATATATATATTAAATTTTATATATATTATTTTAATTATTTTTAAATATTTTTATAAGA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TCTTATAAAAATATTTAAAAATAATTAAAATAATATATATAAAATTTAATATATATATATATTATATTATATTAATATTTTAATATA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TNCACCAAAACATTAACATAATACAATACATATACACACTAAACCCTATATACATCATTTTAATTATTCCCAAACACTCCCACAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TTTTGTGGGAGTGTTTGGGAATAATTAAAATGATGTATATAGGGTTTAGTGTGTATATGTATTGTATTATGTTAATGTTTTGGTGTA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TNCACCAAAACATTAACATAATACAATACATATACACACTAAACCCTATATACATCATTTTAATTATTCCCAAACACTCCCACAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TTTTGTGGGAGTGTTTGGGAATAATTAAAATGATGTATATAGGGTTTAGTGTGTATATGTATTGTATTATGTTAATGTTTTGGTGTA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25455:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 TNTATTAAAATATTAATATAATATAATATATATATATATTAAATTTTATATATATTATTTTAATTATTTTTAAATATTTTTATAAGA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25455:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TCTTATAAAAATATTTAAAAATAATTAAAATAATATATATAAAATTTAATATATATATATATTATATTATATTAATATTTTAATATA FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (56564643 sequences in total) Input files are CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 ANGTGATAAGTATGATGATAAGTAAATGATAAGTTAATGTGTGAAATGGTTTTGATAAA F#FFFFFFF:FF:FF::FFFFFFFFF,FFFFF:FFFFF,F:FFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TTTATCAAAACCATTTCACACATTAACTTATCATTTACTTATCATCATACTTATCACCT ,:FFF:FFFFFFF,,,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 77 * 0 0 * * 0 0 ANATAATAAATATAATAATAAATAAATAATAAATTAATATACAAAATAATTTTAATAAA F#FFFFFFF:FF:FF::FFFFFFFFF,FFFFF:FFFFF,F:FFFFFFF:FFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 141 * 0 0 * * 0 0 TTTATTAAAATTATTTTGTATATTAATTTATTATTTATTTATTATTATATTTATTATTT ,:FFF:FFFFFFF,,,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 83 NC_035787.1_CT_converted 61975843 0 59M = 61975843 -59 TTTATTAAAATTATTTTGTATATTAATTTATTATTTATTTATTATTATATTTATTATNT FFFFFFFFFF:FFFFFFF:F,FFFFF:FFFFF,FFFFFFFFF::FF:FF:FFFFFFF#F AS:i:-25 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:25G3G10G16G0A0 YS:i:-30 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 163 NC_035787.1_CT_converted 61975843 0 59M = 61975843 59 TTTATTAAAATTATTTTGTATATTAATTTATTATTTATTTATTATTATATTTATTATTT ,:FFF:FFFFFFF,,,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:25G3G10G16G0A0 YS:i:-25 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25943:1047_1:N:0:ATGTAAGT+CATAGAGT/1 83 NC_035787.1_GA_converted 61975843 40 59M = 61975843 -59 TTTATCAAAACCATTTCACACATTAACTTATCATTTACTTATCATCATACTTATCACNT FFFFFFFFFF:FFFFFFF:F,FFFFF:FFFFF,FFFFFFFFF::FF:FF:FFFFFFF#F AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:57A0A0 YS:i:-12 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25943:1047_2:N:0:ATGTAAGT+CATAGAGT/2 163 NC_035787.1_GA_converted 61975843 40 59M = 61975843 59 TTTATCAAAACCATTTCACACATTAACTTATCATTTACTTATCATCATACTTATCACCT ,:FFF:FFFFFFF,,,F:FFFFF:FFFF,FF,FF:FFF:,F:FF::FFFF,FFFFF::F AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:57A0A0 YS:i:-7 YT:Z:CP >>> Writing bisulfite mapping results to CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1103:7057:32972_1:N:0:ATGTAAGT+CATAGAGT NC_035781.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1614:17589:7905_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 1 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2330:20166:2910_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 65668335 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2330:21893:1517_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 65668335 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2442:20600:2096_1:N:0:ATGTAAGT+CATAGAGT NC_007175.2 2 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1328:31494:30577_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 65668306 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1336:19967:26177_1:N:0:ATGTAAGT+CATAGAGT NC_007175.2 1 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1665:14000:27148_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 2 Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2345:17770:14982_1:N:0:ATGTAAGT+CATAGAGT NC_035781.1 3 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2474:1289:24361_1:N:0:ATGTAAGT+CATAGAGT NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50555754 (89.38%) aligned concordantly 0 times 2843066 (5.03%) aligned concordantly exactly 1 time 3165823 (5.60%) aligned concordantly >1 times 10.62% overall alignment rate 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50813205 (89.83%) aligned concordantly 0 times 2720880 (4.81%) aligned concordantly exactly 1 time 3030558 (5.36%) aligned concordantly >1 times 10.17% overall alignment rate 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50556611 (89.38%) aligned concordantly 0 times 2851293 (5.04%) aligned concordantly exactly 1 time 3156739 (5.58%) aligned concordantly >1 times 10.62% overall alignment rate 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50816340 (89.84%) aligned concordantly 0 times 2708984 (4.79%) aligned concordantly exactly 1 time 3039319 (5.37%) aligned concordantly >1 times 10.16% overall alignment rate Processed 56564643 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 226258572. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 226258572. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 226258572. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 226258572. Successfully deleted the temporary files CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 56564643 Final Cytosine Methylation Report ================================= Total number of C's analysed: 418960428 Total methylated C's in CpG context: 14182745 Total methylated C's in CHG context: 5001407 Total methylated C's in CHH context: 21115506 Total methylated C's in Unknown context: 806973 Total unmethylated C's in CpG context: 43827071 Total unmethylated C's in CHG context: 81916903 Total unmethylated C's in CHH context: 252916796 Total unmethylated C's in Unknown context: 2517901 C methylated in CpG context: 24.4% C methylated in CHG context: 5.8% C methylated in CHH context: 7.7% C methylated in unknown context (CN or CHN): 24.3% 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50556959 (89.38%) aligned concordantly 0 times 2853424 (5.04%) aligned concordantly exactly 1 time 3154260 (5.58%) aligned concordantly >1 times 10.62% overall alignment rate 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50818584 (89.84%) aligned concordantly 0 times 2709298 (4.79%) aligned concordantly exactly 1 time 3036761 (5.37%) aligned concordantly >1 times 10.16% overall alignment rate 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50812100 (89.83%) aligned concordantly 0 times 2720816 (4.81%) aligned concordantly exactly 1 time 3031727 (5.36%) aligned concordantly >1 times 10.17% overall alignment rate 56564643 reads; of these: 56564643 (100.00%) were paired; of these: 50559131 (89.38%) aligned concordantly 0 times 2843386 (5.03%) aligned concordantly exactly 1 time 3162126 (5.59%) aligned concordantly >1 times 10.62% overall alignment rate Processed 56564643 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 226258572. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 226258572. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 226258572. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 226258572. Successfully deleted the temporary files CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 56564643 Final Cytosine Methylation Report ================================= Total number of C's analysed: 418876193 Total methylated C's in CpG context: 14172131 Total methylated C's in CHG context: 4996397 Total methylated C's in CHH context: 21128495 Total methylated C's in Unknown context: 807083 Total unmethylated C's in CpG context: 43840868 Total unmethylated C's in CHG context: 81907519 Total unmethylated C's in CHH context: 252830783 Total unmethylated C's in Unknown context: 2521980 C methylated in CpG context: 24.4% C methylated in CHG context: 5.7% C methylated in CHH context: 7.7% C methylated in unknown context (CN or CHN): 24.2% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF06-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF06-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF06-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 113129286 Final Cytosine Methylation Report ================================= Total number of C's analysed: 837836621 Total methylated C's in CpG context: 28354876 Total methylated C's in CHG context: 9997804 Total methylated C's in CHH context: 42244001 Total methylated C's in Unknown context: 1614056 Total unmethylated C's in CpG context: 87667939 Total unmethylated C's in CHG context: 163824422 Total unmethylated C's in CHH context: 505747579 Total unmethylated C's in Unknown context: 5039881 C methylated in CpG context: 24.4% C methylated in CHG context: 5.8% C methylated in CHH context: 7.7% C methylated in unknown context (CN or CHN): 24.3% Deleting temporary report files... Bismark completed in 0d 3h 56m 20s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 106708380) Using the subset file >CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 511 and offset 2 (sequences written out: 106708379) Using the subset file >CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 511 and offset 2 (sequences written out: 106708379) Using the subset file >CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 106708380) Using the subset file >CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (106708379 sequences in total) Writing a C -> T converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (106708380 sequences in total) Writing a C -> T converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (106708379 sequences in total) Input files are CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ANTGGGGTGGTTGTGGATTAGTGTTATAATTTTATTTTGTATTTTTGTTTGTAGTTAGTTTTGGTGATATATGGAAATATGTTTTTGGTTTATTGGAGATATTTATGT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ACATAAATATCTCCAATAAACCAAAAACATATTTCCATATATCACCAAAACTAACTACAAACAAAAATACAAAATAAAATTATAACACTAATCCACAACCACCCCAAT :FFFFFFF:FFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ANTAAAATAATTATAAATTAATATTATAATTTTATTTTATATTTTTATTTATAATTAATTTTAATAATATATAAAAATATATTTTTAATTTATTAAAAATATTTATAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 GTATAAATATTTTTAATAAATTAAAAATATATTTTTATATATTATTAAAATTAATTATAAATAAAAATATAAAATAAAATTATAATATTAATTTATAATTATTTTAAT :FFFFFFF:FFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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)) Created C -> T as well as G -> A converted versions of the FastQ file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (106708380 sequences in total) Input files are CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ANTAAAATAATTATAAATTAATATTATAATTTTATTTTATATTTTTATTTATAATTAATTTTAATAATATATAAAAATATATTTTTAATTTATTAAAAATATTTATAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 GTATAAATATTTTTAATAAATTAAAAATATATTTTTATATATTATTAAAATTAATTATAAATAAAAATATAAAATAAAATTATAATATTAATTTATAATTATTTTAAT :FFFFFFF:FFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 TNTGGAATTTATTGAGTGAAAGTGTGGATGTAGTTTGTTGTTTAATTTTATTTGTGGTAATGTTGTGTAGATGTTTTGGTATGTAATAATGTTTATTATTTTTATTTTTTTGGGGTTGGATGGTATGATATTGTTGTGTGAATATGTTGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ACTACCACCACCATAATAACCAACATATTCACACAACAATATCATACCATCCAACCCCAAAAAAATAAAAATAATAAACATTATTACATACCAAAACATCTACACAACATTACCACAAATAAAATTAAACAACAAACTACATCCACACTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26955:1047_1:N:0:GGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 ANTGGGGTGGTTGTGGATTAGTGTTATAATTTTATTTTGTATTTTTGTTTGTAGTTAGTTTTGGTGATATATGGAAATATGTTTTTGGTTTATTGGAGATATTTATGT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26955:1047_2:N:0:GGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ACATAAATATCTCCAATAAACCAAAAACATATTTCCATATATCACCAAAACTAACTACAAACAAAAATACAAAATAAAATTATAACACTAATCCACAACCACCCCAAT :FFFFFFF:FFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 TNTAAAATTTATTAAATAAAAATATAAATATAATTTATTATTTAATTTTATTTATAATAATATTATATAAATATTTTAATATATAATAATATTTATTATTTTTATTTTTTTAAAATTAAATAATATAATATTATTATATAAATATATTAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATTATTATTATTATAATAATTAATATATTTATATAATAATATTATATTATTTAATTTTAAAAAAATAAAAATAATAAATATTATTATATATTAAAATATTTATATAATATTATTATAAATAAAATTAAATAATAAATTATATTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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)) Reading in the sequence files CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 TNTAAAATTTATTAAATAAAAATATAAATATAATTTATTATTTAATTTTATTTATAATAATATTATATAAATATTTTAATATATAATAATATTTATTATTTTTATTTTTTTAAAATTAAATAATATAATATTATTATATAAATATATTAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ATTATTATTATTATAATAATTAATATATTTATATAATAATATTATATTATTTAATTTTAAAAAAATAAAAATAATAAATATTATTATATATTAAAATATTTATATAATATTATTATAAATAAAATTAAATAATAAATTATATTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1 77 * 0 0 * * 0 0 TNTGGAATTTATTGAGTGAAAGTGTGGATGTAGTTTGTTGTTTAATTTTATTTGTGGTAATGTTGTGTAGATGTTTTGGTATGTAATAATGTTTATTATTTTTATTTTTTTGGGGTTGGATGGTATGATATTGTTGTGTGAATATGTTGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2 141 * 0 0 * * 0 0 ACTACCACCACCATAATAACCAACATATTCACACAACAATATCATACCATCCAACCCCAAAAAAATAAAAATAATAAACATTATTACATACCAAAACATCTACACAACATTACCACAAATAAAATTAAACAACAAACTACATCCACACTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1152:20256:34726_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17163 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1275:3206:28087_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1439:10981:1063_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17179 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:24352:18646_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2217:13693:17472_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2217:13991:17613_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2217:13557:16955_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2268:3622:3004_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17180 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2325:7066:3333_1:N:0:GGTACCTT+GACGTCTG NC_007175.2 2 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 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-1012:512:GW210315000:4:2525:5674:35869_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2525:2871:31015_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2526:4752:23531_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2677:11532:34115_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17097 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1116:21495:30890_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1141:19199:23719_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1162:29604:31970_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17176 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1162:29848:31767_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17176 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1177:2058:26631_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1178:2663:3317_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1272:2103:14121_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1275:17246:2425_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17177 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1320:10764:32534_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17118 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1328:8269:27023_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1345:29686:36683_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1346:29414:14544_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17118 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1411:27688:4664_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1411:25536:24862_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17163 Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1425:17815:12962_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1429:31774:19539_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1429:31810:19539_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1431:19714:17660_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1456:12644:31908_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1474:8115:34648_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1503:30300:20650_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17176 Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1505:26856:18975_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17176 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1509:2871:26725_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17106 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1519:22019:1141_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17160 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1549:26250:13667_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17108 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1549:23095:34225_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 1 Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1558:18945:24283_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1564:21296:31704_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 3 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1612:20094:5040_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1623:16170:36385_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1667:31015:17127_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17159 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2128:29722:34616_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2165:30101:1047_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17180 Processed 74000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2277:10312:17879_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 82000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2320:30897:34898_1:N:0:GGTACCTT+GACGTCTT NC_035781.1 2 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2322:12481:34820_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2323:10041:28964_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2323:8811:30373_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 84000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2407:3387:17440_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 89000000 sequence pairs so far Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2421:8621:31078_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2421:7862:26569_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2426:20003:33004_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 90000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2452:30725:3004_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 92000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2467:2844:3443_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 96000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2530:18032:31000_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2533:31060:2550_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17105 Processed 97000000 sequence pairs so far Processed 97000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2550:1154:5901_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 98000000 sequence pairs so far Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2560:20437:20102_1:N:0:GGTACCTT+GACGTCTT NC_035780.1 2 Processed 99000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 102000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2624:17454:27899_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 103000000 sequence pairs so far Processed 103000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2636:5394:8234_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Processed 104000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 106000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2671:9317:9142_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 17173 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2674:19931:36511_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2675:19325:23970_1:N:0:GGTACCTT+GACGTCTT NC_007175.2 2 106708380 reads; of these: 106708380 (100.00%) were paired; of these: 101194943 (94.83%) aligned concordantly 0 times 2454715 (2.30%) aligned concordantly exactly 1 time 3058722 (2.87%) aligned concordantly >1 times 5.17% overall alignment rate 106708380 reads; of these: 106708380 (100.00%) were paired; of these: 99946264 (93.66%) aligned concordantly 0 times 3051615 (2.86%) aligned concordantly exactly 1 time 3710501 (3.48%) aligned concordantly >1 times 6.34% overall alignment rate 106708380 reads; of these: 106708380 (100.00%) were paired; of these: 99885027 (93.61%) aligned concordantly 0 times 3103233 (2.91%) aligned concordantly exactly 1 time 3720120 (3.49%) aligned concordantly >1 times 6.39% overall alignment rate 106708380 reads; of these: 106708380 (100.00%) were paired; of these: 101132959 (94.78%) aligned concordantly 0 times 2509661 (2.35%) aligned concordantly exactly 1 time 3065760 (2.87%) aligned concordantly >1 times 5.22% overall alignment rate Processed 106708380 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 426833520. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 426833520. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 426833520. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 426833520. 106708379 reads; of these: 106708379 (100.00%) were paired; of these: 101189873 (94.83%) aligned concordantly 0 times 2457168 (2.30%) aligned concordantly exactly 1 time 3061338 (2.87%) aligned concordantly >1 times 5.17% overall alignment rate 106708379 reads; of these: 106708379 (100.00%) were paired; of these: 99889253 (93.61%) aligned concordantly 0 times 3103653 (2.91%) aligned concordantly exactly 1 time 3715473 (3.48%) aligned concordantly >1 times 6.39% overall alignment rate 106708379 reads; of these: 106708379 (100.00%) were paired; of these: 99950341 (93.67%) aligned concordantly 0 times 3053077 (2.86%) aligned concordantly exactly 1 time 3704961 (3.47%) aligned concordantly >1 times 6.33% overall alignment rate 106708379 reads; of these: 106708379 (100.00%) were paired; of these: 101129198 (94.77%) aligned concordantly 0 times 2509655 (2.35%) aligned concordantly exactly 1 time 3069526 (2.88%) aligned concordantly >1 times 5.23% overall alignment rate Processed 106708379 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 426833516. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 426833516. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 426833516. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 426833516. Successfully deleted the temporary files CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 106708380 Final Cytosine Methylation Report ================================= Total number of C's analysed: 361994185 Total methylated C's in CpG context: 8561279 Total methylated C's in CHG context: 1553275 Total methylated C's in CHH context: 10723760 Total methylated C's in Unknown context: 541267 Total unmethylated C's in CpG context: 37934759 Total unmethylated C's in CHG context: 69922967 Total unmethylated C's in CHH context: 233298145 Total unmethylated C's in Unknown context: 2049507 C methylated in CpG context: 18.4% C methylated in CHG context: 2.2% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 20.9% Successfully deleted the temporary files CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 106708379 Final Cytosine Methylation Report ================================= Total number of C's analysed: 362074716 Total methylated C's in CpG context: 8560172 Total methylated C's in CHG context: 1557744 Total methylated C's in CHH context: 10741618 Total methylated C's in Unknown context: 541860 Total unmethylated C's in CpG context: 37920578 Total unmethylated C's in CHG context: 69921592 Total unmethylated C's in CHH context: 233373012 Total unmethylated C's in Unknown context: 2050555 C methylated in CpG context: 18.4% C methylated in CHG context: 2.2% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 20.9% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF07-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF07-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF07-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 213416759 Final Cytosine Methylation Report ================================= Total number of C's analysed: 724068901 Total methylated C's in CpG context: 17121451 Total methylated C's in CHG context: 3111019 Total methylated C's in CHH context: 21465378 Total methylated C's in Unknown context: 1083127 Total unmethylated C's in CpG context: 75855337 Total unmethylated C's in CHG context: 139844559 Total unmethylated C's in CHH context: 466671157 Total unmethylated C's in Unknown context: 4100062 C methylated in CpG context: 18.4% C methylated in CHG context: 2.2% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 20.9% Deleting temporary report files... Bismark completed in 0d 6h 8m 23s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 73500072) Using the subset file >CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 30639 and offset 2 (sequences written out: 73500071) Using the subset file >CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 30639 and offset 2 (sequences written out: 73500071) Using the subset file >CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 73500072) Using the subset file >CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a C -> T converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (73500072 sequences in total) Writing a C -> T converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (73500071 sequences in total) Writing a C -> T converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (73500072 sequences in total) Input files are CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 GNGTAGTTTATTATGATGGAATAGGTTAATGTAGGAATGTGTGTAGTTTGTTGGT F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ACCAACAAACTACACACATTCCTACATTAACCTATTCCATCATAATAAACTACCC FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 ANATAATTTATTATAATAAAATAAATTAATATAAAAATATATATAATTTATTAAT F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATTAATAAATTATATATATTTTTATATTAATTTATTTTATTATAATAAATTATTT FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 ANATAATTTATTATAATAAAATAAATTAATATAAAAATATATATAATTTATTAAT F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATTAATAAATTATATATATTTTTATATTAATTTATTTTATTATAATAAATTATTT FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 GNGTAGTTTATTATGATGGAATAGGTTAATGTAGGAATGTGTGTAGTTTGTTGGT F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ACCAACAAACTACACACATTCCTACATTAACCTATTCCATCATAATAAACTACCC FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (73500071 sequences in total) Input files are CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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)) Reading in the sequence files CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TNGTGTGTGAGATGGGGTGATTTGATTGGTGTGTTATGGAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATCCATAACACACCAATCAAATCACCCCATCTCACACACCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TNATATATAAAATAAAATAATTTAATTAATATATTATAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATTTATAATATATTAATTAAATTATTTTATTTTATATATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TNATATATAAAATAAAATAATTTAATTAATATATTATAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATTTATAATATATTAATTAAATTATTTTATTTTATATATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30120:1047_1:N:0:GACCTGAA+CTCACCAA/1 77 * 0 0 * * 0 0 TNGTGTGTGAGATGGGGTGATTTGATTGGTGTGTTATGGAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30120:1047_2:N:0:GACCTGAA+CTCACCAA/2 141 * 0 0 * * 0 0 ATCCATAACACACCAATCAAATCACCCCATCTCACACACCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1101:30969:27946_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17132 Reading in the sequence files CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1406:10710:33254_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17164 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1406:10420:33411_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17164 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1453:18132:6464_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17151 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1522:25409:20447_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1656:32325:32612_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17149 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2124:28221:25661_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17107 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2343:27019:35665_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17151 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2467:22905:30514_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 65668291 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2520:23936:35744_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2521:18132:1141_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1173:24207:17989_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1203:3188:27117_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17179 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1252:25626:36761_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17175 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1261:15103:1783_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17132 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1259:20735:18521_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17132 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1359:23077:21887_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1469:10863:25629_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 3 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1554:3685:6057_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1562:24099:25786_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1621:22652:2738_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2203:2871:32456_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17179 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2204:2437:16642_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17179 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2213:1072:14465_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2351:31693:21214_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17171 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2351:32045:21230_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 17171 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2424:26142:13385_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2425:31232:4038_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2501:19678:15342_1:N:0:GACCTGAA+CTCACCAA NC_007175.2 2 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2529:5150:22842_1:N:0:GACCTGAA+CTCACCAA NC_035780.1 2 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far 73500071 reads; of these: 73500071 (100.00%) were paired; of these: 65226089 (88.74%) aligned concordantly 0 times 3783963 (5.15%) aligned concordantly exactly 1 time 4490019 (6.11%) aligned concordantly >1 times 11.26% overall alignment rate 73500071 reads; of these: 73500071 (100.00%) were paired; of these: 65209939 (88.72%) aligned concordantly 0 times 3801277 (5.17%) aligned concordantly exactly 1 time 4488855 (6.11%) aligned concordantly >1 times 11.28% overall alignment rate 73500071 reads; of these: 73500071 (100.00%) were paired; of these: 67605965 (91.98%) aligned concordantly 0 times 2683668 (3.65%) aligned concordantly exactly 1 time 3210438 (4.37%) aligned concordantly >1 times 8.02% overall alignment rate 73500071 reads; of these: 73500071 (100.00%) were paired; of these: 67596428 (91.97%) aligned concordantly 0 times 2692108 (3.66%) aligned concordantly exactly 1 time 3211535 (4.37%) aligned concordantly >1 times 8.03% overall alignment rate Processed 73500071 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 294000284. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 294000284. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 294000284. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 294000284. Successfully deleted the temporary files CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 73500071 Final Cytosine Methylation Report ================================= Total number of C's analysed: 343257087 Total methylated C's in CpG context: 7883599 Total methylated C's in CHG context: 2295761 Total methylated C's in CHH context: 13966149 Total methylated C's in Unknown context: 515128 Total unmethylated C's in CpG context: 32450126 Total unmethylated C's in CHG context: 59400256 Total unmethylated C's in CHH context: 227261196 Total unmethylated C's in Unknown context: 2329334 C methylated in CpG context: 19.5% C methylated in CHG context: 3.7% C methylated in CHH context: 5.8% C methylated in unknown context (CN or CHN): 18.1% Now waiting for all child processes to complete 73500072 reads; of these: 73500072 (100.00%) were paired; of these: 65215902 (88.73%) aligned concordantly 0 times 3787927 (5.15%) aligned concordantly exactly 1 time 4496243 (6.12%) aligned concordantly >1 times 11.27% overall alignment rate 73500072 reads; of these: 73500072 (100.00%) were paired; of these: 65203027 (88.71%) aligned concordantly 0 times 3803571 (5.17%) aligned concordantly exactly 1 time 4493474 (6.11%) aligned concordantly >1 times 11.29% overall alignment rate 73500072 reads; of these: 73500072 (100.00%) were paired; of these: 67605140 (91.98%) aligned concordantly 0 times 2684902 (3.65%) aligned concordantly exactly 1 time 3210030 (4.37%) aligned concordantly >1 times 8.02% overall alignment rate 73500072 reads; of these: 73500072 (100.00%) were paired; of these: 67591581 (91.96%) aligned concordantly 0 times 2699125 (3.67%) aligned concordantly exactly 1 time 3209366 (4.37%) aligned concordantly >1 times 8.04% overall alignment rate Processed 73500072 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 294000288. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 294000288. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 294000288. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 294000288. Successfully deleted the temporary files CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 73500072 Final Cytosine Methylation Report ================================= Total number of C's analysed: 343378646 Total methylated C's in CpG context: 7886314 Total methylated C's in CHG context: 2300605 Total methylated C's in CHH context: 13999872 Total methylated C's in Unknown context: 513418 Total unmethylated C's in CpG context: 32429549 Total unmethylated C's in CHG context: 59411474 Total unmethylated C's in CHH context: 227350832 Total unmethylated C's in Unknown context: 2334918 C methylated in CpG context: 19.6% C methylated in CHG context: 3.7% C methylated in CHH context: 5.8% C methylated in unknown context (CN or CHN): 18.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF08-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF08-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF08-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 147000143 Final Cytosine Methylation Report ================================= Total number of C's analysed: 686635733 Total methylated C's in CpG context: 15769913 Total methylated C's in CHG context: 4596366 Total methylated C's in CHH context: 27966021 Total methylated C's in Unknown context: 1028546 Total unmethylated C's in CpG context: 64879675 Total unmethylated C's in CHG context: 118811730 Total unmethylated C's in CHH context: 454612028 Total unmethylated C's in Unknown context: 4664252 C methylated in CpG context: 19.6% C methylated in CHG context: 3.7% C methylated in CHH context: 5.8% C methylated in unknown context (CN or CHN): 18.1% Deleting temporary report files... Bismark completed in 0d 4h 40m 5s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 26999708) Using the subset file >CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 19356 and offset 2 (sequences written out: 26999708) Using the subset file >CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 26999708) Using the subset file >CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 19356 and offset 2 (sequences written out: 26999708) Using the subset file >CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (26999708 sequences in total) Writing a C -> T converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (26999708 sequences in total) Writing a C -> T converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (26999708 sequences in total) Input files are CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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 CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (26999708 sequences in total) Input files are CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TNATTATTTTTTGTAATTTGGTTATGTTGGTATGAGATTGTGAATTGTTAATTAAGTAGGGGTATTAGTTAAGTAAATTGGGGT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ACCCCAATTTACTTAACTAATACCCCTACTTAATTAACAATTCACAATCTCATACCAACATAACCAAATTACAAAAAATAATTA FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ANTTAATAAATAATATATTAATTAATAATAAAATATATAAATTAAATAAATTTATATATAAAAATAATATTTTATTATTAATTAATAATATTTATAATTTATTATTTTTAAATATTATTTTTAAAAATATTAAATTATTTTAAATTAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TCATCAAACTCAATAATAACCATAAAAAAAACAAATATATTAACAACATAACATTTATCTTTATCTCACACAAAATACATAAACACATATTATAATCAAATATAAAATTAACCCTTTCCATAACCCAAATAATCAATACTTATTACAAAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ANCCAACAAACAACATACTAACCAACAATAAAATACATAAACTAAATAAACTCACACATAAAAACAATATCCCACTACTAATCAACAATACTTACAACCTACCATTTCCAAACATCATCTTTAAAAATATCAAACCATTCTAAATCAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TTATTAAATTTAATAATAATTATAAAAAAAATAAATATATTAATAATATAATATTTATTTTTATTTTATATAAAATATATAAATATATATTATAATTAAATATAAAATTAATTTTTTTTATAATTTAAATAATTAATATTTATTATAAAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 CNACTATTTTTTATAATTTAATTATATTAATATAAAATTATAAATTATTAATTAAATAAAAATATTAATTAAATAAATTAAAAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 GTTTTAATTTATTTAATTAATATTTTTATTTAATTAATAATTTATAATTTTATATTAATATAATTAAATTATAAAAAATAGTTG FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 CNACTATTTTTTATAATTTAATTATATTAATATAAAATTATAAATTATTAATTAAATAAAAATATTAATTAAATAAATTAAAAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 GTTTTAATTTATTTAATTAATATTTTTATTTAATTAATAATTTATAATTTTATATTAATATAATTAAATTATAAAAAATAGTTG FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ANCCAACAAACAACATACTAACCAACAATAAAATACATAAACTAAATAAACTCACACATAAAAACAATATCCCACTACTAATCAACAATACTTACAACCTACCATTTCCAAACATCATCTTTAAAAATATCAAACCATTCTAAATCAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TTATTAAATTTAATAATAATTATAAAAAAAATAAATATATTAATAATATAATATTTATTTTTATTTTATATAAAATATATAAATATATATTATAATTAAATATAAAATTAATTTTTTTTATAATTTAAATAATTAATATTTATTATAAAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 TNATTATTTTTTGTAATTTGGTTATGTTGGTATGAGATTGTGAATTGTTAATTAAGTAGGGGTATTAGTTAAGTAAATTGGGGT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 ACCCCAATTTACTTAACTAATACCCCTACTTAATTAACAATTCACAATCTCATACCAACATAACCAAATTACAAAAAATAATTA FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29830:1047_1:N:0:GGCATTCT+CAAGCTAG/1 77 * 0 0 * * 0 0 ANTTAATAAATAATATATTAATTAATAATAAAATATATAAATTAAATAAATTTATATATAAAAATAATATTTTATTATTAATTAATAATATTTATAATTTATTATTTTTAAATATTATTTTTAAAAATATTAAATTATTTTAAATTAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29830:1047_2:N:0:GGCATTCT+CAAGCTAG/2 141 * 0 0 * * 0 0 TCATCAAACTCAATAATAACCATAAAAAAAACAAATATATTAACAACATAACATTTATCTTTATCTCACACAAAATACATAAACACATATTATAATCAAATATAAAATTAACCCTTTCCATAACCCAAATAATCAATACTTATTACAAAA FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,F:F:FF:FFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFF,: YT:Z:UP >>> Writing bisulfite mapping results to CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far 26999708 reads; of these: 26999708 (100.00%) were paired; of these: 26852600 (99.46%) aligned concordantly 0 times 60055 (0.22%) aligned concordantly exactly 1 time 87053 (0.32%) aligned concordantly >1 times 0.54% overall alignment rate 26999708 reads; of these: 26999708 (100.00%) were paired; of these: 26828919 (99.37%) aligned concordantly 0 times 69557 (0.26%) aligned concordantly exactly 1 time 101232 (0.37%) aligned concordantly >1 times 0.63% overall alignment rate 26999708 reads; of these: 26999708 (100.00%) were paired; of these: 26852107 (99.45%) aligned concordantly 0 times 59739 (0.22%) aligned concordantly exactly 1 time 87862 (0.33%) aligned concordantly >1 times 0.55% overall alignment rate 26999708 reads; of these: 26999708 (100.00%) were paired; of these: 26829420 (99.37%) aligned concordantly 0 times 69652 (0.26%) aligned concordantly exactly 1 time 100636 (0.37%) aligned concordantly >1 times 0.63% overall alignment rate Processed 26999708 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 107998832. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 107998832. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 107998832. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 107998832. Successfully deleted the temporary files CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 26999708 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9916033 Total methylated C's in CpG context: 220914 Total methylated C's in CHG context: 51282 Total methylated C's in CHH context: 885469 Total methylated C's in Unknown context: 28085 Total unmethylated C's in CpG context: 946758 Total unmethylated C's in CHG context: 1674804 Total unmethylated C's in CHH context: 6136806 Total unmethylated C's in Unknown context: 55303 C methylated in CpG context: 18.9% C methylated in CHG context: 3.0% C methylated in CHH context: 12.6% C methylated in unknown context (CN or CHN): 33.7% Now waiting for all child processes to complete 26999708 reads; of these: 26999708 (26999708 reads; of these:100.00 % ) were paired; of these:26999708 ( 26827937 (99.36%) aligned concordantly 0 times 70207 (0.26100.00%%) aligned concordantly exactly 1 time) were paired; of these: 10156426852699 ( (0.3899.46%%) aligned concordantly >1 times) aligned concordantly 0 times 0.64 %60516 overall alignment rate ( 0.22%) aligned concordantly exactly 1 time 86493 (0.32%) aligned concordantly >1 times 0.54% overall alignment rate 26999708 reads; of these: 26999708 (100.00%) were paired; of these: 26851562 (99.45%) aligned concordantly 0 times 60344 (0.22%) aligned concordantly exactly 1 time 87802 (0.33%) aligned concordantly >1 times 0.55% overall alignment rate 26999708 reads; of these: 26999708 (100.00%) were paired; of these: 26828026 (99.36%) aligned concordantly 0 times 70417 (0.26%) aligned concordantly exactly 1 time 101265 (0.38%) aligned concordantly >1 times 0.64% overall alignment rate Processed 26999708 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 107998832. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 107998832. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 107998832. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 107998832. Successfully deleted the temporary files CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 26999708 Final Cytosine Methylation Report ================================= Total number of C's analysed: 9922688 Total methylated C's in CpG context: 219419 Total methylated C's in CHG context: 50997 Total methylated C's in CHH context: 887628 Total methylated C's in Unknown context: 28011 Total unmethylated C's in CpG context: 953736 Total unmethylated C's in CHG context: 1679314 Total unmethylated C's in CHH context: 6131594 Total unmethylated C's in Unknown context: 54986 C methylated in CpG context: 18.7% C methylated in CHG context: 2.9% C methylated in CHH context: 12.6% C methylated in unknown context (CN or CHN): 33.7% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF08-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF08-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF08-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 53999416 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19838721 Total methylated C's in CpG context: 440333 Total methylated C's in CHG context: 102279 Total methylated C's in CHH context: 1773097 Total methylated C's in Unknown context: 56096 Total unmethylated C's in CpG context: 1900494 Total unmethylated C's in CHG context: 3354118 Total unmethylated C's in CHH context: 12268400 Total unmethylated C's in Unknown context: 110289 C methylated in CpG context: 18.8% C methylated in CHG context: 3.0% C methylated in CHH context: 12.6% C methylated in unknown context (CN or CHN): 33.7% Deleting temporary report files... Bismark completed in 0d 1h 29m 1s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 1966 and offset 2 (sequences written out: 40341858) Using the subset file >CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 40341859) Using the subset file >CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 1966 and offset 2 (sequences written out: 40341858) Using the subset file >CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 40341859) Using the subset file >CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (40341858 sequences in total) Writing a C -> T converted version of the input file CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (40341859 sequences in total) Writing a C -> T converted version of the input file CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (40341859 sequences in total) Input files are CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (40341858 sequences in total) Input files are CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26503:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 TNATAATAATTAAATTAAATAAAATTATATAAATATATATTTTTGAAAATTTATTTATTTAATTAAAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26503:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 ATTTTTAATTAAATAAATAAATTTTCAAAAATATATATTTATATAATTTTATTTAATTTAATTATTATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25780:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 TNTTAATTTTAGAGGTATTATTGTGATGGTTTGTATTAATGTTTTAAATTTGGTGATTTTGTAGTTTTTTATTAATATTTTAAATAATTTTTAGTTTGATTATAGTGTTAGTGGTGTTGGTTATGTGGTGTTTGGTTGAGTGATTGTGGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25780:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 ACCACTTCCATACCCACAATCACTCAACCAAACACCACATAACCAACACCACTAACACTATAATCAAACTAAAAATTATTTAAAATATTAATAAAAAACTACAAAATCACCAAATTTAAAACATTAATACAAACCATCACAATAATACCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26503:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 CNACAATAATTAAACCAAATAAAACCACACAAACACATACTCCTAAAAACTCATTCATCTAACCAAAAAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26503:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 GTTTTTGGTTAGATGAATGAGTTTTTAGGAGTATGTGTTTGTGTGGTTTTATTTGGTTTAATTATTGTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25780:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 CNCTAATTTTAAAAATATTATTATAATAATTTATATTAATATTTTAAATTTAATAATTTTATAATTTTTTATTAATATTTTAAATAATTTTTAATTTAATTATAATATTAATAATATTAATTATATAATATTTAATTAAATAATTATAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25780:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 ATTATTTTTATATTTATAATTATTTAATTAAATATTATATAATTAATATTATTAATATTATAATTAAATTAAAAATTATTTAAAATATTAATAAAAAATTATAAAATTATTAAATTTAAAATATTAATATAAATTATTATAATAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26503:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 CNACAATAATTAAACCAAATAAAACCACACAAACACATACTCCTAAAAACTCATTCATCTAACCAAAAAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26503:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 GTTTTTGGTTAGATGAATGAGTTTTTAGGAGTATGTGTTTGTGTGGTTTTATTTGGTTTAATTATTGTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25780:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 CNCTAATTTTAAAAATATTATTATAATAATTTATATTAATATTTTAAATTTAATAATTTTATAATTTTTTATTAATATTTTAAATAATTTTTAATTTAATTATAATATTAATAATATTAATTATATAATATTTAATTAAATAATTATAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25780:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 ATTATTTTTATATTTATAATTATTTAATTAAATATTATATAATTAATATTATTAATATTATAATTAAATTAAAAATTATTTAAAATATTAATAAAAAATTATAAAATTATTAAATTTAAAATATTAATATAAATTATTATAATAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26503:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 TNATAATAATTAAATTAAATAAAATTATATAAATATATATTTTTGAAAATTTATTTATTTAATTAAAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26503:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 ATTTTTAATTAAATAAATAAATTTTCAAAAATATATATTTATATAATTTTATTTAATTTAATTATTATTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25780:1047_1:N:0:CGTTAGAA+GACCTGAA/1 77 * 0 0 * * 0 0 TNTTAATTTTAGAGGTATTATTGTGATGGTTTGTATTAATGTTTTAAATTTGGTGATTTTGTAGTTTTTTATTAATATTTTAAATAATTTTTAGTTTGATTATAGTGTTAGTGGTGTTGGTTATGTGGTGTTTGGTTGAGTGATTGTGGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF:FFFFFFFFF:FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25780:1047_2:N:0:CGTTAGAA+GACCTGAA/2 141 * 0 0 * * 0 0 ACCACTTCCATACCCACAATCACTCAACCAAACACCACATAACCAACACCACTAACACTATAATCAAACTAAAAATTATTTAAAATATTAATAAAAAACTACAAAATCACCAAATTTAAAACATTAATACAAACCATCACAATAATACCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far 40341859 reads; of these: 40341859 (100.00%) were paired; of these: 39929111 (98.98%) aligned concordantly 0 times 185783 (0.46%) aligned concordantly exactly 1 time 226965 (0.56%) aligned concordantly >1 times 1.02% overall alignment rate 40341859 reads; of these: 40341859 (100.00%) were paired; of these: 39947576 (99.02%) aligned concordantly 0 times 177428 (0.44%) aligned concordantly exactly 1 time 216855 (0.54%) aligned concordantly >1 times 0.98% overall alignment rate 40341859 reads; of these: 40341859 (100.00%) were paired; of these: 39928611 (98.98%) aligned concordantly 0 times 186683 (0.46%) aligned concordantly exactly 1 time 226565 (0.56%) aligned concordantly >1 times 1.02% overall alignment rate 40341859 reads; of these: 40341859 (100.00%) were paired; of these: 39947379 (99.02%) aligned concordantly 0 times 176223 (0.44%) aligned concordantly exactly 1 time 218257 (0.54%) aligned concordantly >1 times 0.98% overall alignment rate Processed 40341859 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 161367436. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 161367436. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 161367436. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 161367436. Successfully deleted the temporary files CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 40341859 Final Cytosine Methylation Report ================================= Total number of C's analysed: 36968220 Total methylated C's in CpG context: 754046 Total methylated C's in CHG context: 119060 Total methylated C's in CHH context: 877784 Total methylated C's in Unknown context: 49314 Total unmethylated C's in CpG context: 3945951 Total unmethylated C's in CHG context: 6771358 Total unmethylated C's in CHH context: 24500021 Total unmethylated C's in Unknown context: 170235 C methylated in CpG context: 16.0% C methylated in CHG context: 1.7% C methylated in CHH context: 3.5% C methylated in unknown context (CN or CHN): 22.5% 40341858 reads; of these: 40341858 (100.00%) were paired; of these: 39948525 (99.03%) aligned concordantly 0 times 176342 (0.44%) aligned concordantly exactly 1 time 216991 (0.54%) aligned concordantly >1 times 0.97% overall alignment rate 40341858 reads; of these: 40341858 (100.00%) were paired; of these: 39928256 (98.97%) aligned concordantly 0 times 186943 (0.46%) aligned concordantly exactly 1 time 226659 (0.56%) aligned concordantly >1 times 1.03% overall alignment rate 40341858 reads; of these: 40341858 (100.00%) were paired; of these: 39947859 (99.02%) aligned concordantly 0 times 176615 (0.44%) aligned concordantly exactly 1 time 217384 (0.54%) aligned concordantly >1 times 0.98% overall alignment rate 40341858 reads; of these: 40341858 (100.00%) were paired; of these: 39928115 (98.97%) aligned concordantly 0 times 186963 (0.46%) aligned concordantly exactly 1 time 226780 (0.56%) aligned concordantly >1 times 1.03% overall alignment rate Processed 40341858 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 161367432. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 161367432. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 161367432. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 161367432. Successfully deleted the temporary files CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 40341858 Final Cytosine Methylation Report ================================= Total number of C's analysed: 37015584 Total methylated C's in CpG context: 752008 Total methylated C's in CHG context: 118111 Total methylated C's in CHH context: 872398 Total methylated C's in Unknown context: 49026 Total unmethylated C's in CpG context: 3944830 Total unmethylated C's in CHG context: 6781081 Total unmethylated C's in CHH context: 24547156 Total unmethylated C's in Unknown context: 169324 C methylated in CpG context: 16.0% C methylated in CHG context: 1.7% C methylated in CHH context: 3.4% C methylated in unknown context (CN or CHN): 22.5% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> CF08-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF08-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF08-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 80683717 Final Cytosine Methylation Report ================================= Total number of C's analysed: 73983804 Total methylated C's in CpG context: 1506054 Total methylated C's in CHG context: 237171 Total methylated C's in CHH context: 1750182 Total methylated C's in Unknown context: 98340 Total unmethylated C's in CpG context: 7890781 Total unmethylated C's in CHG context: 13552439 Total unmethylated C's in CHH context: 49047177 Total unmethylated C's in Unknown context: 339559 C methylated in CpG context: 16.0% C methylated in CHG context: 1.7% C methylated in CHH context: 3.4% C methylated in unknown context (CN or CHN): 22.5% Deleting temporary report files... Bismark completed in 0d 2h 57m 33s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 61777294) Using the subset file >EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 20449 and offset 2 (sequences written out: 61777294) Using the subset file >EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 20449 and offset 2 (sequences written out: 61777294) Using the subset file >EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 61777294) Using the subset file >EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz to EF01-EM01-Zygote_R1_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz to EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF01-EM01-Zygote_R1_001.fastp-trim.20220827.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.20220827.fq.gz.temp.1.gz to EF01-EM01-Zygote_R1_001.fastp-trim.20220827.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.20220827.fq.gz.temp.1.gz (61777294 sequences in total) Writing a C -> T converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.1.gz to EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz (61777294 sequences in total) Writing a C -> T converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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.20220827.fq.gz.temp.2.gz to EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (61777294 sequences in total) Input files are EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 ANTAATATTTTTTTTTTAATAATTATTTTTTTTTTTTTATAATTAATATATAATATATTTTTTTTTTTTTATTTTTAATAATATTAGAA F#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TTCTAATATTATTAAAAATAAAAAAAAAAAAATATATTATATATTAATTATAAAAAAAAAAAAATAATTATTAAAAAAAAAATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 ANCAACACTTTTTCTTTAATAATCATTTTTTTCTTTTTATAACTAACATATAATATACTTTTTTCCTCTTATTTCTAACAACATTAAAA F#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TTTTAATGTTGTTAGAAATAAGAGGAAAAAAGTATATTATATGTTAGTTATAAAAAGAAAAAAATGATTATTAAAGAAAAAGTGTTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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)) Created C -> T as well as G -> A converted versions of the FastQ file EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (61777294 sequences in total) Input files are EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 ANCAACACTTTTTCTTTAATAATCATTTTTTTCTTTTTATAACTAACATATAATATACTTTTTTCCTCTTATTTCTAACAACATTAAAA F#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TTTTAATGTTGTTAGAAATAAGAGGAAAAAAGTATATTATATGTTAGTTATAAAAAGAAAAAAATGATTATTAAAGAAAAAGTGTTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: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.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30373:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 ANGTTAGTGGTGTGGTGTTGGGATATTATGTTAGTGAGGATGGGTATTTTGGTTGGATGTTGTAGAAATGGATATTATTTTGTGAGTTATTTGGTGGGTGTGTTTTGTTTATTTATGTTTTTGAATTTGTGGAGGATGGGT F#FFFFFFFFF:FFFFFFFFFFFFFF: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 ACCCATCCTCCACAAATTCAAAAACATAAATAAACAAAACACACCCACCAAATAACTCACAAAATAATATCCATTTCTACAACATCCAACCAAAATACCCATCCTCACTAACATAATATCCCAACACCACACCACTAACAT :FFFFFFFFF:FFFFF,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.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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 ANTAATATTTTTTTTTTAATAATTATTTTTTTTTTTTTATAATTAATATATAATATATTTTTTTTTTTTTATTTTTAATAATATTAGAA F#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2 141 * 0 0 * * 0 0 TTCTAATATTATTAAAAATAAAAAAAAAAAAATATATTATATATTAATTATAAAAAAAAAAAAATAATTATTAAAAAAAAAATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP >>> Writing bisulfite mapping results to EF01-EM01-Zygote_R1_001.fastp-trim.20220827.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 ANACTAATAATATAATATTAAAATATTATATTAATAAAAATAAATATTTTAATTAAATATTATAAAAATAAATATTATTTTATAAATTATTTAATAAATATATTTTATTTATTTATATTTTTAAATTTATAAAAAATAAAC F#FFFFFFFFF:FFFFFFFFFFFFFF: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 GTTTATTTTTTATAAATTTAAAAATATAAATAAATAAAATATATTTATTAAATAATTTATAAAATAATATTTATTTTTATAATATTTAATTAAAATATTTATTTTTATTAATATAATATTTTAATATTATATTATTAGTAT :FFFFFFFFF:FFFFF,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.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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)) Reading in the sequence files EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:30373:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 ANACTAATAATATAATATTAAAATATTATATTAATAAAAATAAATATTTTAATTAAATATTATAAAAATAAATATTATTTTATAAATTATTTAATAAATATATTTTATTTATTTATATTTTTAAATTTATAAAAAATAAAC F#FFFFFFFFF:FFFFFFFFFFFFFF: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 GTTTATTTTTTATAAATTTAAAAATATAAATAAATAAAATATATTTATTAAATAATTTATAAAATAATATTTATTTTTATAATATTTAATTAAAATATTTATTTTTATTAATATAATATTTTAATATTATATTATTAGTAT :FFFFFFFFF:FFFFF,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.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30373:1047_1:N:0:TAATACAG+GTGAATAT/1 77 * 0 0 * * 0 0 ANGTTAGTGGTGTGGTGTTGGGATATTATGTTAGTGAGGATGGGTATTTTGGTTGGATGTTGTAGAAATGGATATTATTTTGTGAGTTATTTGGTGGGTGTGTTTTGTTTATTTATGTTTTTGAATTTGTGGAGGATGGGT F#FFFFFFFFF:FFFFFFFFFFFFFF: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 ACCCATCCTCCACAAATTCAAAAACATAAATAAACAAAACACACCCACCAAATAACTCACAAAATAATATCCATTTCTACAACATCCAACCAAAATACCCATCCTCACTAACATAATATCCCAACACCACACCACTAACAT :FFFFFFFFF:FFFFF,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.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1305:16459:27962_1:N:0:TAATACAG+ATGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1305:15555:28494_1:N:0:TAATACAG+ATGAATAT NC_007175.2 1 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 6000000 sequence pairs so far Processed 6000000 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 7000000 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 17153 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1473:18295:22874_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17153 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1473:19108:23657_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17153 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 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1540:11749:5212_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 10000000 sequence pairs so far Processed 10000000 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 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 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 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 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 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2252:3170:20071_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 16000000 sequence pairs so far Processed 16000000 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 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 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 Processed 19000000 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 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2474:15275:13573_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17153 Processed 20000000 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 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2571:15908:32863_1:N:0:TAATACAG+GTGTATAT NC_007175.2 2 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 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 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2678:17707:2002_1:N:0:TAATACAG+GTGAATAT NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1107:22616:31641_1:N:0:TAATACAG+GTGAATAT NC_035780.1 1 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 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:2:1171:16260:25175_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1171:14326:25801_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1202:22643:19601_1:N:0:TAATACAG+GTGAATAT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1202:22083:16282_1:N:0:TAATACAG+GTGAATAT NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1355:12572:16752_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1361:22381:21089_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17160 Processed 33000000 sequence pairs so far Processed 33000000 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 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1433:7798:1595_1:N:0:TAATACAG+GTGAATAT NC_007175.2 1 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1465:18873:33426_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1474:4101:18396_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1545:3839:18035_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1545:6108:20337_1:N:0:TAATACAG+GTGAATAT NC_007175.2 17163 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far 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 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 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 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2239:11017:21574_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 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 Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far 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 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2468:7337:17080_1:N:0:TAATACAG+GTGAATAT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2468:7238:17284_1:N:0:TAATACAG+GTGAATAT NC_035780.1 2 Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far 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 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:5330:19022_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:5204:19398_1:N:0:TAATACAG+GTGAATAT NC_007175.2 2 Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 55284369 (89.49%) aligned concordantly 0 times 3146610 (5.09%) aligned concordantly exactly 1 time 3346315 (5.42%) aligned concordantly >1 times 10.51% overall alignment rate 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 55312692 (89.54%) aligned concordantly 0 times 3139756 (5.08%) aligned concordantly exactly 1 time 3324846 (5.38%) aligned concordantly >1 times 10.46% overall alignment rate 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 54988970 (89.01%) aligned concordantly 0 times 3305198 (5.35%) aligned concordantly exactly 1 time 3483126 (5.64%) aligned concordantly >1 times 10.99% overall alignment rate 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 54963782 (88.97%) aligned concordantly 0 times 3305927 (5.35%) aligned concordantly exactly 1 time 3507585 (5.68%) aligned concordantly >1 times 11.03% overall alignment rate Processed 61777294 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 247109176. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 247109176. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 247109176. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 247109176. Successfully deleted the temporary files EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 61777294 Final Cytosine Methylation Report ================================= Total number of C's analysed: 454663931 Total methylated C's in CpG context: 14720909 Total methylated C's in CHG context: 4852089 Total methylated C's in CHH context: 20757025 Total methylated C's in Unknown context: 883464 Total unmethylated C's in CpG context: 46111615 Total unmethylated C's in CHG context: 87825655 Total unmethylated C's in CHH context: 280396638 Total unmethylated C's in Unknown context: 2709101 C methylated in CpG context: 24.2% C methylated in CHG context: 5.2% C methylated in CHH context: 6.9% C methylated in unknown context (CN or CHN): 24.6% Now waiting for all child processes to complete 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 54960363 (88.97%) aligned concordantly 0 times 3308741 (5.36%) aligned concordantly exactly 1 time 3508190 (5.68%) aligned concordantly >1 times 11.03% overall alignment rate 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 55315244 (89.54%) aligned concordantly 0 times 3137557 (5.08%) aligned concordantly exactly 1 time 3324493 (5.38%) aligned concordantly >1 times 10.46% overall alignment rate 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 55285047 (89.49%) aligned concordantly 0 times 3145583 (5.09%) aligned concordantly exactly 1 time 3346664 (5.42%) aligned concordantly >1 times 10.51% overall alignment rate 61777294 reads; of these: 61777294 (100.00%) were paired; of these: 54989668 (89.01%) aligned concordantly 0 times 3306795 (5.35%) aligned concordantly exactly 1 time 3480831 (5.63%) aligned concordantly >1 times 10.99% overall alignment rate Processed 61777294 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 247109176. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 247109176. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 247109176. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 247109176. Successfully deleted the temporary files EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 61777294 Final Cytosine Methylation Report ================================= Total number of C's analysed: 454640946 Total methylated C's in CpG context: 14739771 Total methylated C's in CHG context: 4854649 Total methylated C's in CHH context: 20749116 Total methylated C's in Unknown context: 884305 Total unmethylated C's in CpG context: 46114320 Total unmethylated C's in CHG context: 87832989 Total unmethylated C's in CHH context: 280350101 Total unmethylated C's in Unknown context: 2709237 C methylated in CpG context: 24.2% C methylated in CHG context: 5.2% C methylated in CHH context: 6.9% C methylated in unknown context (CN or CHN): 24.6% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF01-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF01-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF01-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 123554588 Final Cytosine Methylation Report ================================= Total number of C's analysed: 909304877 Total methylated C's in CpG context: 29460680 Total methylated C's in CHG context: 9706738 Total methylated C's in CHH context: 41506141 Total methylated C's in Unknown context: 1767769 Total unmethylated C's in CpG context: 92225935 Total unmethylated C's in CHG context: 175658644 Total unmethylated C's in CHH context: 560746739 Total unmethylated C's in Unknown context: 5418338 C methylated in CpG context: 24.2% C methylated in CHG context: 5.2% C methylated in CHH context: 6.9% C methylated in unknown context (CN or CHN): 24.6% Deleting temporary report files... Bismark completed in 0d 4h 12m 27s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 44838 and offset 2 (sequences written out: 72135316) Using the subset file >EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 72135316) Using the subset file >EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 72135316) Using the subset file >EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 44838 and offset 2 (sequences written out: 72135316) Using the subset file >EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (72135316 sequences in total) Writing a C -> T converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (72135316 sequences in total) Writing a C -> T converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (72135316 sequences in total) Input files are EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (72135316 sequences in total) Input files are EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 ANAAAAAAAATTTATTTTTATATTTATAAAAAAAATTTATTTTTATATATAAATTTTATTTTTTTTTTTTTTAATTTTTTTATTAAAATATTAATTTTATTAAATAATTTTTTAATATTTTTAAAAAAATAATTAATAATAAAAATTAAT F#FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TCATAAATCATTAAAACAAATAATAACAATAAAAACTAATAAAATTAATTTTATTAATTTTTATTATTAATTATTTTTTTAAAAATATTAAAAAATTATTTAATAAAATTAATATTTTAATAAAAAAATTAAAAAAAAAAAAAATAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF,FFFFF:FFFFFFF:FF:FF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TNTAAAATTTTAAAATTGGAATTATTGTGAAATTTTGGTGATTGGAAATGGTTTTGGTTTTTTTTTTTTTTTTGTTTTGAAAAAAATGTTGATAAATATATAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TTATATATTTATCAACATTTTTTTCAAAACAAAAAAAAAAAAAAAACCAAAACCATTTCCAATCACCAAAATTTCACAATAATTCCAATTTTAAAATTTTAAA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 ANAAAAAAAATCTATCTCTATACCTACAAAAAAAATCTATCTCTATACATAAATTTTATCTCTCTCTTCTCTAACTTTTTTATTAAAATACCAACTCTACCAAATAATTTTTCAACATTTTTAAAAAAATAACCAACAATAAAAACTAAT F#FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TTATAAATTATTAAAATAAATAATAATAATAAAAATTAATGAGATTAGTTTTATTAGTTTTTATTGTTGGTTATTTTTTTAAAAATGTTGAAAAATTATTTGGTAGAGTTGGTATTTTAATAAAAAAGTTAGAGAAGAGAGAGATAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF,FFFFF:FFFFFFF:FF:FF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 CNCAAAATTTTAAAATTAAAATTATTATAAAATTTTAATAATTAAAAATAATTTTAATTTTTTTTTTTTTTTTATTTTAAAAAAAATATTAATAAATATATAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TTATATATTTATTAATATTTTTTTTAAAATAAAAAAAAAAAAAAAATTAAAATTATTTTTAATTATTAAAATTTTATAATAATTTTAATTTTAAAATTTTGAG FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 ANAAAAAAAATCTATCTCTATACCTACAAAAAAAATCTATCTCTATACATAAATTTTATCTCTCTCTTCTCTAACTTTTTTATTAAAATACCAACTCTACCAAATAATTTTTCAACATTTTTAAAAAAATAACCAACAATAAAAACTAAT F#FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TTATAAATTATTAAAATAAATAATAATAATAAAAATTAATGAGATTAGTTTTATTAGTTTTTATTGTTGGTTATTTTTTTAAAAATGTTGAAAAATTATTTGGTAGAGTTGGTATTTTAATAAAAAAGTTAGAGAAGAGAGAGATAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF,FFFFF:FFFFFFF:FF:FF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 CNCAAAATTTTAAAATTAAAATTATTATAAAATTTTAATAATTAAAAATAATTTTAATTTTTTTTTTTTTTTTATTTTAAAAAAAATATTAATAAATATATAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TTATATATTTATTAATATTTTTTTTAAAATAAAAAAAAAAAAAAAATTAAAATTATTTTTAATTATTAAAATTTTATAATAATTTTAATTTTAAAATTTTGAG FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27064:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 TNTAAAATTTTAAAATTGGAATTATTGTGAAATTTTGGTGATTGGAAATGGTTTTGGTTTTTTTTTTTTTTTTGTTTTGAAAAAAATGTTGATAAATATATAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFF::,FFF,:FFFFFF:::FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27064:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TTATATATTTATCAACATTTTTTTCAAAACAAAAAAAAAAAAAAAACCAAAACCATTTCCAATCACCAAAATTTCACAATAATTCCAATTTTAAAATTTTAAA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF::FFFFFFF:FFF,FF::FFFFFFFFFF:F::F:::FFFF:FFFFFFFFFFFFF::: YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26811:1047_1:N:0:ATCCACTG+ACGCACCT/1 77 * 0 0 * * 0 0 ANAAAAAAAATTTATTTTTATATTTATAAAAAAAATTTATTTTTATATATAAATTTTATTTTTTTTTTTTTTAATTTTTTTATTAAAATATTAATTTTATTAAATAATTTTTTAATATTTTTAAAAAAATAATTAATAATAAAAATTAAT F#FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFF:FFFF:F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26811:1047_2:N:0:ATCCACTG+ACGCACCT/2 141 * 0 0 * * 0 0 TCATAAATCATTAAAACAAATAATAACAATAAAAACTAATAAAATTAATTTTATTAATTTTTATTATTAATTATTTTTTTAAAAATATTAAAAAATTATTTAATAAAATTAATATTTTAATAAAAAAATTAAAAAAAAAAAAAATAAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF,FFFFF:FFFFFFF:FF:FF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1125:12147:26005_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1132:18502:12054_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17137 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1158:7907:2816_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1213:18177:13338_1:N:0:GTCCACTG+ACGCACCT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1213:18457:13855_1:N:0:GTCCACTG+ACGCACCT NC_007175.2 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1353:15528:34554_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1437:19208:17816_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1545:9118:10457_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:29107:32205_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:28339:32910_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1616:13376:24001_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2138:11288:10582_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2155:12915:14340_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2226:23122:2268_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17091 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2244:30843:27915_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2443:1669:10207_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2454:14751:31485_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17137 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2461:26250:24940_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17107 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2461:24885:24142_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17107 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2467:7446:32299_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2546:22083:10895_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17162 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1108:22516:13651_1:N:0:CTCCACTG+ACGCCCCT NC_007175.2 2 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1176:5132:4930_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17099 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1177:8278:4711_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17099 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1216:25988:28494_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1245:14380:24048_1:N:0:ATCCACTG+ACGCACCT NC_035781.1 2 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1364:18774:30968_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1371:1850:32189_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17116 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1413:7274:24893_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1413:6985:21574_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1413:8757:22232_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1421:19063:32189_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17160 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1430:30617:10739_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1566:26648:3803_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1566:26829:20619_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1627:15157:33285_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17206 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2131:8142:5885_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2270:2139:19789_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17165 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2270:2003:19805_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17165 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2270:2058:19836_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17165 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2317:2202:5588_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17162 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2321:32425:24017_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17158 Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2374:25021:14199_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17161 Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2420:23827:11631_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2420:23845:11631_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2422:21070:3443_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17160 Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2457:28194:24455_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 1 Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2471:20428:18834_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17166 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2536:26223:6230_1:N:0:ATCCACTG+ACGCACCT NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2539:22200:28604_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17158 Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2564:28854:27383_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2566:29767:14935_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 2 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2575:9851:25379_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17178 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2577:28682:26115_1:N:0:ATCCACTG+ACGCACCT NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2602:8477:17300_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2603:9742:18552_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17163 Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2641:9706:14888_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2642:6054:31516_1:N:0:ATCCACTG+ACGCACCT NC_007175.2 17161 Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 64412133 (89.29%) aligned concordantly 0 times 3429434 (4.75%) aligned concordantly exactly 1 time 4293749 (5.95%) aligned concordantly >1 times 10.71% overall alignment rate 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 62355761 (86.44%) aligned concordantly 0 times 4382903 (6.08%) aligned concordantly exactly 1 time 5396652 (7.48%) aligned concordantly >1 times 13.56% overall alignment rate 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 62435947 (86.55%) aligned concordantly 0 times 4326440 (6.00%) aligned concordantly exactly 1 time 5372929 (7.45%) aligned concordantly >1 times 13.45% overall alignment rate 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 64479954 (89.39%) aligned concordantly 0 times 3378764 (4.68%) aligned concordantly exactly 1 time 4276598 (5.93%) aligned concordantly >1 times 10.61% overall alignment rate Processed 72135316 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 288541264. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 288541264. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 288541264. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 288541264. Successfully deleted the temporary files EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 72135316 Final Cytosine Methylation Report ================================= Total number of C's analysed: 535019454 Total methylated C's in CpG context: 12098906 Total methylated C's in CHG context: 2304107 Total methylated C's in CHH context: 10866420 Total methylated C's in Unknown context: 722564 Total unmethylated C's in CpG context: 66444842 Total unmethylated C's in CHG context: 110902742 Total unmethylated C's in CHH context: 332402437 Total unmethylated C's in Unknown context: 3716529 C methylated in CpG context: 15.4% C methylated in CHG context: 2.0% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 16.3% Now waiting for all child processes to complete 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 62349217 (86.43%) aligned concordantly 0 times 4383843 (6.08%) aligned concordantly exactly 1 time 5402256 (7.49%) aligned concordantly >1 times 13.57% overall alignment rate 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 64481321 (89.39%) aligned concordantly 0 times 3379111 (4.68%) aligned concordantly exactly 1 time 4274884 (5.93%) aligned concordantly >1 times 10.61% overall alignment rate 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 62429781 (86.55%) aligned concordantly 0 times 4327733 (6.00%) aligned concordantly exactly 1 time 5377802 (7.46%) aligned concordantly >1 times 13.45% overall alignment rate 72135316 reads; of these: 72135316 (100.00%) were paired; of these: 64416122 (89.30%) aligned concordantly 0 times 3426606 (4.75%) aligned concordantly exactly 1 time 4292588 (5.95%) aligned concordantly >1 times 10.70% overall alignment rate Processed 72135316 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 288541264. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 288541264. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 288541264. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 288541264. Successfully deleted the temporary files EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 72135316 Final Cytosine Methylation Report ================================= Total number of C's analysed: 534964613 Total methylated C's in CpG context: 12096786 Total methylated C's in CHG context: 2304348 Total methylated C's in CHH context: 10860105 Total methylated C's in Unknown context: 723276 Total unmethylated C's in CpG context: 66406207 Total unmethylated C's in CHG context: 110884779 Total unmethylated C's in CHH context: 332412388 Total unmethylated C's in Unknown context: 3722187 C methylated in CpG context: 15.4% C methylated in CHG context: 2.0% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 16.3% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF02-EM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF02-EM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF02-EM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 144270632 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1069984067 Total methylated C's in CpG context: 24195692 Total methylated C's in CHG context: 4608455 Total methylated C's in CHH context: 21726525 Total methylated C's in Unknown context: 1445840 Total unmethylated C's in CpG context: 132851049 Total unmethylated C's in CHG context: 221787521 Total unmethylated C's in CHH context: 664814825 Total unmethylated C's in Unknown context: 7438716 C methylated in CpG context: 15.4% C methylated in CHG context: 2.0% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 16.3% Deleting temporary report files... Bismark completed in 0d 4h 41m 27s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 33391 and offset 2 (sequences written out: 67635918) Using the subset file >EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 67635918) Using the subset file >EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 33391 and offset 2 (sequences written out: 67635918) Using the subset file >EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 67635918) Using the subset file >EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (67635918 sequences in total) Writing a C -> T converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (67635918 sequences in total) Writing a C -> T converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (67635918 sequences in total) Input files are EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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 EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (67635918 sequences in total) Input files are EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TNGTATAAGTTTATTTGTGGTTGTGGTGGAGGTAGATGTGGTGGTTGATTGTTGTGATGTTGTAGTATTTGTTTTTTTTGAGGTTATTGTATTTTGTGTTGAAGTGGTGGTTTTTGATGTTTTGTGGTTATG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 CATAACCACAAAACATCAAAAACCACCACTTCAACACAAAATACAATAACCTCAAAAAAAACAAATACTACAACATCACAACAATCAACCACCACATCTACCTCCACCACAACCACAAATAAACTTATACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ANATTATTATAAAATATATATATAAATAAAAATTAAATAAAAAAAATTGATTAATTAATTAATAAATTATTATAAATTATTATAATAATAAATAAATATTATTATATAAAATAAAATTATTAATAAAATTTATATTTATTAAAATAATAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTTAATATTTTTATATTATTTTAATAAATATAAATTTTATTAATAATTTTATTTTATATAATAATATTTATTTATTATTATAATAATTTATAATAATTTATTAATTAATTAATCAATTTTTTTTATTTAATTTTTATTTATATATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TNATATAAATTTATTTATAATTATAATAAAAATAAATATAATAATTAATTATTATAATATTATAATATTTATTTTTTTTAAAATTATTATATTTTATATTAAAATAATAATTTTTAATATTTTATAATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TATAATTATAAAATATTAAAAATTATTATTTTAATATAAAATATAATAATTTTAAAAAAAATAAATATTATAATATTATAATAATTAATTATTATATTTATTTTTATTATAATTATAAATAAATTTATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ANACCACTACAAAATACACATATAAATAAAAACCAAATAAAAAAAACTAACTAATTAACCAACAAATTATTATAAACCACCACAACAATAAACAAACACTACTACATAAAATAAAACCATCAATAAAACCTATACCCACCAAAATAATAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTTGATATTTTTGTATTATTTTGGTGGGTATAGGTTTTATTGATGGTTTTATTTTATGTAGTAGTGTTTGTTTATTGTTGTGGTGGTTTATAATAATTTGTTGGTTAATTAGTTAGTTTTTTTTATTTGGTTTTTATTTATATGTGTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TNATATAAATTTATTTATAATTATAATAAAAATAAATATAATAATTAATTATTATAATATTATAATATTTATTTTTTTTAAAATTATTATATTTTATATTAAAATAATAATTTTTAATATTTTATAATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TATAATTATAAAATATTAAAAATTATTATTTTAATATAAAATATAATAATTTTAAAAAAAATAAATATTATAATATTATAATAATTAATTATTATATTTATTTTTATTATAATTATAAATAAATTTATATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ANACCACTACAAAATACACATATAAATAAAAACCAAATAAAAAAAACTAACTAATTAACCAACAAATTATTATAAACCACCACAACAATAAACAAACACTACTACATAAAATAAAACCATCAATAAAACCTATACCCACCAAAATAATAC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTTGATATTTTTGTATTATTTTGGTGGGTATAGGTTTTATTGATGGTTTTATTTTATGTAGTAGTGTTTGTTTATTGTTGTGGTGGTTTATAATAATTTGTTGGTTAATTAGTTAGTTTTTTTTATTTGGTTTTTATTTATATGTGTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27245:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 TNGTATAAGTTTATTTGTGGTTGTGGTGGAGGTAGATGTGGTGGTTGATTGTTGTGATGTTGTAGTATTTGTTTTTTTTGAGGTTATTGTATTTTGTGTTGAAGTGGTGGTTTTTGATGTTTTGTGGTTATG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27245:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 CATAACCACAAAACATCAAAAACCACCACTTCAACACAAAATACAATAACCTCAAAAAAAACAAATACTACAACATCACAACAATCAACCACCACATCTACCTCCACCACAACCACAAATAAACTTATACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26250:1047_1:N:0:CTCTCGTC+AGGTTATA/1 77 * 0 0 * * 0 0 ANATTATTATAAAATATATATATAAATAAAAATTAAATAAAAAAAATTGATTAATTAATTAATAAATTATTATAAATTATTATAATAATAAATAAATATTATTATATAAAATAAAATTATTAATAAAATTTATATTTATTAAAATAATAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26250:1047_2:N:0:CTCTCGTC+AGGTTATA/2 141 * 0 0 * * 0 0 TTTAATATTTTTATATTATTTTAATAAATATAAATTTTATTAATAATTTTATTTTATATAATAATATTTATTTATTATTATAATAATTTATAATAATTTATTAATTAATTAATCAATTTTTTTTATTTAATTTTTATTTATATATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1107:6958:14450_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1173:2401:20400_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1173:1714:34053_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1213:6750:35477_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1233:8666:22701_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 17194 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1235:23836:23672_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1313:15564:2801_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1373:7039:2284_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1450:21721:19758_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1558:29884:26475_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2235:23863:25347_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2364:12897:12179_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2374:18358:34976_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 17114 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2378:12536:13839_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2374:18430:35070_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 17114 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2409:27661:36871_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2432:5565:21433_1:N:0:CTCTCGTC+AGGTTATA NC_007175.2 1 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2447:30544:21605_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 3 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2558:25373:19194_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2643:24695:28322_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2643:25265:25300_1:N:0:CTCTCGTC+AGGTTATA NC_035780.1 2 Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far 67635918 reads; of these: 67635918 (100.00%) were paired; of these: 61126333 (90.38%) aligned concordantly 0 times 2924288 (4.32%) aligned concordantly exactly 1 time 3585297 (5.30%) aligned concordantly >1 times 9.62% overall alignment rate 67635918 reads; of these: 67635918 (100.00%) were paired; of these: 61125374 (90.37%) aligned concordantly 0 times 2925387 (4.33%) aligned concordantly exactly 1 time 3585157 (5.30%) aligned concordantly >1 times 9.63% overall alignment rate 6763591867635918 reads; of these: reads; of these: 6763591867635918 ( (100.00100.00%%) were paired; of these:) were paired; of these: 6237695862376904 ( (92.2292.22%%) aligned concordantly 0 times) aligned concordantly 0 times 23117232320320 ( (3.423.43%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 29472372938694 ( (4.364.34%%) aligned concordantly >1 times) aligned concordantly >1 times 7.787.78%% overall alignment rate overall alignment rate Processed 67635918 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 270543672. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 270543672. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 270543672. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 270543672. Successfully deleted the temporary files EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 67635918 Final Cytosine Methylation Report ================================= Total number of C's analysed: 290772110 Total methylated C's in CpG context: 7681343 Total methylated C's in CHG context: 2540458 Total methylated C's in CHH context: 12573483 Total methylated C's in Unknown context: 572347 Total unmethylated C's in CpG context: 28118379 Total unmethylated C's in CHG context: 52277686 Total unmethylated C's in CHH context: 187580761 Total unmethylated C's in Unknown context: 2058772 C methylated in CpG context: 21.5% C methylated in CHG context: 4.6% C methylated in CHH context: 6.3% C methylated in unknown context (CN or CHN): 21.8% Now waiting for all child processes to complete 67635918 reads; of these: 67635918 (100.00%) were paired; of these: 62379082 (92.23%) aligned concordantly 0 times 2317426 (3.43%) aligned concordantly exactly 1 time 2939410 (4.35%) aligned concordantly >1 times 7.77% overall alignment rate 67635918 reads; of these: 67635918 (100.00%) were paired; of these: 62375536 (92.22%) aligned concordantly 0 times 2313599 (3.42%) aligned concordantly exactly 1 time 2946783 (4.36%) aligned concordantly >1 times 7.78% overall alignment rate 67635918 reads; of these: 67635918 (100.00%) were paired; of these: 61126728 (90.38%) aligned concordantly 0 times 2923139 (4.32%) aligned concordantly exactly 1 time 3586051 (5.30%) aligned concordantly >1 times 9.62% overall alignment rate 67635918 reads; of these: 67635918 (100.00%) were paired; of these: 61126318 (90.38%) aligned concordantly 0 times 2926081 (4.33%) aligned concordantly exactly 1 time 3583519 (5.30%) aligned concordantly >1 times 9.62% overall alignment rate Processed 67635918 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 270543672. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 270543672. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 270543672. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 270543672. Successfully deleted the temporary files EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 67635918 Final Cytosine Methylation Report ================================= Total number of C's analysed: 290583411 Total methylated C's in CpG context: 7671044 Total methylated C's in CHG context: 2537412 Total methylated C's in CHH context: 12565484 Total methylated C's in Unknown context: 568191 Total unmethylated C's in CpG context: 28115114 Total unmethylated C's in CHG context: 52240775 Total unmethylated C's in CHH context: 187453582 Total unmethylated C's in Unknown context: 2057804 C methylated in CpG context: 21.4% C methylated in CHG context: 4.6% C methylated in CHH context: 6.3% C methylated in unknown context (CN or CHN): 21.6% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF03-EM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF03-EM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF03-EM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 135271836 Final Cytosine Methylation Report ================================= Total number of C's analysed: 581355521 Total methylated C's in CpG context: 15352387 Total methylated C's in CHG context: 5077870 Total methylated C's in CHH context: 25138967 Total methylated C's in Unknown context: 1140538 Total unmethylated C's in CpG context: 56233493 Total unmethylated C's in CHG context: 104518461 Total unmethylated C's in CHH context: 375034343 Total unmethylated C's in Unknown context: 4116576 C methylated in CpG context: 21.4% C methylated in CHG context: 4.6% C methylated in CHH context: 6.3% C methylated in unknown context (CN or CHN): 21.7% Deleting temporary report files... Bismark completed in 0d 4h 2m 45s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 3536 and offset 2 (sequences written out: 66557646) Using the subset file >EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 66557646) Using the subset file >EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 3536 and offset 2 (sequences written out: 66557646) Using the subset file >EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 66557646) Using the subset file >EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (66557646 sequences in total) Writing a C -> T converted version of the input file EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (66557646 sequences in total) Writing a C -> T converted version of the input file EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (66557646 sequences in total) Input files are EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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 EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (66557646 sequences in total) Input files are EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27968:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNTTAATTAATTAATTTTTTATTAGAAATAAAGGGTTAATTGATTAGGAAGATTAAATTTTGTTAAAATGAAGATTATAAAGTTTTAGGGGTTATTTTGTTAATTAGAAATTTTATTTGTGTTTTGGAATATTGTTG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,::,FFFFFFFF,,:FFFFFF:F:FFFFFFFF,FFFF:FF:,FFF,F,F:FFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27968:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 CAACAATATTCCAAAACACAAATAAAATTTCTAATTAACAAAATAACCCCTAAAACTTTATAATCTTCATTTTAACAAAATTTAATCTTCCTAATCAATTAACCCTTTATTTCTAATAAAAAATTAATTAATTAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26521:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNTAAAATTAAATATATAAAATATAATTTTTTATTATATTTTAAATTTATTATTAATATTTTTAAAATTAATTTTTTTTTTTTATTTTTTTTAATTATTTTTTATAAAATATATTTTTAATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26521:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 TATAATTAAAAATATATTTTATAAAAAATAATTAAAAAAAATAAAAAAAAAAAATTAATTTTAAAAATATTAATAATAAATTTAATATATAATAAAAAATTATATTTTATATATTTAATTTTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFF,F:FF:FFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27968:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNCTAATCAATTAACCCTTTATTAAAAATAAAAAATTAATTAATTAAAAAAATTAAATTTTATTAAAATAAAAATTATAAAATTTTAAAAATTATTTTATTAATTAAAAATTTTATCTATATTTTAAAATATTATTA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,::,FFFFFFFF,,:FFFFFF:F:FFFFFFFF,FFFF:FF:,FFF,F,F:FFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27968:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 TAATAATATTTTAAAATATAGATAAAATTTTTAATTAATAAAATAATTTTTAAAATTTTATAATTTTTATTTTAATAAAATTTAATTTTTTTAATTAATTAATTTTTTATTTTTAATAAAGGGTTAATTGATTAGGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26521:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNTAAAACTAAACACATAAAATATAATTTTTCATCATATTTTAAATCTACTATTAATATTTCTAAAATCAATTTTTTTTCTTCATTTTCTCTAACTATTTTCCATAAAATACATTTTTAATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26521:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 TATAATTAAAAATGTATTTTATGGAAAATAGTTAGAGAAAATGAAGAAAAAAAATTGATTTTAGAAATATTAATAGTAGATTTAATATATGATGAAAAATTATATTTTATGTGTTTAGTTTTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFF,F:FF:FFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27968:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNCTAATCAATTAACCCTTTATTAAAAATAAAAAATTAATTAATTAAAAAAATTAAATTTTATTAAAATAAAAATTATAAAATTTTAAAAATTATTTTATTAATTAAAAATTTTATCTATATTTTAAAATATTATTA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,::,FFFFFFFF,,:FFFFFF:F:FFFFFFFF,FFFF:FF:,FFF,F,F:FFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27968:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 TAATAATATTTTAAAATATAGATAAAATTTTTAATTAATAAAATAATTTTTAAAATTTTATAATTTTTATTTTAATAAAATTTAATTTTTTTAATTAATTAATTTTTTATTTTTAATAAAGGGTTAATTGATTAGGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26521:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNTAAAACTAAACACATAAAATATAATTTTTCATCATATTTTAAATCTACTATTAATATTTCTAAAATCAATTTTTTTTCTTCATTTTCTCTAACTATTTTCCATAAAATACATTTTTAATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26521:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 TATAATTAAAAATGTATTTTATGGAAAATAGTTAGAGAAAATGAAGAAAAAAAATTGATTTTAGAAATATTAATAGTAGATTTAATATATGATGAAAAATTATATTTTATGTGTTTAGTTTTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFF,F:FF:FFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27968:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNTTAATTAATTAATTTTTTATTAGAAATAAAGGGTTAATTGATTAGGAAGATTAAATTTTGTTAAAATGAAGATTATAAAGTTTTAGGGGTTATTTTGTTAATTAGAAATTTTATTTGTGTTTTGGAATATTGTTG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,::,FFFFFFFF,,:FFFFFF:F:FFFFFFFF,FFFF:FF:,FFF,F,F:FFF:F YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27968:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 CAACAATATTCCAAAACACAAATAAAATTTCTAATTAACAAAATAACCCCTAAAACTTTATAATCTTCATTTTAACAAAATTTAATCTTCCTAATCAATTAACCCTTTATTTCTAATAAAAAATTAATTAATTAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26521:1047_1:N:0:GGCTTAAG+GGTCACGA/1 77 * 0 0 * * 0 0 TNTAAAATTAAATATATAAAATATAATTTTTTATTATATTTTAAATTTATTATTAATATTTTTAAAATTAATTTTTTTTTTTTATTTTTTTTAATTATTTTTTATAAAATATATTTTTAATTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26521:1047_2:N:0:GGCTTAAG+GGTCACGA/2 141 * 0 0 * * 0 0 TATAATTAAAAATATATTTTATAAAAAATAATTAAAAAAAATAAAAAAAAAAAATTAATTTTAAAAATATTAATAATAAATTTAATATATAATAAAAAATTATATTTTATATATTTAATTTTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFF,F:FF:FFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1104:24080:1266_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1140:5529:2143_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1168:19542:24377_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1177:1118:7059_1:N:0:NGCTTAAG+GGTCACNA NC_007175.2 17165 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1216:20934:1799_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1237:27914:33082_1:N:0:GGCTTAAG+GGTCACGA NC_007175.2 17165 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1242:13521:7153_1:N:0:GGCTTAAG+GGTCACGA NC_007175.2 17165 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1403:7934:13260_1:N:0:GGCTTAAG+GGTCACGA NC_035781.1 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1437:25283:7075_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 3 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1441:28583:25692_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1441:28402:26475_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1504:16071:23657_1:N:0:GGCTTAAG+GGTCACGA NC_007175.2 17165 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:17472:35415_1:N:0:GGCTTAAG+GGTCACGA NC_007175.2 17105 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:17237:35759_1:N:0:GGCTTAAG+GGTCACGA NC_007175.2 17105 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2103:22146:30264_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2335:25581:2644_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2420:16342:2832_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2420:15917:3568_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2642:24225:25692_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1207:5195:24048_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1229:27425:7686_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1308:7907:35164_1:N:0:GGCTTAAG+GGTCACGA NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1309:8413:2503_1:N:0:GGCTTAAG+GGTCACGA NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1313:17996:10050_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1545:15609:27555_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1549:2645:31031_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1618:18855:34648_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2147:30517:10629_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2229:25870:12070_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2327:11966:21590_1:N:0:GGCTTAAG+GGTCACGA NC_007175.2 2 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2468:24695:23062_1:N:0:GGCTTAAG+GGTCACGA NC_035781.1 2 Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2526:32588:15875_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2537:10140:22091_1:N:0:GGCTTAAG+GGTCACGA NC_035780.1 2 Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 55834846 (83.89%) aligned concordantly 0 times 5001362 (7.51%) aligned concordantly exactly 1 time 5721438 (8.60%) aligned concordantly >1 times 16.11% overall alignment rate 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 57648980 (86.62%) aligned concordantly 0 times 4101452 (6.16%) aligned concordantly exactly 1 time 4807214 (7.22%) aligned concordantly >1 times 13.38% overall alignment rate 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 57663185 (86.64%) aligned concordantly 0 times 4106559 (6.17%) aligned concordantly exactly 1 time 4787902 (7.19%) aligned concordantly >1 times 13.36% overall alignment rate 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 55815664 (83.86%) aligned concordantly 0 times 4991450 (7.50%) aligned concordantly exactly 1 time 5750532 (8.64%) aligned concordantly >1 times 16.14% overall alignment rate Processed 66557646 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 266230584. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 266230584. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 266230584. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 266230584. Successfully deleted the temporary files EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 66557646 Final Cytosine Methylation Report ================================= Total number of C's analysed: 742552333 Total methylated C's in CpG context: 23299462 Total methylated C's in CHG context: 8357202 Total methylated C's in CHH context: 30956412 Total methylated C's in Unknown context: 1341990 Total unmethylated C's in CpG context: 82250088 Total unmethylated C's in CHG context: 149066429 Total unmethylated C's in CHH context: 448622740 Total unmethylated C's in Unknown context: 4503207 C methylated in CpG context: 22.1% C methylated in CHG context: 5.3% C methylated in CHH context: 6.5% C methylated in unknown context (CN or CHN): 23.0% Now waiting for all child processes to complete 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 57658795 (86.63%) aligned concordantly 0 times 4107760 (6.17%) aligned concordantly exactly 1 time 4791091 (7.20%) aligned concordantly >1 times 13.37% overall alignment rate 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 57648831 (86.61%) aligned concordantly 0 times 4097748 (6.16%) aligned concordantly exactly 1 time 4811067 (7.23%) aligned concordantly >1 times 13.39% overall alignment rate 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 55832872 (83.89%) aligned concordantly 0 times 5004233 (7.52%) aligned concordantly exactly 1 time 5720541 (8.59%) aligned concordantly >1 times 16.11% overall alignment rate 66557646 reads; of these: 66557646 (100.00%) were paired; of these: 55816377 (83.86%) aligned concordantly 0 times 4988739 (7.50%) aligned concordantly exactly 1 time 5752530 (8.64%) aligned concordantly >1 times 16.14% overall alignment rate Processed 66557646 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 266230584. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 266230584. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 266230584. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 266230584. Successfully deleted the temporary files EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 66557646 Final Cytosine Methylation Report ================================= Total number of C's analysed: 742592340 Total methylated C's in CpG context: 23271615 Total methylated C's in CHG context: 8357175 Total methylated C's in CHH context: 30944726 Total methylated C's in Unknown context: 1342191 Total unmethylated C's in CpG context: 82269225 Total unmethylated C's in CHG context: 149027655 Total unmethylated C's in CHH context: 448721944 Total unmethylated C's in Unknown context: 4496271 C methylated in CpG context: 22.0% C methylated in CHG context: 5.3% C methylated in CHH context: 6.5% C methylated in unknown context (CN or CHN): 23.0% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF03-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF03-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF03-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 133115292 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1485144673 Total methylated C's in CpG context: 46571077 Total methylated C's in CHG context: 16714377 Total methylated C's in CHH context: 61901138 Total methylated C's in Unknown context: 2684181 Total unmethylated C's in CpG context: 164519313 Total unmethylated C's in CHG context: 298094084 Total unmethylated C's in CHH context: 897344684 Total unmethylated C's in Unknown context: 8999478 C methylated in CpG context: 22.1% C methylated in CHG context: 5.3% C methylated in CHH context: 6.5% C methylated in unknown context (CN or CHN): 23.0% Deleting temporary report files... Bismark completed in 0d 5h 8m 59s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 68663545) Using the subset file >EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 7422 and offset 2 (sequences written out: 68663545) Using the subset file >EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 7422 and offset 2 (sequences written out: 68663545) Using the subset file >EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 68663545) Using the subset file >EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (68663545 sequences in total) Writing a C -> T converted version of the input file EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (68663545 sequences in total) Writing a C -> T converted version of the input file EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (68663545 sequences in total) Input files are EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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 EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (68663545 sequences in total) Input files are EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26901:1047_1:N:0:AATCCGGA+AACTGTAG/1 77 * 0 0 * * 0 0 TNTTTATAAAAAAAAAAAATAAAATTAATAAATATATAAAAAAAAATTTATTTTAATATTTATTTAAATTATTATATATTAATTATTTATAATATTATAAAATTAATAAAAAATTTATTATTTATATATTTAATAATAATATTAAATTTT F#FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFF:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26901:1047_2:N:0:AATCCGGA+AACTGTAG/2 141 * 0 0 * * 0 0 ACCTACTCTTCCAATAATTATATATTAAATATATTTTATTATATATTTTTAAAATTTAATATTATTATTAAATATATAAATAATAAATTTTTTATTAATTTTATAATATTATAAATAATTAATATATAATAATTTAAATAAATATTAAAA :FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF::FFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FF,FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26775:1047_1:N:0:AATCCGGA+AACTGTAG/1 99 NC_035782.1_CT_converted 29879545 7 4M3I143M = 29879574 179 GNATTTATTAAATTTATTAAATTTAATGAATGGAGGAGGATGTGTTATTTTATTTGTTTTTAGTTGTAAAATAGTAATGTTTAATTTTTTATTGTGATAAAGAATTTTAGGTTTTAGAGAAAATTTTAAGGAATTAATTTGATAGTGTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,F:FFFF:FF AS:i:-27 XS:i:-45 XN:i:0 XM:i:3 XO:i:1 XG:i:3 NM:i:6 MD:Z:1T0G1G142 YS:i:0 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26775:1047_2:N:0:AATCCGGA+AACTGTAG/2 147 NC_035782.1_CT_converted 29879574 7 150M = 29879545 -179 GAGGAGGATGTGTTATTTTATTTGTTTTTAGTTGTAAAATAGTAATGTTTAATTTTTTATTGTGATAAAGAATTTTAGGTTTTAGAGAAAATTTTAAGGAATTAATTTGATAGTGTTTTTTAAATTTAAAATTGATAAATATTTTAGGAT FFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-18 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:150 YS:i:-27 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26901:1047_1:N:0:AATCCGGA+AACTGTAG/1 77 * 0 0 * * 0 0 CNCCCATAAAAAAAAAAAACAAAACTAACAAACACATAAAAAAAAACCTACCCCAACACCTATTTAAATCACTATACATCAATCATTTACAACACCACAAAACCAACAAAAAATCCATTACCCATACATTTAATAACAATATTAAATTTC F#FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFF:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26901:1047_2:N:0:AATCCGGA+AACTGTAG/2 141 * 0 0 * * 0 0 GTTTGTTTTTTTGATAATTATGTATTGGATGTGTTTTGTTATGTGTTTTTGAAATTTAATATTGTTATTAAATGTATGGGTAATGGATTTTTTGTTGGTTTTGTGGTGTTGTAAATGATTGATGTATAGTGATTTAAATAGGTGTTGGGG :FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF::FFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FF,FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26775:1047_1:N:0:AATCCGGA+AACTGTAG/1 77 * 0 0 * * 0 0 ANATTCATTAAATTTATTAAATTTAATAAATAAAAAAAAATATATTATTTTATTTATTTTTAATTATAAAATAATAATATTTAATTTTTTATTATAATAAAAAATTTTAAATTTTAAAAAAAATTTTAAAAAATTAATTTAATAATATTC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,F:FFFF:FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26775:1047_2:N:0:AATCCGGA+AACTGTAG/2 141 * 0 0 * * 0 0 ATTTTAAAATATTTATTAATTTTAAATTTAAAGAATATTATTAAATTAATTTTTTAAAATTTTTTTTAAAATTTAAAATTTTTTATTATAATAAAAAATTAAATATTATTATTTTATAATTAAAAATAAATAAAATAATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26901:1047_1:N:0:AATCCGGA+AACTGTAG/1 77 * 0 0 * * 0 0 CNCCCATAAAAAAAAAAAACAAAACTAACAAACACATAAAAAAAAACCTACCCCAACACCTATTTAAATCACTATACATCAATCATTTACAACACCACAAAACCAACAAAAAATCCATTACCCATACATTTAATAACAATATTAAATTTC F#FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFF:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26901:1047_2:N:0:AATCCGGA+AACTGTAG/2 141 * 0 0 * * 0 0 GTTTGTTTTTTTGATAATTATGTATTGGATGTGTTTTGTTATGTGTTTTTGAAATTTAATATTGTTATTAAATGTATGGGTAATGGATTTTTTGTTGGTTTTGTGGTGTTGTAAATGATTGATGTATAGTGATTTAAATAGGTGTTGGGG :FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF::FFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FF,FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26775:1047_1:N:0:AATCCGGA+AACTGTAG/1 77 * 0 0 * * 0 0 ANATTCATTAAATTTATTAAATTTAATAAATAAAAAAAAATATATTATTTTATTTATTTTTAATTATAAAATAATAATATTTAATTTTTTATTATAATAAAAAATTTTAAATTTTAAAAAAAATTTTAAAAAATTAATTTAATAATATTC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,F:FFFF:FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26775:1047_2:N:0:AATCCGGA+AACTGTAG/2 141 * 0 0 * * 0 0 ATTTTAAAATATTTATTAATTTTAAATTTAAAGAATATTATTAAATTAATTTTTTAAAATTTTTTTTAAAATTTAAAATTTTTTATTATAATAAAAAATTAAATATTATTATTTTATAATTAAAAATAAATAAAATAATATATTTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26901:1047_1:N:0:AATCCGGA+AACTGTAG/1 77 * 0 0 * * 0 0 TNTTTATAAAAAAAAAAAATAAAATTAATAAATATATAAAAAAAAATTTATTTTAATATTTATTTAAATTATTATATATTAATTATTTATAATATTATAAAATTAATAAAAAATTTATTATTTATATATTTAATAATAATATTAAATTTT F#FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFF:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26901:1047_2:N:0:AATCCGGA+AACTGTAG/2 141 * 0 0 * * 0 0 ACCTACTCTTCCAATAATTATATATTAAATATATTTTATTATATATTTTTAAAATTTAATATTATTATTAAATATATAAATAATAAATTTTTTATTAATTTTATAATATTATAAATAATTAATATATAATAATTTAAATAAATATTAAAA :FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF::FFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FF,FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFF:FF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26775:1047_1:N:0:AATCCGGA+AACTGTAG/1 77 * 0 0 * * 0 0 GNATTTATTAAATTTATTAAATTTAATGAATGGAGGAGGATGTGTTATTTTATTTGTTTTTAGTTGTAAAATAGTAATGTTTAATTTTTTATTGTGATAAAGAATTTTAGGTTTTAGAGAAAATTTTAAGGAATTAATTTGATAGTGTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,F:FFFF:FF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26775:1047_2:N:0:AATCCGGA+AACTGTAG/2 141 * 0 0 * * 0 0 ATCCTAAAATATTTATCAATTTTAAATTTAAAAAACACTATCAAATTAATTCCTTAAAATTTTCTCTAAAACCTAAAATTCTTTATCACAATAAAAAATTAAACATTACTATTTTACAACTAAAAACAAATAAAATAACACATCCTCCTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1171:5059:13479_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1226:14380:3223_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1330:1452:9361_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 3 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1614:16495:4852_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 3 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2171:1353:5212_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2215:5972:13056_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 3 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2270:15609:7357_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2270:15700:7576_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2270:17671:8891_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2316:11523:2253_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2563:26458:35603_1:N:0:AATCCGGA+AACTGTAG NC_035781.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2621:28411:26741_1:N:0:AATCCGGA+AACTGTAG NC_035781.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1122:19768:34256_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 3 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1161:18566:32550_1:N:0:AATCCGGA+AACTGTAG NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1163:20609:23782_1:N:0:AATCCGGA+AACTGTAG NC_035781.1 2 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1441:19868:7498_1:N:0:AATCCGGA+AACTGTAG NC_007175.2 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1556:26295:17221_1:N:0:AATCCGGA+AACTGTAG NC_007175.2 17101 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2120:32633:12414_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 3 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2351:28944:32612_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2548:15953:29590_1:N:0:AATCCGGA+AACTGTAG NC_007175.2 1 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2558:30490:16752_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2558:31222:18333_1:N:0:AATCCGGA+ACCTGTAG NC_035780.1 1 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2612:16947:29496_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2669:3215:23688_1:N:0:AATCCGGA+AACTGTAG NC_035780.1 2 68663545 reads; of these: 68663545 (100.00%) were paired; of these: 59487985 (86.64%) aligned concordantly 0 times 4350424 (6.34%) aligned concordantly exactly 1 time 4825136 (7.03%) aligned concordantly >1 times 13.36% overall alignment rate 68663545 reads; of these: 68663545 (100.00%) were paired; of these: 59554688 (86.73%) aligned concordantly 0 times 4303772 (6.27%) aligned concordantly exactly 1 time 4805085 (7.00%) aligned concordantly >1 times 13.27% overall alignment rate 68663545 reads; of these: 68663545 (100.00%) were paired; of these: 59575275 (86.76%) aligned concordantly 0 times 4319289 (6.29%) aligned concordantly exactly 1 time 4768981 (6.95%) aligned concordantly >1 times 13.24% overall alignment rate 68663545 reads; of these: 68663545 (100.00%) were paired; of these: 59480249 (86.63%) aligned concordantly 0 times 4331965 (6.31%) aligned concordantly exactly 1 time 4851331 (7.07%) aligned concordantly >1 times 13.37% overall alignment rate Processed 68663545 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 274654180. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 274654180. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 274654180. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 274654180. Successfully deleted the temporary files EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 68663545 Final Cytosine Methylation Report ================================= Total number of C's analysed: 732002777 Total methylated C's in CpG context: 21403292 Total methylated C's in CHG context: 5822586 Total methylated C's in CHH context: 22290181 Total methylated C's in Unknown context: 1254872 Total unmethylated C's in CpG context: 85047315 Total unmethylated C's in CHG context: 148923524 Total unmethylated C's in CHH context: 448515879 Total unmethylated C's in Unknown context: 4107963 C methylated in CpG context: 20.1% C methylated in CHG context: 3.8% C methylated in CHH context: 4.7% C methylated in unknown context (CN or CHN): 23.4% Now waiting for all child processes to complete 68663545 reads; of these: 68663545 (100.00%) were paired; of these: 59577857 (86.77%) aligned concordantly 0 times 4318012 (6.29%) aligned concordantly exactly 1 time 4767676 (6.94%) aligned concordantly >1 times 13.23% overall alignment rate 68663545 reads; of these: 68663545 (100.00%) were paired; of these: 59486330 (86.63%) aligned concordantly 0 times 4350380 (6.34%) aligned concordantly exactly 1 time 4826835 (7.03%) aligned concordantly >1 times 13.37% overall alignment rate 68663545 reads; of these: 68663545 (100.00%) were paired; of these: 59474558 (86.62%) aligned concordantly 0 times 68663545 reads; of these:4335513 ( 6.31 %68663545) aligned concordantly exactly 1 time ( 4853474 (7.07%) aligned concordantly >1 times 13.38100.00%% overall alignment rate) were paired; of these: 59557366 (86.74%) aligned concordantly 0 times 4305465 (6.27%) aligned concordantly exactly 1 time 4800714 (6.99%) aligned concordantly >1 times 13.26% overall alignment rate Processed 68663545 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 274654180. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 274654180. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 274654180. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 274654180. Successfully deleted the temporary files EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 68663545 Final Cytosine Methylation Report ================================= Total number of C's analysed: 732327121 Total methylated C's in CpG context: 21435627 Total methylated C's in CHG context: 5824950 Total methylated C's in CHH context: 22293894 Total methylated C's in Unknown context: 1253323 Total unmethylated C's in CpG context: 85052855 Total unmethylated C's in CHG context: 148962010 Total unmethylated C's in CHH context: 448757785 Total unmethylated C's in Unknown context: 4108572 C methylated in CpG context: 20.1% C methylated in CHG context: 3.8% C methylated in CHH context: 4.7% C methylated in unknown context (CN or CHN): 23.4% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF03-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF03-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF03-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 137327090 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1464329898 Total methylated C's in CpG context: 42838919 Total methylated C's in CHG context: 11647536 Total methylated C's in CHH context: 44584075 Total methylated C's in Unknown context: 2508195 Total unmethylated C's in CpG context: 170100170 Total unmethylated C's in CHG context: 297885534 Total unmethylated C's in CHH context: 897273664 Total unmethylated C's in Unknown context: 8216535 C methylated in CpG context: 20.1% C methylated in CHG context: 3.8% C methylated in CHH context: 4.7% C methylated in unknown context (CN or CHN): 23.4% Deleting temporary report files... Bismark completed in 0d 5h 22m 20s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 31384 and offset 2 (sequences written out: 78618344) Using the subset file >EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 78618345) Using the subset file >EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 31384 and offset 2 (sequences written out: 78618344) Using the subset file >EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 78618345) Using the subset file >EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (78618345 sequences in total) Writing a C -> T converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (78618344 sequences in total) Writing a C -> T converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (78618345 sequences in total) Input files are EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (78618344 sequences in total) Input files are EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 ANGTTGAAATTGGTTTATTAGTTTTGGATAAGAAGATTTTTTATTTTTTAATGTTTTAATTTTATATATAAGTTTTTAGAATGATTTAAATTTTTTTTTTTTTTTTGTATTTTTTTGTTTTTTTTTTATTAAATTTTTTTTAGGTATTGT F#FFFFF:FFFFFFFFFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAATTAATAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAACATTAAAAAATAAAAAAAAATAATATACAAAACAAATAAAACAAATTAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TNTTGTTTTTTTGATTTGATTAATATTAAATTTTTATAAAATATTATATT F#FFFFF::FFFFFFF,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AATATAATATTTTATAAAAATTTAATATTAATCAAATCAAAAAAACAAAA FFF,F:FFFFFFFF:,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CNCTACTCTTCCAATCTAATCAATATTAAATTTCCACAAAACACTACACC F#FFFFF::FFFFFFF,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 GGTGTAGTGTTTTGTGGAAATTTAATATTGATTAGATTGGAAGAGTAGGG FFF,F:FFFFFFFF:,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 ANATTAAAATTAATTCATTAATTTTAAATAAAAAAATTTTTTATTTTTTAATATTTTAATTTTATATATAAATTTTTAAAATAATTTAAATTTTTTTTTTTTTTTTATATTTTTTTATTTTTTTTTTATTAAATTTTTTTTAAATATTAC F#FFFFF:FFFFFFFFFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAATTAATAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAATATTAAAAAATAAAAAAAAATAATATATAAAATAAATGAAATAAATTAAAAAAAGAAAGGAAGAAG FFFFFFFFFFFFFFFFFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 ANATTAAAATTAATTCATTAATTTTAAATAAAAAAATTTTTTATTTTTTAATATTTTAATTTTATATATAAATTTTTAAAATAATTTAAATTTTTTTTTTTTTTTTATATTTTTTTATTTTTTTTTTATTAAATTTTTTTTAAATATTAC F#FFFFF:FFFFFFFFFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAATTAATAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAATATTAAAAAATAAAAAAAAATAATATATAAAATAAATGAAATAAATTAAAAAAAGAAAGGAAGAAG FFFFFFFFFFFFFFFFFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 CNCTACTCTTCCAATCTAATCAATATTAAATTTCCACAAAACACTACACC F#FFFFF::FFFFFFF,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 GGTGTAGTGTTTTGTGGAAATTTAATATTGATTAGATTGGAAGAGTAGGG FFF,F:FFFFFFFF:,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28076:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 ANGTTGAAATTGGTTTATTAGTTTTGGATAAGAAGATTTTTTATTTTTTAATGTTTTAATTTTATATATAAGTTTTTAGAATGATTTAAATTTTTTTTTTTTTTTTGTATTTTTTTGTTTTTTTTTTATTAAATTTTTTTTAGGTATTGT F#FFFFF:FFFFFFFFFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFF:FF:FFFFFF:F,:F:::FFF:,FFFFFFFFFF::FFF,FFF:,,,,,,,,F,,,: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28076:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AAAAATTAATAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAATAATTAAAAAAAAATATATAAAAAAATAAAACATTAAAAAATAAAAAAAAATAATATACAAAACAAATAAAACAAATTAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFFFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFF,FF,FF,,F,F,,FFFFFF,::,F,F,FFFF,F:FFF,F,F,FFFFF,FFFFFF,:,F,,,,,:,:FFF,,FF,:FFFFFF,,FFFF:,:F,,,,,:FF,,,, YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27010:1047_1:N:0:CAAGCTAG+CGCTATGT/1 77 * 0 0 * * 0 0 TNTTGTTTTTTTGATTTGATTAATATTAAATTTTTATAAAATATTATATT F#FFFFF::FFFFFFF,:FFFFF:FF:FFF,,,FFFFFFFFFF,FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27010:1047_2:N:0:CAAGCTAG+CGCTATGT/2 141 * 0 0 * * 0 0 AATATAATATTTTATAAAAATTTAATATTAATCAAATCAAAAAAACAAAA FFF,F:FFFFFFFF:,FFFFF,FFFFFFFFFF:FFFFFF:FF,FF:FFF: YT:Z:UP >>> Writing bisulfite mapping results to EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1154:23502:8656_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17200 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1258:4408:29199_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1267:12843:2534_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1267:11894:2957_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 3 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1345:8648:21605_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17146 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1511:21531:13917_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17165 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1537:30870:34632_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2122:15863:13745_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17154 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2443:14615:13870_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2443:16486:11600_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17161 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2511:21820:5181_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17165 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2617:14199:34820_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2617:14326:34820_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2619:17553:11537_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2677:29532:10050_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17176 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1157:1931:23281_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1168:24840:9283_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17179 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1506:6253:17394_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17161 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1552:3712:22576_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1569:15971:31908_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 3 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1572:16857:5854_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 3 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1645:2311:19366_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1645:2266:16845_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2104:12418:1329_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17161 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2113:8278:5337_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17173 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2113:8223:5400_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17173 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2112:8938:26991_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17173 Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2132:16622:25363_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 1 Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2237:21847:36980_1:N:0:CAAGCTAG+CGCGATGT NC_007175.2 17163 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2253:18014:19445_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17131 Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2325:21441:29512_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2325:21423:34491_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2325:21323:29496_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2471:13648:14544_1:N:0:CAAGCTAG+CGCTATGT NC_007175.2 17163 Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2576:16052:27477_1:N:0:CAAGCTAG+CGCTATGT NC_035780.1 2 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 78000000 sequence pairs so far 78618345 reads; of these: 78618345 (100.00%) were paired; of these: 74859544 (95.22%) aligned concordantly 0 times 1693372 (2.15%) aligned concordantly exactly 1 time 2065429 (2.63%) aligned concordantly >1 times 4.78% overall alignment rate 78618345 reads; of these: 78618345 (100.00%) were paired; of these: 75032122 (95.44%) aligned concordantly 0 times 1632084 (2.08%) aligned concordantly exactly 1 time 1954139 (2.49%) aligned concordantly >1 times 4.56% overall alignment rate 78618345 reads; of these: 78618345 (100.00%) were paired; of these: 74865012 (95.23%) aligned concordantly 0 times 1700033 (2.16%) aligned concordantly exactly 1 time 2053300 (2.61%) aligned concordantly >1 times 4.77% overall alignment rate 78618345 reads; of these: 78618345 (100.00%) were paired; of these: 75033678 (95.44%) aligned concordantly 0 times 1625331 (2.07%) aligned concordantly exactly 1 time 1959336 (2.49%) aligned concordantly >1 times 4.56% overall alignment rate Processed 78618345 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 314473380. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 314473380. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 314473380. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 314473380. Successfully deleted the temporary files EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 78618345 Final Cytosine Methylation Report ================================= Total number of C's analysed: 168006467 Total methylated C's in CpG context: 4026353 Total methylated C's in CHG context: 1664829 Total methylated C's in CHH context: 7018667 Total methylated C's in Unknown context: 451591 Total unmethylated C's in CpG context: 18622537 Total unmethylated C's in CHG context: 30552732 Total unmethylated C's in CHH context: 106121349 Total unmethylated C's in Unknown context: 1643076 C methylated in CpG context: 17.8% C methylated in CHG context: 5.2% C methylated in CHH context: 6.2% C methylated in unknown context (CN or CHN): 21.6% 78618344 reads; of these: 78618344 (100.00%) were paired; of these: 75033777 (95.44%) aligned concordantly 0 times 1627120 (2.07%) aligned concordantly exactly 1 time 1957447 (2.49%) aligned concordantly >1 times 4.56% overall alignment rate 78618344 reads; of these: 78618344 (100.00%) were paired; of these: 74859795 (95.22%) aligned concordantly 0 times 1693765 (2.15%) aligned concordantly exactly 1 time 2064784 (2.63%) aligned concordantly >1 times 4.78% overall alignment rate 78618344 reads; of these: 78618344 (100.00%) were paired; of these: 75035326 (95.44%) aligned concordantly 0 times 1633639 (2.08%) aligned concordantly exactly 1 time 1949379 (2.48%) aligned concordantly >1 times 4.56% overall alignment rate 78618344 reads; of these: 78618344 (100.00%) were paired; of these: 74864526 (95.23%) aligned concordantly 0 times 1700059 (2.16%) aligned concordantly exactly 1 time 2053759 (2.61%) aligned concordantly >1 times 4.77% overall alignment rate Processed 78618344 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 314473376. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 314473376. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 314473376. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 314473376. Successfully deleted the temporary files EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 78618344 Final Cytosine Methylation Report ================================= Total number of C's analysed: 167994343 Total methylated C's in CpG context: 4019103 Total methylated C's in CHG context: 1663596 Total methylated C's in CHH context: 7012007 Total methylated C's in Unknown context: 452302 Total unmethylated C's in CpG context: 18623246 Total unmethylated C's in CHG context: 30551090 Total unmethylated C's in CHH context: 106125301 Total unmethylated C's in Unknown context: 1647857 C methylated in CpG context: 17.8% C methylated in CHG context: 5.2% C methylated in CHH context: 6.2% C methylated in unknown context (CN or CHN): 21.5% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF04-EM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF04-EM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF04-EM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 157236689 Final Cytosine Methylation Report ================================= Total number of C's analysed: 336000810 Total methylated C's in CpG context: 8045456 Total methylated C's in CHG context: 3328425 Total methylated C's in CHH context: 14030674 Total methylated C's in Unknown context: 903893 Total unmethylated C's in CpG context: 37245783 Total unmethylated C's in CHG context: 61103822 Total unmethylated C's in CHH context: 212246650 Total unmethylated C's in Unknown context: 3290933 C methylated in CpG context: 17.8% C methylated in CHG context: 5.2% C methylated in CHH context: 6.2% C methylated in unknown context (CN or CHN): 21.5% Deleting temporary report files... Bismark completed in 0d 8h 53m 39s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 70518396) Using the subset file >EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 26163 and offset 2 (sequences written out: 70518396) Using the subset file >EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 70518396) Using the subset file >EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 26163 and offset 2 (sequences written out: 70518396) Using the subset file >EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (70518396 sequences in total) Writing a C -> T converted version of the input file EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (70518396 sequences in total) Writing a C -> T converted version of the input file EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (70518396 sequences in total) Input files are EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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 EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (70518396 sequences in total) Input files are EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27606:1047_1:N:0:CTTGGTAT+GGACTTGG/1 77 * 0 0 * * 0 0 TNTTATTTTATAATAAAATTAAAGGATTTAATTTTATTATAAAGTAGTGATTTAAGGGAGTGGATTAAAGGATTTAATTTTAATTAGATTGTTAATTTGT F#FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,FF:FFFFFFFFFF:FFFFFFFF:FFFFFFFFFF,:F:FFFFF:FFFFFFFFFF:FFFFFF:F,FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27606:1047_2:N:0:CTTGGTAT+GGACTTGG/2 141 * 0 0 * * 0 0 ACAAATTAACAATCTAATTAAAATTAAATCCTTTAATCCACTCCCTTAAATCACTACTTTATAATAAAATTAAATCCTTTAATTTTATTATAAAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF:FFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25979:1047_1:N:0:CTTGGTAT+GGACTTGG/1 77 * 0 0 * * 0 0 ANTAATGGGGAGTTATAGATTTTTTATGTGATAGTATAAATAGTGGTTTGATTATAGTTTGATTAAATTTTATTTAAAGATTTTTTTGTTAAGTTTGGTTGTAATTGGTTTAGTTATTTTGGTAAAGGAAATGAAAATGTGAAAAAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFF:FFFFFFFFF:FFFF:FFFFFFF,FFFFFF:FFFFFF:FFFFFFFFFF:FFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25979:1047_2:N:0:CTTGGTAT+GGACTTGG/2 141 * 0 0 * * 0 0 ATCAAAATTTAAATATAATCAAATAAAAAACCACTCTCCCTTTTAAATAATAAATTATTTAAATTAACAAAAATATAAAAATAATATCATAAATAAATTTTCTCCTAAAAATCAAACTTTTTCACTAAATCTCATATTTAAACTCATCCA FF:FFFFFFFFFFFF:FFFFFFFFFFFFFFF:F:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF,FF,FFFFF:FFFF,:F:FF:FFF:FFFF,FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27606:1047_1:N:0:CTTGGTAT+GGACTTGG/1 77 * 0 0 * * 0 0 CNCTACTTTATAATAAAATTAAAAAATTTAATTTTATTATAAAATAATAATTTAAAAAAATAAATTAAAAAATTTAATTTTAATTAAATTATTAATTTAT F#FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,FF:FFFFFFFFFF:FFFFFFFF:FFFFFFFFFF,:F:FFFFF:FFFFFFFFFF:FFFFFF:F,FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27606:1047_2:N:0:CTTGGTAT+GGACTTGG/2 141 * 0 0 * * 0 0 ATAAATTAATAATTTAATTAAAATTAAATTTTTTAATTTATTTTTTTAAATTATTATTTTATAATAAAATTAAATTTTTTAATTTTATTATAAAGTAGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF:FFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25979:1047_1:N:0:CTTGGTAT+GGACTTGG/1 77 * 0 0 * * 0 0 ANTAATAAAAAATTATAAATTTTTTATATAATAATATAAATAATAATTTAATTATAATTTAATTAAATTTTATTTAAAAATTTTTTTATTAAATTTAATTATAATTAATTTAATTATTTTAATAAAAAAAATAAAAATATAAAAAAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFF:FFFFFFFFF:FFFF:FFFFFFF,FFFFFF:FFFFFF:FFFFFFFFFF:FFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25979:1047_2:N:0:CTTGGTAT+GGACTTGG/2 141 * 0 0 * * 0 0 ATTAAAATTTAAATATAATTAAATAAAAAATTATTTTTTTTTTTAAATAATAAATTATTTAAATTAATAAAAATATAAAAATAATATTATAAATAAATTTTTTTTTAAAAATTGAATTTTTTTATTAAATTTTATATTTAAATTTATTTG FF:FFFFFFFFFFFF:FFFFFFFFFFFFFFF:F:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF,FF,FFFFF:FFFF,:F:FF:FFF:FFFF,FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27606:1047_1:N:0:CTTGGTAT+GGACTTGG/1 77 * 0 0 * * 0 0 CNCTACTTTATAATAAAATTAAAAAATTTAATTTTATTATAAAATAATAATTTAAAAAAATAAATTAAAAAATTTAATTTTAATTAAATTATTAATTTAT F#FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,FF:FFFFFFFFFF:FFFFFFFF:FFFFFFFFFF,:F:FFFFF:FFFFFFFFFF:FFFFFF:F,FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27606:1047_2:N:0:CTTGGTAT+GGACTTGG/2 141 * 0 0 * * 0 0 ATAAATTAATAATTTAATTAAAATTAAATTTTTTAATTTATTTTTTTAAATTATTATTTTATAATAAAATTAAATTTTTTAATTTTATTATAAAGTAGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF:FFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25979:1047_1:N:0:CTTGGTAT+GGACTTGG/1 77 * 0 0 * * 0 0 ANTAATAAAAAATTATAAATTTTTTATATAATAATATAAATAATAATTTAATTATAATTTAATTAAATTTTATTTAAAAATTTTTTTATTAAATTTAATTATAATTAATTTAATTATTTTAATAAAAAAAATAAAAATATAAAAAAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFF:FFFF:FFFFFFFFF:FFFF:FFFFFFF,FFFFFF:FFFFFF:FFFFFFFFFF:FFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25979:1047_2:N:0:CTTGGTAT+GGACTTGG/2 141 * 0 0 * * 0 0 ATTAAAATTTAAATATAATTAAATAAAAAATTATTTTTTTTTTTAAATAATAAATTATTTAAATTAATAAAAATATAAAAATAATATTATAAATAAATTTTTTTTTAAAAATTGAATTTTTTTATTAAATTTTATATTTAAATTTATTTG FF:FFFFFFFFFFFF:FFFFFFFFFFFFFFF:F:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF,FF,FFFFF:FFFF,:F:FF:FFF:FFFF,FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27606:1047_1:N:0:CTTGGTAT+GGACTTGG/1 77 * 0 0 * * 0 0 TNTTATTTTATAATAAAATTAAAGGATTTAATTTTATTATAAAGTAGTGATTTAAGGGAGTGGATTAAAGGATTTAATTTTAATTAGATTGTTAATTTGT F#FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,FF:FFFFFFFFFF:FFFFFFFF:FFFFFFFFFF,:F:FFFFF:FFFFFFFFFF:FFFFFF:F,FFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27606:1047_2:N:0:CTTGGTAT+GGACTTGG/2 141 * 0 0 * * 0 0 ACAAATTAACAATCTAATTAAAATTAAATCCTTTAATCCACTCCCTTAAATCACTACTTTATAATAAAATTAAATCCTTTAATTTTATTATAAAATAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF:FFFF,FF YT:Z:UP >>> Writing bisulfite mapping results to EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25979:1047_1:N:0:CTTGGTAT+GGACTTGG/1 83 NC_035785.1_GA_converted 37740619 24 134M1D16M = 37740383 -387 AAATTTTTTCACATTTTCATTTCCTTTACCAAAATAACTAAACCAATTACAACCAAACTTAACAAAAAAATCTTTAAATAAAATTTAATCAAACTATAATCAAACCACTATTTATACTATCACATAAAAAATCTATAACTCCCCATTANT FFFF:FFFFFFFFFF:FFFFFF:FFFFFF,FFFFFFF:FFFF:FFFFFFFFF:FFFF:FFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-33 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:2T61T3T27A37^A14C1 YS:i:-26 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25979:1047_2:N:0:CTTGGTAT+GGACTTGG/2 163 NC_035785.1_GA_converted 37740383 24 44M1D106M = 37740619 387 ATCAAAATTTAAATATAATCAAATAAAAAACCACTCTCCCTTTTAAATAATAAATTATTTAAATTAACAAAAATATAAAAATAATATCATAAATAAATTTTCTCCTAAAAATCAAACTTTTTCACTAAATCTCATATTTAAACTCATCCA FF:FFFFFFFFFFFF:FFFFFFFFFFFFFFF:F:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF,FF,FFFFF:FFFF,:F:FF:FFF:FFFF,FFFFFFFFFFF AS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A0A41^A101T4 YS:i:-33 YT:Z:CP >>> Writing bisulfite mapping results to EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1248:11107:10802_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1303:19895:20854_1:N:0:CTTGGTAT+GGACTTGG NC_035781.1 2 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1308:31901:28620_1:N:0:CTTGGTAT+AGACTTGG NC_007175.2 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1376:4707:21230_1:N:0:CTTGGTAT+AGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1409:21305:25582_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1452:6849:27633_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1521:8712:27884_1:N:0:CTTGGTAT+GGACTTGG NC_035784.1 1 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1564:28040:7560_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2139:11632:4476_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2301:14407:26788_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2301:14443:22279_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2402:6994:30138_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2409:17192:29888_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2409:18159:30624_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2410:21576:11115_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2501:14136:20181_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2575:16685:22842_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2642:9010:1407_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2652:9417:10629_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2652:9100:10958_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1108:26937:36714_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1112:30065:20776_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1112:30201:20854_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1174:1533:31516_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1216:7464:11224_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1235:25898:10113_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1307:1759:34851_1:N:0:CTTGGTAT+AGACTTGG NC_035780.1 2 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1333:11270:20697_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1362:26711:7545_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 3 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1420:19144:19241_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1420:19461:19413_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1439:7166:9142_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1455:29053:9408_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 3 Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1528:13621:15812_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1544:11849:21230_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1556:32877:33160_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1558:21974:28902_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1620:32714:12806_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 3 Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1656:1425:25066_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1661:6090:17519_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2104:15402:33739_1:N:0:CTTGGTAT+GGACTTGG NC_007175.2 2 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2131:7464:35650_1:N:0:CTTGGTAT+GGACTTGG NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2133:5204:27884_1:N:0:CTTGGTAT+GGACTTGG NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2135:26241:25770_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 3 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2218:5086:35603_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2236:23529:10426_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2254:25545:23187_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2308:31069:11177_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 3 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2317:19443:34788_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2344:27769:19366_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2357:2239:11068_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2442:27579:19977_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2516:25807:12555_1:N:0:CTTGGTAT+GGACTTGG NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2517:15329:6151_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2526:1660:30765_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2548:25455:23249_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 3 Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2621:17038:3474_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2637:29875:12743_1:N:0:CTTGGTAT+GGACTTGG NC_007175.2 17165 Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2677:6397:36370_1:N:0:CTTGGTAT+GGACTTGG NC_035780.1 2 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 57700132 (81.82%) aligned concordantly 0 times 5748483 (8.15%) aligned concordantly exactly 1 time 7069781 (10.03%) aligned concordantly >1 times 18.18% overall alignment rate 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 59056434 (83.75%) aligned concordantly 0 times 5160095 (7.32%) aligned concordantly exactly 1 time 6301867 (8.94%) aligned concordantly >1 times 16.25% overall alignment rate 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 57686181 (81.80%) aligned concordantly 0 times 5738832 (8.14%) aligned concordantly exactly 1 time 7093383 (10.06%) aligned concordantly >1 times 18.20% overall alignment rate 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 59037442 (83.72%) aligned concordantly 0 times 5151288 (7.30%) aligned concordantly exactly 1 time 6329666 (8.98%) aligned concordantly >1 times 16.28% overall alignment rate Processed 70518396 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 282073584. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 282073584. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 282073584. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 282073584. Successfully deleted the temporary files EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 70518396 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1061652867 Total methylated C's in CpG context: 27327244 Total methylated C's in CHG context: 3695924 Total methylated C's in CHH context: 14476009 Total methylated C's in Unknown context: 994816 Total unmethylated C's in CpG context: 131748969 Total unmethylated C's in CHG context: 223562397 Total unmethylated C's in CHH context: 660842324 Total unmethylated C's in Unknown context: 5013089 C methylated in CpG context: 17.2% C methylated in CHG context: 1.6% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 16.6% Now waiting for all child processes to complete 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 57685790 (81.80%) aligned concordantly 0 times 5734984 (8.13%) aligned concordantly exactly 1 time 7097622 (10.06%) aligned concordantly >1 times 18.20% overall alignment rate 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 59040725 (83.72%) aligned concordantly 0 times 5151203 (7.30%) aligned concordantly exactly 1 time 6326468 (8.97%) aligned concordantly >1 times 16.28% overall alignment rate 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 57700170 (81.82%) aligned concordantly 0 times 5746408 (8.15%) aligned concordantly exactly 1 time 7071818 (10.03%) aligned concordantly >1 times 18.18% overall alignment rate 70518396 reads; of these: 70518396 (100.00%) were paired; of these: 59058356 (83.75%) aligned concordantly 0 times 5158329 (7.31%) aligned concordantly exactly 1 time 6301711 (8.94%) aligned concordantly >1 times 16.25% overall alignment rate Processed 70518396 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 282073584. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 282073584. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 282073584. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 282073584. Successfully deleted the temporary files EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 70518396 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1060985348 Total methylated C's in CpG context: 27312651 Total methylated C's in CHG context: 3689849 Total methylated C's in CHH context: 14483732 Total methylated C's in Unknown context: 992565 Total unmethylated C's in CpG context: 131660572 Total unmethylated C's in CHG context: 223378624 Total unmethylated C's in CHH context: 660459920 Total unmethylated C's in Unknown context: 5013717 C methylated in CpG context: 17.2% C methylated in CHG context: 1.6% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 16.5% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF04-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF04-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF04-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 141036792 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2122638215 Total methylated C's in CpG context: 54639895 Total methylated C's in CHG context: 7385773 Total methylated C's in CHH context: 28959741 Total methylated C's in Unknown context: 1987381 Total unmethylated C's in CpG context: 263409541 Total unmethylated C's in CHG context: 446941021 Total unmethylated C's in CHH context: 1321302244 Total unmethylated C's in Unknown context: 10026806 C methylated in CpG context: 17.2% C methylated in CHG context: 1.6% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 16.5% Deleting temporary report files... Bismark completed in 0d 15h 24m 29s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 24706 and offset 2 (sequences written out: 53242710) Using the subset file >EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 53242711) Using the subset file >EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 24706 and offset 2 (sequences written out: 53242710) Using the subset file >EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 53242711) Using the subset file >EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (53242710 sequences in total) Writing a C -> T converted version of the input file EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (53242711 sequences in total) Writing a C -> T converted version of the input file EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (53242710 sequences in total) Input files are EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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 EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (53242711 sequences in total) Input files are EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30246:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 GNGTTTAATTTGAATGTTTTTTTATTTATTATAAAAAATTAAAAATTTAATTATTTTATAAAAATATTAAATTTATGATTTATGGATTATTATGAATAAAGATGATATTTTTAAATAAAAAGAG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30246:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 CTCTTTTTATTTAAAAATATCATCTTTATTCATAATAATCCATAAATCATAAATTTAATATTTTTATAAAATAATTAAATTTTTAATTTTTTATAATAAATAAAAAAACATTCAAATTAAACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,:F:FF:FFF::FFFF:FFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28402:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 ANTTAAAATTATTAATTATTTAAATAAAAATTATATTAATAATAAAATTAATTTAATTATAATTTTTTTTAATTTATTAATATTTATTAATAATAATTTAATTTTAAATAAAATTATTAATATATTAATATATAATTTAATTTATTAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28402:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 CAACCCATCTTATTAATTTAATAAATTAAATTATATATTAATATATTAATAATTTTATTTAAAATTAAATTATTATTAATAAATATTAATAAATTAAAAAAAATTATAATTAAATTAATTTTATTATTAATATAATTTTTATTTAAATAA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFFFFFF:FFFFF::F,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFF:FF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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)) Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30246:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 ANATTCAACTCAAACATTTCCTTATCTACCACAAAAAACCAAAAATTTAATTATCTTATAAAAATATCAAATTTATAATTTATAAATTATTATAAATAAAAATAATATTTTTAAATAAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30246:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 TTTTTTTTATTTAAAAATATTATTTTTATTTATAATAATTTATAAATTATAAATTTGATATTTTTATAAGATAATTAAATTTTTGGTTTTTTGTGGTAGATAAGGAAATGTTTGAGTTGAATGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,:F:FF:FFF::FFFF:FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28402:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 ANCCAAAACCATCAACCACCTAAATAAAAACTACATCAACAACAAAATTAACCTAATCACAACCTTCCTCAACCCACTAACATTCACCAACAACAACCCAACCCCAAACAAAACCACCAACACACTAACACACAACCTAACCCATCAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28402:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 TAATTTATTTTATTGATTTGATGGGTTAGGTTGTGTGTTAGTGTGTTGGTGGTTTTGTTTGGGGTTGGGTTGTTGTTGGTGAATGTTAGTGGGTTGAGGAAGGTTGTGATTAGGTTAATTTTGTTGTTGATGTAGTTTTTATTTAGGTGG FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFFFFFF:FFFFF::F,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFF:FF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:28402:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 ANCCAAAACCATCAACCACCTAAATAAAAACTACATCAACAACAAAATTAACCTAATCACAACCTTCCTCAACCCACTAACATTCACCAACAACAACCCAACCCCAAACAAAACCACCAACACACTAACACACAACCTAACCCATCAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28402:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 TAATTTATTTTATTGATTTGATGGGTTAGGTTGTGTGTTAGTGTGTTGGTGGTTTTGTTTGGGGTTGGGTTGTTGTTGGTGAATGTTAGTGGGTTGAGGAAGGTTGTGATTAGGTTAATTTTGTTGTTGATGTAGTTTTTATTTAGGTGG FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFFFFFF:FFFFF::F,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFF:FF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30246:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 ANATTCAACTCAAACATTTCCTTATCTACCACAAAAAACCAAAAATTTAATTATCTTATAAAAATATCAAATTTATAATTTATAAATTATTATAAATAAAAATAATATTTTTAAATAAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30246:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 TTTTTTTTATTTAAAAATATTATTTTTATTTATAATAATTTATAAATTATAAATTTGATATTTTTATAAGATAATTAAATTTTTGGTTTTTTGTGGTAGATAAGGAAATGTTTGAGTTGAATGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,:F:FF:FFF::FFFF:FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:30246:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 GNGTTTAATTTGAATGTTTTTTTATTTATTATAAAAAATTAAAAATTTAATTATTTTATAAAAATATTAAATTTATGATTTATGGATTATTATGAATAAAGATGATATTTTTAAATAAAAAGAG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:30246:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 CTCTTTTTATTTAAAAATATCATCTTTATTCATAATAATCCATAAATCATAAATTTAATATTTTTATAAAATAATTAAATTTTTAATTTTTTATAATAAATAAAAAAACATTCAAATTAAACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,:F:FF:FFF::FFFF:FFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:28402:1047_1:N:0:CCGCGGTT+CTAGCGCT/1 77 * 0 0 * * 0 0 ANTTAAAATTATTAATTATTTAAATAAAAATTATATTAATAATAAAATTAATTTAATTATAATTTTTTTTAATTTATTAATATTTATTAATAATAATTTAATTTTAAATAAAATTATTAATATATTAATATATAATTTAATTTATTAAAT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:28402:1047_2:N:0:CCGCGGTT+CTAGCGCT/2 141 * 0 0 * * 0 0 CAACCCATCTTATTAATTTAATAAATTAAATTATATATTAATATATTAATAATTTTATTTAAAATTAAATTATTATTAATAAATATTAATAAATTAAAAAAAATTATAATTAAATTAATTTTATTATTAATATAATTTTTATTTAAATAA FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFFFFFF:FFFFF::F,FFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFF:FF:FFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Reading in the sequence files EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1503:4670:12868_1:N:0:CCGCGGTT+CTCGCGCT NC_007175.2 17163 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1517:10438:36980_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1623:16785:20071_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1623:15067:25300_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1636:4942:35947_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1643:1624:14857_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1664:29930:9486_1:N:0:CCGCGGTT+CTAGCGCT NC_007175.2 17099 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2567:8133:10567_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2567:10646:17331_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1151:19235:26600_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 3 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1212:9815:4116_1:N:0:CCGCGGTT+CTAGCGCT NC_007175.2 17161 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1513:24523:21793_1:N:0:CCGCGGTT+CTAGCGCT NC_035781.1 3 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1566:7238:27430_1:N:0:CCGCGGTT+CTAGCGCT NC_035781.1 2 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1674:14534:16172_1:N:0:CCGCGGTT+GTAGCGCT NC_035780.1 2 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2145:9941:28197_1:N:0:CCGCGGTT+CTAGCGCT NC_007175.2 17163 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2273:21603:31109_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2353:23131:12305_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2353:24523:27837_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2548:22309:27946_1:N:0:CCGCGGTT+CTAGCGCT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2558:21549:1110_1:N:0:CCGCGGTT+CTAGCGCT NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far 53242710 reads; of these: 53242710 (100.00%) were paired; of these: 45663917 (85.77%) aligned concordantly 0 times 532427103399164 reads; of these: ( 6.38 %53242710) aligned concordantly exactly 1 time ( 4179629 (7.85%) aligned concordantly >1 times100.00 %14.23) were paired; of these:% overall alignment rate 45682030 (85.80%) aligned concordantly 0 times 3405697 (6.40%) aligned concordantly exactly 1 time 4154983 (7.80%) aligned concordantly >1 times 14.20% overall alignment rate 53242710 reads; of these: 53242710 (100.00%) were paired; of these: 46078248 (86.54%) aligned concordantly 0 times 3240800 (6.09%) aligned concordantly exactly 1 time 3923662 (7.37%) aligned concordantly >1 times 13.46% overall alignment rate 53242710 reads; of these: 53242710 (100.00%) were paired; of these: 46094237 (86.57%) aligned concordantly 0 times 3248548 (6.10%) aligned concordantly exactly 1 time 3899925 (7.32%) aligned concordantly >1 times 13.43% overall alignment rate Processed 53242710 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 212970840. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 212970840. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 212970840. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 212970840. Successfully deleted the temporary files EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 53242710 Final Cytosine Methylation Report ================================= Total number of C's analysed: 614407068 Total methylated C's in CpG context: 18013292 Total methylated C's in CHG context: 3058470 Total methylated C's in CHH context: 11649587 Total methylated C's in Unknown context: 1039018 Total unmethylated C's in CpG context: 76188129 Total unmethylated C's in CHG context: 130257417 Total unmethylated C's in CHH context: 375240173 Total unmethylated C's in Unknown context: 3205967 C methylated in CpG context: 19.1% C methylated in CHG context: 2.3% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 24.5% Now waiting for all child processes to complete 53242711 reads; of these: 53242711 (100.00%) were paired; of these: 45663716 (85.77%) aligned concordantly 0 times 3399310 (6.38%) aligned concordantly exactly 1 time 4179685 (7.85%) aligned concordantly >1 times 14.23% overall alignment rate 53242711 reads; of these: 53242711 (100.00%) were paired; of these: 45681506 (85.80%) aligned concordantly 0 times 3406028 (6.40%) aligned concordantly exactly 1 time 4155177 (7.80%) aligned concordantly >1 times 14.20% overall alignment rate 53242711 reads; of these: 53242711 (100.00%) were paired; of these: 46091669 (86.57%) aligned concordantly 0 times 3245835 (6.10%) aligned concordantly exactly 1 time 3905207 (7.33%) aligned concordantly >1 times 13.43% overall alignment rate 53242711 reads; of these: 53242711 (100.00%) were paired; of these: 46070117 (86.53%) aligned concordantly 0 times 3243546 (6.09%) aligned concordantly exactly 1 time 3929048 (7.38%) aligned concordantly >1 times 13.47% overall alignment rate Processed 53242711 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 212970844. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 212970844. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 212970844. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 212970844. Successfully deleted the temporary files EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 53242711 Final Cytosine Methylation Report ================================= Total number of C's analysed: 614683222 Total methylated C's in CpG context: 18020339 Total methylated C's in CHG context: 3060788 Total methylated C's in CHH context: 11630617 Total methylated C's in Unknown context: 1037399 Total unmethylated C's in CpG context: 76275844 Total unmethylated C's in CHG context: 130306729 Total unmethylated C's in CHH context: 375388905 Total unmethylated C's in Unknown context: 3209194 C methylated in CpG context: 19.1% C methylated in CHG context: 2.3% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 24.4% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF05-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF05-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF05-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 106485421 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1229090290 Total methylated C's in CpG context: 36033631 Total methylated C's in CHG context: 6119258 Total methylated C's in CHH context: 23280204 Total methylated C's in Unknown context: 2076417 Total unmethylated C's in CpG context: 152463973 Total unmethylated C's in CHG context: 260564146 Total unmethylated C's in CHH context: 750629078 Total unmethylated C's in Unknown context: 6415161 C methylated in CpG context: 19.1% C methylated in CHG context: 2.3% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 24.5% Deleting temporary report files... Bismark completed in 0d 5h 33m 59s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 43829 and offset 2 (sequences written out: 60738863) Using the subset file >EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 60738863) Using the subset file >EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 43829 and offset 2 (sequences written out: 60738863) Using the subset file >EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 60738863) Using the subset file >EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (60738863 sequences in total) Writing a C -> T converted version of the input file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (60738863 sequences in total) Writing a C -> T converted version of the input file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (60738863 sequences in total) Input files are EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (60738863 sequences in total) Input files are EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 TNTTGATTATTATGAAGGTGATGTTTTTAAAAATTAAGTTTTGAAGAAGGGTAGTATTTAAAGTAGAAGGTTTTGGGGTGTGTGATATGAAATGAAGTATTGGTTGTAAGTGTGATTTTGGATTAGTTGTTAATGTGTTAATTGTGGGGG F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 TTTAACTTTAATAATATATAACAATTATAATCCTAAACAAAAACCCCCCACAATTAACACATTAACAACTAATCCAAAATCACACTTACAACCAATACTTCATTTCATATCACACACCCCAAAACCTTCTACTTTAAATACTACCCTTCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25852:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 TNATAAAAAAAAAATTTAATATTAATATTAAAATTATTTTTATAAAAATAATTAATATATATT F#FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25852:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 AATATATATTAATTATTTTTATAAAAATAATTTTAATATTAATATTAAATTTTTTTTTTATAA FFFFFFFF:FFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 CNTTAATTATTATAAAAATAATATTTTTAAAAATTAAATTTTAAAAAAAAATAATATTTAAAATAAAAAATTTTAAAATATATAATATAAAATAAAATATTAATTATAAATATAATTCTAAATTAATTATTAATATATTAATTATAAAAA F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 TTTAATTTTAATAATATATAATAATTATAATTTTAAATAAAAATTTTTTATAATTAATATATTAATAATTAATTTAGAATTATATTTATAATTAATATTTTATTTTATATTATATATTTTAAAATTTTTTATTTTAAATATTATTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25852:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 TNACAAAAAAAAAATTTAATATTAATATCAAAATCACCTTTACAAAAACAACCAATACACACC F#FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25852:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 GGTGTGTATTGGTTGTTTTTGTAAAGGTGATTTTGATATTAATATTAAATTTTTTTTTTGTAA FFFFFFFF:FFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 CNTTAATTATTATAAAAATAATATTTTTAAAAATTAAATTTTAAAAAAAAATAATATTTAAAATAAAAAATTTTAAAATATATAATATAAAATAAAATATTAATTATAAATATAATTCTAAATTAATTATTAATATATTAATTATAAAAA F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 TTTAATTTTAATAATATATAATAATTATAATTTTAAATAAAAATTTTTTATAATTAATATATTAATAATTAATTTAGAATTATATTTATAATTAATATTTTATTTTATATTATATATTTTAAAATTTTTTATTTTAAATATTATTTTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25852:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 TNACAAAAAAAAAATTTAATATTAATATCAAAATCACCTTTACAAAAACAACCAATACACACC F#FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25852:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 GGTGTGTATTGGTTGTTTTTGTAAAGGTGATTTTGATATTAATATTAAATTTTTTTTTTGTAA FFFFFFFF:FFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 TNTTGATTATTATGAAGGTGATGTTTTTAAAAATTAAGTTTTGAAGAAGGGTAGTATTTAAAGTAGAAGGTTTTGGGGTGTGTGATATGAAATGAAGTATTGGTTGTAAGTGTGATTTTGGATTAGTTGTTAATGTGTTAATTGTGGGGG F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 TTTAACTTTAATAATATATAACAATTATAATCCTAAACAAAAACCCCCCACAATTAACACATTAACAACTAATCCAAAATCACACTTACAACCAATACTTCATTTCATATCACACACCCCAAAACCTTCTACTTTAAATACTACCCTTCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25852:1047_1:N:0:AAGTCCAA+TACTCATA/1 77 * 0 0 * * 0 0 TNATAAAAAAAAAATTTAATATTAATATTAAAATTATTTTTATAAAAATAATTAATATATATT F#FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25852:1047_2:N:0:AAGTCCAA+TACTCATA/2 141 * 0 0 * * 0 0 AATATATATTAATTATTTTTATAAAAATAATTTTAATATTAATATTAAATTTTTTTTTTATAA FFFFFFFF:FFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Reading in the sequence files EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1210:30870:24079_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17123 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1343:16152:7921_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 1 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1523:12572:29465_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17184 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2137:15176:14873_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17164 Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2334:32515:2002_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17199 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2334:31566:3270_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17199 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2403:28673:10128_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17177 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2444:30427:32863_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17199 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2547:31702:9142_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17179 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1378:6551:1438_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17169 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1667:25102:32534_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 2 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2130:4200:26553_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17199 Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2343:13910:5384_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17193 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2344:6081:30968_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17193 Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:31485:1376_1:N:0:AAGTCCAA+TACTCATA NC_007175.2 17177 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2646:4580:30718_1:N:0:AAGTCCAA+TACTCATA NC_035780.1 2 Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58326330 (96.03%) aligned concordantly 0 times 1043477 (1.72%) aligned concordantly exactly 1 time 1369056 (2.25%) aligned concordantly >1 times 3.97% overall alignment rate 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58149372 (95.74%) aligned concordantly 0 times 1125608 (1.85%) aligned concordantly exactly 1 time 1463883 (2.41%) aligned concordantly >1 times 4.26% overall alignment rate 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58144734 (95.73%) aligned concordantly 0 times 1128479 (1.86%) aligned concordantly exactly 1 time 1465650 (2.41%) aligned concordantly >1 times 4.27% overall alignment rate 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58331057 (96.04%) aligned concordantly 0 times 1038918 (1.71%) aligned concordantly exactly 1 time 1368888 (2.25%) aligned concordantly >1 times 3.96% overall alignment rate Processed 60738863 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 242955452. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 242955452. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 242955452. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 242955452. Successfully deleted the temporary files EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 60738863 Final Cytosine Methylation Report ================================= Total number of C's analysed: 99015892 Total methylated C's in CpG context: 1694975 Total methylated C's in CHG context: 447393 Total methylated C's in CHH context: 2754172 Total methylated C's in Unknown context: 129463 Total unmethylated C's in CpG context: 11206931 Total unmethylated C's in CHG context: 18028356 Total unmethylated C's in CHH context: 64884065 Total unmethylated C's in Unknown context: 938877 C methylated in CpG context: 13.1% C methylated in CHG context: 2.4% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 12.1% 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58147688 (95.73%) aligned concordantly 0 times 1124496 (1.85%) aligned concordantly exactly 1 time 1466679 (2.41%) aligned concordantly >1 times 4.27% overall alignment rate 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58328101 (96.03%) aligned concordantly 0 times 1039568 (1.71%) aligned concordantly exactly 1 time 1371194 (2.26%) aligned concordantly >1 times 3.97% overall alignment rate 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58142621 (95.73%) aligned concordantly 0 times 1129423 (1.86%) aligned concordantly exactly 1 time 1466819 (2.41%) aligned concordantly >1 times 4.27% overall alignment rate 60738863 reads; of these: 60738863 (100.00%) were paired; of these: 58323391 (96.02%) aligned concordantly 0 times 1045571 (1.72%) aligned concordantly exactly 1 time 1369901 (2.26%) aligned concordantly >1 times 3.98% overall alignment rate Processed 60738863 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 242955452. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 242955452. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 242955452. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 242955452. Successfully deleted the temporary files EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 60738863 Final Cytosine Methylation Report ================================= Total number of C's analysed: 99042010 Total methylated C's in CpG context: 1696893 Total methylated C's in CHG context: 445960 Total methylated C's in CHH context: 2761343 Total methylated C's in Unknown context: 130547 Total unmethylated C's in CpG context: 11210457 Total unmethylated C's in CHG context: 18035319 Total unmethylated C's in CHH context: 64892038 Total unmethylated C's in Unknown context: 939571 C methylated in CpG context: 13.1% C methylated in CHG context: 2.4% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 12.2% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF05-EM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF05-EM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF05-EM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 121477726 Final Cytosine Methylation Report ================================= Total number of C's analysed: 198057902 Total methylated C's in CpG context: 3391868 Total methylated C's in CHG context: 893353 Total methylated C's in CHH context: 5515515 Total methylated C's in Unknown context: 260010 Total unmethylated C's in CpG context: 22417388 Total unmethylated C's in CHG context: 36063675 Total unmethylated C's in CHH context: 129776103 Total unmethylated C's in Unknown context: 1878448 C methylated in CpG context: 13.1% C methylated in CHG context: 2.4% C methylated in CHH context: 4.1% C methylated in unknown context (CN or CHN): 12.2% Deleting temporary report files... Bismark completed in 0d 3h 45m 38s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 99385432) Using the subset file >EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 8248 and offset 2 (sequences written out: 99385431) Using the subset file >EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 8248 and offset 2 (sequences written out: 99385431) Using the subset file >EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 99385432) Using the subset file >EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (99385432 sequences in total) Writing a C -> T converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (99385431 sequences in total) Writing a C -> T converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (99385432 sequences in total) Input files are EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (99385431 sequences in total) Input files are EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 ANTATAATAAAAATTTTTTTATTAATATTAATATTAATAAAATTATAATTTTAAATATTTTAATTAAAATATATTAATAAATTATTTTATTATTTTATTATTTAAATTTATGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 CCATAAATTTAAATAATAAAATAATAAAATAATTTATTAATATATTTTAATTAAAATATTTAAAATTATAATTTTATTAATATTAATATTAATAAAAAAATTTTTATTATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TNTGGTGTTTTTATATGATATTATTGAATATATTTTATGTATGTATTTGTTTAATATTATTAAAATTTATGTTTGTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 AACAAACATAAATTTTAATAATATTAAACAAATACATACATAAAATATATTCAATAATATCATATAAAAACACCAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 99 NC_035784.1_GA_converted 20135244 1 113M = 20135244 113 ANTATAATAAAAACCCCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-13 XS:i:-13 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1T108T1T0 YS:i:-12 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 147 NC_035784.1_GA_converted 20135244 1 113M = 20135244 -113 ATTATAATAAAAACCCCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:110T1T0 YS:i:-13 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TNTAATATTTTTATATAATATTATTAAATATATTTTATATATATATTTATTTAATATTATTAAAATTTATATTTACC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 GGTAAATATAAATTTTAATAATATTAAATAAATATATATATAAAATATATTTAATAATATTATATAAAAATATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 ANTATAATAAAAACCCCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 TTGTAGGTTTAGATAATAAAGTAATAAAGTAGTTTGTTGGTGTGTTTTAGTTGAAATGTTTAGAGTTGTGATTTTATTAATGTTAATATTAATGGAGGGGTTTTTATTATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 TNTAATATTTTTATATAATATTATTAAATATATTTTATATATATATTTATTTAATATTATTAAAATTTATATTTACC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 GGTAAATATAAATTTTAATAATATTAAATAAATATATATATAAAATATATTTAATAATATTATATAAAAATATTAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1 77 * 0 0 * * 0 0 ANTATAATAAAAATTTTTTTATTAATATTAATATTAATAAAATTATAATTTTAAATATTTTAATTAAAATATATTAATAAATTATTTTATTATTTTATTATTTAAATTTATGG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2 141 * 0 0 * * 0 0 CCATAAATTTAAATAATAAAATAATAAAATAATTTATTAATATATTTTAATTAAAATATTTAAAATTATAATTTTATTAATATTAATATTAATAAAAAAATTTTTATTATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:29035:1047_1:N:0:TTACAGGA+GCTTGTCA/1 83 NC_035788.1_GA_converted 21798571 1 77M = 21798571 -77 AACAAACATAAATTTTAATAATATTAAACAAATACATACATAAAATATATTCAATAATATCATATAAAAACACCANA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-7 XS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0T74A1 YS:i:-6 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:29035:1047_2:N:0:TTACAGGA+GCTTGTCA/2 163 NC_035788.1_GA_converted 21798571 1 77M = 21798571 77 AACAAACATAAATTTTAATAATATTAAACAAATACATACATAAAATATATTCAATAATATCATATAAAAACACCAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F::FFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0T76 YS:i:-7 YT:Z:CP >>> Writing bisulfite mapping results to EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1234:3586:1689_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17121 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1677:32027:21136_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1677:31855:21339_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2251:28971:18192_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2406:23827:33708_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:25247:16877_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:23348:13808_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2543:25192:17065_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1115:8856:12320_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17121 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1121:8061:20494_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1121:8260:24439_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1168:31584:9878_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1332:23863:32330_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17112 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1378:31548:21371_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 1 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1419:18285:9298_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1511:11595:33661_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 65668288 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1608:29378:20619_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1647:31792:35164_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1647:32976:22467_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2244:19045:7294_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 75000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2311:14253:31939_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 78000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2430:10728:26772_1:N:0:TTACAGGA+GCTTGTCA NC_007175.2 17121 Processed 85000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2511:11939:31939_1:N:0:TTACAGGA+GCTGGTCA NC_035780.1 65668288 Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2517:8024:22279_1:N:0:TTACAGGA+GCTTGTCA NC_035780.1 2 Processed 90000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 99000000 sequence pairs so far 99385432 reads; of these: 99385432 (100.00%) were paired; of these: 83138012 (83.65%) aligned concordantly 0 times 7545455 (7.59%) aligned concordantly exactly 1 time 8701965 (8.76%) aligned concordantly >1 times 16.35% overall alignment rate 99385432 reads; of these: 99385432 (100.00%) were paired; of these: 84302169 (84.82%) aligned concordantly 0 times 7040443 (7.08%) aligned concordantly exactly 1 time 8042820 (8.09%) aligned concordantly >1 times 15.18% overall alignment rate 99385432 reads; of these: 99385432 (100.00%) were paired; of these: 83127603 (83.64%) aligned concordantly 0 times 7528580 (7.58%) aligned concordantly exactly 1 time 8729249 (8.78%) aligned concordantly >1 times 16.36% overall alignment rate 99385432 reads; of these: 99385432 (100.00%) were paired; of these: 84302314 (84.82%) aligned concordantly 0 times 7014824 (7.06%) aligned concordantly exactly 1 time 8068294 (8.12%) aligned concordantly >1 times 15.18% overall alignment rate Processed 99385432 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 397541728. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 397541728. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 397541728. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 397541728. Successfully deleted the temporary files EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 99385432 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1520086795 Total methylated C's in CpG context: 42199311 Total methylated C's in CHG context: 14928152 Total methylated C's in CHH context: 59010591 Total methylated C's in Unknown context: 1801712 Total unmethylated C's in CpG context: 170696530 Total unmethylated C's in CHG context: 287173577 Total unmethylated C's in CHH context: 946078634 Total unmethylated C's in Unknown context: 6873350 C methylated in CpG context: 19.8% C methylated in CHG context: 4.9% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 20.8% 99385431 reads; of these: 99385431 (100.00%) were paired; of these: 84309149 (84.83%) aligned concordantly 0 times 7033458 (7.08%) aligned concordantly exactly 1 time 8042824 (8.09%) aligned concordantly >1 times 15.17% overall alignment rate 99385431 reads; of these: 99385431 (100.00%) were paired; of these: 83140512 (83.65%) aligned concordantly 0 times 7545542 (7.59%) aligned concordantly exactly 1 time 8699377 (8.75%) aligned concordantly >1 times 16.35% overall alignment rate 99385431 reads; of these: 99385431 (100.00%) were paired; of these: 84306153 (84.83%) aligned concordantly 0 times 7008263 (7.05%) aligned concordantly exactly 1 time 8071015 (8.12%) aligned concordantly >1 times 15.17% overall alignment rate 99385431 reads; of these: 99385431 (100.00%) were paired; of these: 83124944 (83.64%) aligned concordantly 0 times 7530967 (7.58%) aligned concordantly exactly 1 time 8729520 (8.78%) aligned concordantly >1 times 16.36% overall alignment rate Processed 99385431 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 397541724. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 397541724. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 397541724. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 397541724. Successfully deleted the temporary files EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 99385431 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1519949808 Total methylated C's in CpG context: 42190970 Total methylated C's in CHG context: 14928535 Total methylated C's in CHH context: 59071191 Total methylated C's in Unknown context: 1802075 Total unmethylated C's in CpG context: 170687532 Total unmethylated C's in CHG context: 287095187 Total unmethylated C's in CHH context: 945976393 Total unmethylated C's in Unknown context: 6878044 C methylated in CpG context: 19.8% C methylated in CHG context: 4.9% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 20.8% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF05-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF05-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF05-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 198770863 Final Cytosine Methylation Report ================================= Total number of C's analysed: 3040036603 Total methylated C's in CpG context: 84390281 Total methylated C's in CHG context: 29856687 Total methylated C's in CHH context: 118081782 Total methylated C's in Unknown context: 3603787 Total unmethylated C's in CpG context: 341384062 Total unmethylated C's in CHG context: 574268764 Total unmethylated C's in CHH context: 1892055027 Total unmethylated C's in Unknown context: 13751394 C methylated in CpG context: 19.8% C methylated in CHG context: 4.9% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 20.8% Deleting temporary report files... Bismark completed in 0d 12h 25m 0s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 13693 and offset 2 (sequences written out: 71369801) Using the subset file >EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 71369801) Using the subset file >EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 13693 and offset 2 (sequences written out: 71369801) Using the subset file >EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 71369801) Using the subset file >EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (71369801 sequences in total) Writing a C -> T converted version of the input file EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (71369801 sequences in total) Writing a C -> T converted version of the input file EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (71369801 sequences in total) Input files are EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26142:1047_1:N:0:ATGAGGCC+CAATTAAC/1 77 * 0 0 * * 0 0 TNTAAAATAAATAATTAATTATTAAATAATAAATATTATAATTAATTTTTATTTTTTATTAAATTAAATTTTTTAAAATAAAATTTTTATAATAAAAATTTTATTAAATATTTAAAAATTAAATATATAAAATAATTAAAAAATTATAAA F#FFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFF:FF::FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26142:1047_2:N:0:ATGAGGCC+CAATTAAC/2 141 * 0 0 * * 0 0 AATTAATTTTTTTTTTAAAATTATTATTTATTTTTTTTATAATTTTTTAATTATTTTATATATTTAATTTTTAAATATTTAATAAAATTTTTATTATAAAAATTTTATTTTAAAAAATTTAATTTAATAAAAAATAAAAATTAATTATAA FF,FFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFF:FFFFFFFFF::F,FFFFF:F:F:FF:FFFFFFFF:FFFFFFF,:FFFFFFFFFFF,FFFFFFFFFFFFF::FFFFFFFFF:FF:FFFF:FFFF,:FFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (71369801 sequences in total) Input files are EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26142:1047_1:N:0:ATGAGGCC+CAATTAAC/1 99 NC_035783.1_GA_converted 33762010 42 150M = 33762045 186 CNTAAAATAAACAATCAACCACCAAATAACAAATATTACAACCAATCTCTACCCTTCATTAAATTAAATTCTTTAAAACAAAACTTTTACAACAAAAATCTCACTAAATATCCAAAAATCAAACACACAAAACAACTAAAAAATTATAAA F#FFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFF:FF::FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:1C101A46 YS:i:-20 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26142:1047_2:N:0:ATGAGGCC+CAATTAAC/2 147 NC_035783.1_GA_converted 33762045 42 134M1D16M = 33762010 -186 TTACAACCAATCTCTACCCTTCATTAAATTAAATTCTTTAAAACAAAACTTTTACAACAAAAATCTCACTAAATATCCAAAAATCAAACACACAAAACAACTAAAAAATTATAAAAAAAATAAACAACAATCCCAAAAAAAAAACTAACC FFFFFFFFFFF:FFF:,FFFF:FFFF:FF:FFFFFFFFF::FFFFFFFFFFFFF,FFFFFFFFFFF:,FFFFFFF:FFFFFFFF:FF:F:F:FFFFF,F::FFFFFFFFF:FFFFFFFF,FFFFFF,FFFFFFFFFFFFFFFFFFFF,FF AS:i:-20 XN:i:0 XM:i:2 XO:i:1 XG:i:1 NM:i:3 MD:Z:68A50C14^A16 YS:i:-7 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26359:1047_1:N:0:ATGAGGCC+CAATTAAC/1 77 * 0 0 * * 0 0 TNATATTAATATAAATTTTAATAAATAAAATATAAAAATAAAATATTTTTATATTAAATTATTTTTTTTTAAAATAAAATTTTATTATTATATTATAAATTTTTAAAATAATAATAATATTAAATTATAATTTATATTAAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26359:1047_2:N:0:ATGAGGCC+CAATTAAC/2 141 * 0 0 * * 0 0 TATTTAATATAAATTATAATTTAATATTATTATTATTTTAAAAATTTATAATATAATAATAAAATTTTATTTTAAAAAAAAATAATTTAATATAAAAATATTTTATTTTTATATTTTATTTATTAAAATTTATATTAATATAA FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26142:1047_1:N:0:ATGAGGCC+CAATTAAC/1 83 NC_035783.1_CT_converted 21935408 40 150M = 21935372 -186 TTTATAATTTTTTAGTTGTTTTGTGTGTTTGATTTTTGGATATTTAGTGAGATTTTTGTTGTAAAAGTTTTGTTTTAAAGAATTTAATTTAATGAAGGGTAGAGATTGGTTGTAATATTTGTTATTTGGTGGTTGATTGTTTATTTTANG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF::FF:FFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF#F AS:i:-13 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:48A1A97G1 YS:i:-32 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26142:1047_2:N:0:ATGAGGCC+CAATTAAC/2 163 NC_035783.1_CT_converted 21935372 40 6M1D144M = 21935408 186 GGTTAGTTTTTTTTTTGGGATTGTTGTTTATTTTTTTTATAATTTTTTAGTTGTTTTGTGTGTTTGATTTTTGGATATTTAGTGAGATTTTTGTTGTAAAAGTTTTGTTTTAAAGAATTTAATTTAATGAAGGGTAGAGATTGGTTGTAA FF,FFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFF:FFFFFFFFF::F,FFFFF:F:F:FF:FFFFFFFF:FFFFFFF,:FFFFFFFFFFF,FFFFFFFFFFFFF::FFFFFFFFF:FF:FFFF:FFFF,:FFF:FFFFFFFFFFF AS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:6^T16T7G52A1A64 YS:i:-13 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26359:1047_1:N:0:ATGAGGCC+CAATTAAC/1 77 * 0 0 * * 0 0 CNACACCAATACAAACCTCAACAAACAAAATATAAAAATAAAACATTTTCATATCAAACCACTTCTTTCCAAAACAAAATTTTACTATCACATTATAAACTTCTAAAACAATAATAACACCAAACCATAATTTATACCAAACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26359:1047_2:N:0:ATGAGGCC+CAATTAAC/2 141 * 0 0 * * 0 0 TGTTTGGTATAAATTATGGTTTGGTGTTATTATTGTTTTAGAAGTTTATAATGTGATAGTAAAATTTTGTTTTGGAAAGAAGTGGTTTGATATGAAAATGTTTTATTTTTATATTTTGTTTGTTGAGGTTTGTATTGGTGTGG FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26142:1047_1:N:0:ATGAGGCC+CAATTAAC/1 77 * 0 0 * * 0 0 TNTAAAATAAATAATTAATTATTAAATAATAAATATTATAATTAATTTTTATTTTTTATTAAATTAAATTTTTTAAAATAAAATTTTTATAATAAAAATTTTATTAAATATTTAAAAATTAAATATATAAAATAATTAAAAAATTATAAA F#FFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFF:FF::FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26142:1047_2:N:0:ATGAGGCC+CAATTAAC/2 141 * 0 0 * * 0 0 AATTAATTTTTTTTTTAAAATTATTATTTATTTTTTTTATAATTTTTTAATTATTTTATATATTTAATTTTTAAATATTTAATAAAATTTTTATTATAAAAATTTTATTTTAAAAAATTTAATTTAATAAAAAATAAAAATTAATTATAA FF,FFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFF:FFFFFFFFF::F,FFFFF:F:F:FF:FFFFFFFF:FFFFFFF,:FFFFFFFFFFF,FFFFFFFFFFFFF::FFFFFFFFF:FF:FFFF:FFFF,:FFF:FFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26359:1047_1:N:0:ATGAGGCC+CAATTAAC/1 77 * 0 0 * * 0 0 CNACACCAATACAAACCTCAACAAACAAAATATAAAAATAAAACATTTTCATATCAAACCACTTCTTTCCAAAACAAAATTTTACTATCACATTATAAACTTCTAAAACAATAATAACACCAAACCATAATTTATACCAAACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26359:1047_2:N:0:ATGAGGCC+CAATTAAC/2 141 * 0 0 * * 0 0 TGTTTGGTATAAATTATGGTTTGGTGTTATTATTGTTTTAGAAGTTTATAATGTGATAGTAAAATTTTGTTTTGGAAAGAAGTGGTTTGATATGAAAATGTTTTATTTTTATATTTTGTTTGTTGAGGTTTGTATTGGTGTGG FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.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)) Reading in the sequence files EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26359:1047_1:N:0:ATGAGGCC+CAATTAAC/1 77 * 0 0 * * 0 0 TNATATTAATATAAATTTTAATAAATAAAATATAAAAATAAAATATTTTTATATTAAATTATTTTTTTTTAAAATAAAATTTTATTATTATATTATAAATTTTTAAAATAATAATAATATTAAATTATAATTTATATTAAATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26359:1047_2:N:0:ATGAGGCC+CAATTAAC/2 141 * 0 0 * * 0 0 TATTTAATATAAATTATAATTTAATATTATTATTATTTTAAAAATTTATAATATAATAATAAAATTTTATTTTAAAAAAAAATAATTTAATATAAAAATATTTTATTTTTATATTTTATTTATTAAAATTTATATTAATATAA FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1123:10176:4429_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1139:17571:23500_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1156:5367:20776_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1308:16486:11162_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1326:31566:33614_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 3 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1362:26476:32033_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1424:19217:8594_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1516:8621:34397_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1516:8368:35180_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1516:8612:34381_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1518:12463:1658_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1567:5321:13745_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1620:6406:23202_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1632:21621:3771_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2136:29451:22592_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2139:15854:13730_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2144:7563:10551_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2148:1280:13322_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2221:13792:10222_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 1 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2362:4128:17472_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2417:2917:6825_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2451:24587:30076_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2554:21486:11741_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2636:20338:12790_1:N:0:CTGAGGCC+CAATTAAC NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1133:30725:11021_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1139:21603:36965_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1211:24560:1376_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1238:30156:30107_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1241:23637:3787_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 3 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1275:7916:18145_1:N:0:ATGAGGCC+CAATTAAC NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1275:10682:22999_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1309:22037:7279_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1320:9896:10582_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1335:28167:17080_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1335:25744:19116_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1375:15347:10755_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1430:17833:9706_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1437:16423:2785_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1436:14769:33301_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1544:9760:1705_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1547:15600:21934_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1561:10167:35884_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1606:11216:5478_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1609:26286:27602_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1609:24605:33113_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1628:4101:30702_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1630:3513:8077_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 3 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1662:17598:3505_1:N:0:ATGAGGCC+CAATTAAC NC_007175.2 17108 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1676:4273:30592_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1676:4164:30843_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2210:24216:12336_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2211:23827:10034_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2212:21233:12493_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2213:7988:6026_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2214:8449:20478_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2219:1741:34444_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2220:1832:4100_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2266:7319:28792_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2307:25762:22623_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2318:9408:3850_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2318:11722:14779_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2374:13268:10786_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2374:11939:23860_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2376:12879:9956_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2433:13901:5650_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2542:26684:29543_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2556:26250:13730_1:N:0:ATAAGGCC+CAATTAAC NC_035780.1 2 Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2567:2501:31814_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2567:10917:19774_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2607:13105:22874_1:N:0:ATGAGGCC+CAATTAAC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2610:27028:3803_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2610:25979:5932_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2629:30300:30984_1:N:0:ATGAGGCC+CAATTAAC NC_035780.1 2 Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 60437555 (84.68%) aligned concordantly 0 times 4859937 (6.81%) aligned concordantly exactly 1 time 6072309 (8.51%) aligned concordantly >1 times 15.32% overall alignment rate 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 59148478 (82.88%) aligned concordantly 0 times 5436981 (7.62%) aligned concordantly exactly 1 time 6784342 (9.51%) aligned concordantly >1 times 17.12% overall alignment rate 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 60449363 (84.70%) aligned concordantly 0 times 4869888 (6.82%) aligned concordantly exactly 1 time 6050550 (8.48%) aligned concordantly >1 times 15.30% overall alignment rate 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 59146783 (82.87%) aligned concordantly 0 times 5416853 (7.59%) aligned concordantly exactly 1 time 6806165 (9.54%) aligned concordantly >1 times 17.13% overall alignment rate Processed 71369801 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 285479204. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 285479204. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 285479204. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 285479204. Successfully deleted the temporary files EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 71369801 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1002621369 Total methylated C's in CpG context: 25170460 Total methylated C's in CHG context: 3764548 Total methylated C's in CHH context: 14970772 Total methylated C's in Unknown context: 941344 Total unmethylated C's in CpG context: 121659942 Total unmethylated C's in CHG context: 205539020 Total unmethylated C's in CHH context: 631516627 Total unmethylated C's in Unknown context: 4668446 C methylated in CpG context: 17.1% C methylated in CHG context: 1.8% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 16.8% Now waiting for all child processes to complete 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 59150768 (82.88%) aligned concordantly 0 times 5433982 (7.61%) aligned concordantly exactly 1 time 6785051 (9.51%) aligned concordantly >1 times 17.12% overall alignment rate 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 60435440 (84.68%) aligned concordantly 0 times 4858753 (6.81%) aligned concordantly exactly 1 time 6075608 (8.51%) aligned concordantly >1 times 15.32% overall alignment rate 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 60451449 (84.70%) aligned concordantly 0 times 4867525 (6.82%) aligned concordantly exactly 1 time 6050827 (8.48%) aligned concordantly >1 times 15.30% overall alignment rate 71369801 reads; of these: 71369801 (100.00%) were paired; of these: 59143303 (82.87%) aligned concordantly 0 times 5420890 (7.60%) aligned concordantly exactly 1 time 6805608 (9.54%) aligned concordantly >1 times 17.13% overall alignment rate Processed 71369801 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 285479204. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 285479204. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 285479204. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 285479204. Successfully deleted the temporary files EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 71369801 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1002608279 Total methylated C's in CpG context: 25201804 Total methylated C's in CHG context: 3764892 Total methylated C's in CHH context: 14963393 Total methylated C's in Unknown context: 944867 Total unmethylated C's in CpG context: 121633874 Total unmethylated C's in CHG context: 205604184 Total unmethylated C's in CHH context: 631440132 Total unmethylated C's in Unknown context: 4666768 C methylated in CpG context: 17.2% C methylated in CHG context: 1.8% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 16.8% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF06-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF06-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF06-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 142739602 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2005229648 Total methylated C's in CpG context: 50372264 Total methylated C's in CHG context: 7529440 Total methylated C's in CHH context: 29934165 Total methylated C's in Unknown context: 1886211 Total unmethylated C's in CpG context: 243293816 Total unmethylated C's in CHG context: 411143204 Total unmethylated C's in CHH context: 1262956759 Total unmethylated C's in Unknown context: 9335214 C methylated in CpG context: 17.2% C methylated in CHG context: 1.8% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 16.8% Deleting temporary report files... Bismark completed in 0d 6h 24m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 48624 and offset 2 (sequences written out: 58061310) Using the subset file >EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 58061311) Using the subset file >EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 58061311) Using the subset file >EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 48624 and offset 2 (sequences written out: 58061310) Using the subset file >EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (58061311 sequences in total) Writing a C -> T converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (58061310 sequences in total) Writing a C -> T converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (58061310 sequences in total) Input files are EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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 EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (58061311 sequences in total) Input files are EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 ANAAATAAATTTTTATTTGTTATTGAAATAAATTAATTTTTTTTTTAGTGTTTTTGTATGGTAGAATATTGGTTTGTTTGTTGTGTTAATGGTGTATTTTGTATTTTTGGAGATAAATAGTATTATGTTTTTTTGGTATATTATGTGGGT F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 CAATATCTATATAAAATTCACCACAACACAAACATTTTTAATTTAAAAAAAACCTTACCACACCTACACCATACCTTAAACTTTATAACCCACATAATATACCAAAAAAACATAATACTATTTATCTCCAAAAATACAAAATACACCATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 ANTTTAAAATATATAAAAAAATTTTAATATATAAAAAATTGTTTAAAATTTTTATAATGAAAGAAAATAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 AAATTATTTTCTTTCATTATAAAAATTTTAAACAATTTTTTATATATTAAAATTTTTTTATATATTTTAAATT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 ANAAACAAACCCTTACCCACTACCAAAACAAACTAACCCCCTCTTTAATATTTTTATATAATAAAATATTAACTTATTTATTATATTAATAATATATTTTATATTTTTAAAAATAAATAATATTATATTTTTTTAATATATTATATAAAT F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 TAATATTTATATAAAATTTATTATAATATAAATATTTTTAATTTAAAAAAAATTTTATTATATTTATATTATATTTTAAATTTTATAATTTATATAATATATTAAAAAAATATAATATTATTTATTTTTAAAAATATAAAATATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 ANTCCAAAACATACAAAAAAATTCCAACATACAAAAAATCATCCAAAACCTCTACAACAAAAAAAAACAACTC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 GAGTTGTTTTTTTTTGTTGTAGAGGTTTTGGATGATTTTTTGTATGTTGGAATTTTTTTGTATGTTTTGGATT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 83 NC_035789.1_CT_converted 8475991 42 73M = 8475991 -73 GAGTTGTTTTTTTTTGTTGTAGAGGTTTTGGATGATTTTTTGTATGTTGGAATTTTTTTGTATGTTTTGGANT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:51T19T1 YS:i:-6 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 163 NC_035789.1_CT_converted 8475991 42 73M = 8475991 73 GAGTTGTTTTTTTTTGTTGTAGAGGTTTTGGATGATTTTTTGTATGTTGGAATTTTTTTGTATGTTTTGGATT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:51T21 YS:i:-7 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 ANAAACAAACCCTTACCCACTACCAAAACAAACTAACCCCCTCTTTAATATTTTTATATAATAAAATATTAACTTATTTATTATATTAATAATATATTTTATATTTTTAAAAATAAATAATATTATATTTTTTTAATATATTATATAAAT F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 TAATATTTATATAAAATTTATTATAATATAAATATTTTTAATTTAAAAAAAATTTTATTATATTTATATTATATTTTAAATTTTATAATTTATATAATATATTAAAAAAATATAATATTATTTATTTTTAAAAATATAAAATATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 ANAAATAAATTTTTATTTGTTATTGAAATAAATTAATTTTTTTTTTAGTGTTTTTGTATGGTAGAATATTGGTTTGTTTGTTGTGTTAATGGTGTATTTTGTATTTTTGGAGATAAATAGTATTATGTTTTTTTGGTATATTATGTGGGT F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 CAATATCTATATAAAATTCACCACAACACAAACATTTTTAATTTAAAAAAAACCTTACCACACCTACACCATACCTTAAACTTTATAACCCACATAATATACCAAAAAAACATAATACTATTTATCTCCAAAAATACAAAATACACCATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25834:1047_1:N:0:GCAGAATT+TGGCCGGT/1 77 * 0 0 * * 0 0 ANTTTAAAATATATAAAAAAATTTTAATATATAAAAAATTGTTTAAAATTTTTATAATGAAAGAAAATAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25834:1047_2:N:0:GCAGAATT+TGGCCGGT/2 141 * 0 0 * * 0 0 AAATTATTTTCTTTCATTATAAAAATTTTAAACAATTTTTTATATATTAAAATTTTTTTATATATTTTAAATT FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF,FFFFFF:FFFFFFFF,FFFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1131:6424:5228_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1131:6388:5259_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1610:3631:10034_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1646:19895:36636_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2346:22372:15937_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2349:31376:22263_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2360:20247:6684_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 3 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2509:7111:23046_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 3 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2645:9968:35196_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1229:22290:27821_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1242:4734:13448_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1318:30409:33771_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1320:15176:21887_1:N:0:GCAGAAGT+TGGCCGGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1318:30038:15969_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1349:16586:22294_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1340:26639:6981_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 3 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1373:6162:10629_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 3 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1462:12807:1282_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 2 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1565:6515:5729_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1605:3016:7310_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2232:32000:29919_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 2 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2276:10520:20400_1:N:0:ACAGAATT+TGGCCGGT NC_035780.1 2 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2351:7157:35086_1:N:0:GCAGAATT+TGGCCGGT NC_035780.1 2 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2375:19904:2018_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2414:31846:18568_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 17158 Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2529:22173:20509_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 2 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2608:8784:29230_1:N:0:GCAGAATT+TGGCCGGT NC_035781.1 2 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2619:1850:30342_1:N:0:GCAGAATT+TGGCCGGT NC_007175.2 17101 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far 58061310 reads; of these: 58061310 (100.00%) were paired; of these: 48571390 (83.66%) aligned concordantly 0 times 4401574 (7.58%) aligned concordantly exactly 1 time 5088346 (8.76%) aligned concordantly >1 times 16.34% overall alignment rate 58061310 reads; of these: 58061310 (100.00%) were paired; of these: 48164262 (82.95%) aligned concordantly 0 times 4586146 (7.90%) aligned concordantly exactly 1 time 5310902 (9.15%) aligned concordantly >1 times 17.05% overall alignment rate 58061310 reads; of these: 58061310 (100.00%) were paired; of these: 48589251 (83.69%) aligned concordantly 0 times 4408015 (7.59%) aligned concordantly exactly 1 time 5064044 (8.72%) aligned concordantly >1 times 16.31% overall alignment rate 58061310 reads; of these: 58061310 (100.00%) were paired; of these: 48155485 (82.94%) aligned concordantly 0 times 4575559 (7.88%) aligned concordantly exactly 1 time 5330266 (9.18%) aligned concordantly >1 times 17.06% overall alignment rate Processed 58061310 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 232245240. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 232245240. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 232245240. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 232245240. Successfully deleted the temporary files EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 58061310 Final Cytosine Methylation Report ================================= Total number of C's analysed: 784886337 Total methylated C's in CpG context: 23876801 Total methylated C's in CHG context: 4950590 Total methylated C's in CHH context: 17886490 Total methylated C's in Unknown context: 1207399 Total unmethylated C's in CpG context: 94871095 Total unmethylated C's in CHG context: 167152345 Total unmethylated C's in CHH context: 476149016 Total unmethylated C's in Unknown context: 4111239 C methylated in CpG context: 20.1% C methylated in CHG context: 2.9% C methylated in CHH context: 3.6% C methylated in unknown context (CN or CHN): 22.7% Now waiting for all child processes to complete Processed 58000000 sequence pairs so far 58061311 reads; of these: 58061311 (100.00%) were paired; of these: 48580217 (83.67%) aligned concordantly 0 times 4399698 (7.58%) aligned concordantly exactly 1 time 5081396 (8.75%) aligned concordantly >1 times 16.33% overall alignment rate 58061311 reads; of these: 58061311 (100.00%) were paired; of these: 48596766 (83.70%) aligned concordantly 0 times 4403007 (7.58%) aligned concordantly exactly 1 time 5061538 (8.72%) aligned concordantly >1 times 16.30% overall alignment rate 58061311 reads; of these: 58061311 (100.00%) were paired; of these: 48160433 (82.95%) aligned concordantly 0 times 4587873 (7.90%) aligned concordantly exactly 1 time 5313005 (9.15%) aligned concordantly >1 times 17.05% overall alignment rate 58061311 reads; of these: 58061311 (100.00%) were paired; of these: 48153196 (82.94%) aligned concordantly 0 times 4576382 (7.88%) aligned concordantly exactly 1 time 5331733 (9.18%) aligned concordantly >1 times 17.06% overall alignment rate Processed 58061311 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 232245244. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 232245244. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 232245244. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 232245244. Successfully deleted the temporary files EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 58061311 Final Cytosine Methylation Report ================================= Total number of C's analysed: 785035675 Total methylated C's in CpG context: 23892149 Total methylated C's in CHG context: 4948862 Total methylated C's in CHH context: 17865089 Total methylated C's in Unknown context: 1206269 Total unmethylated C's in CpG context: 94887978 Total unmethylated C's in CHG context: 167171211 Total unmethylated C's in CHH context: 476270386 Total unmethylated C's in Unknown context: 4115842 C methylated in CpG context: 20.1% C methylated in CHG context: 2.9% C methylated in CHH context: 3.6% C methylated in unknown context (CN or CHN): 22.7% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF06-EM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF06-EM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF06-EM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 116122621 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1569922012 Total methylated C's in CpG context: 47768950 Total methylated C's in CHG context: 9899452 Total methylated C's in CHH context: 35751579 Total methylated C's in Unknown context: 2413668 Total unmethylated C's in CpG context: 189759073 Total unmethylated C's in CHG context: 334323556 Total unmethylated C's in CHH context: 952419402 Total unmethylated C's in Unknown context: 8227081 C methylated in CpG context: 20.1% C methylated in CHG context: 2.9% C methylated in CHH context: 3.6% C methylated in unknown context (CN or CHN): 22.7% Deleting temporary report files... Bismark completed in 0d 5h 32m 5s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 80553258) Using the subset file >EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 7791 and offset 2 (sequences written out: 80553258) Using the subset file >EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 7791 and offset 2 (sequences written out: 80553258) Using the subset file >EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 80553258) Using the subset file >EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (80553258 sequences in total) Writing a C -> T converted version of the input file EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (80553258 sequences in total) Writing a C -> T converted version of the input file EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (80553258 sequences in total) Input files are EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (80553258 sequences in total) Input files are EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26178:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 ANATTATTAATATAATTTTTTAATTATTTAATTTTTTATTATTTATAATTATATATATTTTTTTTTAATTAAATATATAAAAAAAAGTTGGATTAATTAGAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26178:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 TTTTCTAATTAATCCAACTTTTTTTTATATATTTAATTAAAAAAAAATATATATAATTATAAATAATAAAAAATTTAATAATTATAAAATTATATTTATTATTT FFFFFFFFFFFFFF:FF:FFFFFFFFFFFF,:FFFF:FFFF:,FFF,FFF:FFFFF:FF:,FF:FF,,FFFF,FF,FFF,,FFF,FFF,FFFFFFF,FF,,FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27100:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 TNAAGTAGATAAGGTATAATTGTTTTTTTTTTGTTGTTTGGATTTTTTTTATAAAGTATTAG F#FF:FFFFFFF::FFFFFFFFFFFFF:FFFF,FFFFFF,,FF::FFFFFFFFFF::F,FF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27100:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 CTAATACTTTATAAAAAAAATCCAAACAACAAAAAAAAAACAATTATACCTTATCTACTTAA FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26178:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 ANACCATCAATATAACTTTCTAACCATTCAACTTTTCATTATTCATAATTATACATACTTTCCTTTAATTAAACATATAAAAAAAAATTAAATTAATTAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26178:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 TTTTTTAATTAATTTAATTTTTTTTTATATGTTTAATTAAAGGAAAGTATGTATAATTATGAATAATGAAAAGTTTAATGGTTATAAAGTTATATTTATTGTTT FFFFFFFFFFFFFF:FF:FFFFFFFFFFFF,:FFFF:FFFF:,FFF,FFF:FFFFF:FF:,FF:FF,,FFFF,FF,FFF,,FFF,FFF,FFFFFFF,FF,,FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27100:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 TNAAATAAATAAAATATAATTATTTTTTTTTTATTATTTAAATTTTTTTTATAAAATATTAA F#FF:FFFFFFF::FFFFFFFFFFFFF:FFFF,FFFFFF,,FF::FFFFFFFFFF::F,FF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27100:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 TTAATATTTTATAAAAAAAATTTAAATAATAAAAAAAAAATAATTATATTTTATTTATTTAA FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26178:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 ANACCATCAATATAACTTTCTAACCATTCAACTTTTCATTATTCATAATTATACATACTTTCCTTTAATTAAACATATAAAAAAAAATTAAATTAATTAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26178:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 TTTTTTAATTAATTTAATTTTTTTTTATATGTTTAATTAAAGGAAAGTATGTATAATTATGAATAATGAAAAGTTTAATGGTTATAAAGTTATATTTATTGTTT FFFFFFFFFFFFFF:FF:FFFFFFFFFFFF,:FFFF:FFFF:,FFF,FFF:FFFFF:FF:,FF:FF,,FFFF,FF,FFF,,FFF,FFF,FFFFFFF,FF,,FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27100:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 TNAAATAAATAAAATATAATTATTTTTTTTTTATTATTTAAATTTTTTTTATAAAATATTAA F#FF:FFFFFFF::FFFFFFFFFFFFF:FFFF,FFFFFF,,FF::FFFFFFFFFF::F,FF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27100:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 TTAATATTTTATAAAAAAAATTTAAATAATAAAAAAAAAATAATTATATTTTATTTATTTAA FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27100:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 TNAAGTAGATAAGGTATAATTGTTTTTTTTTTGTTGTTTGGATTTTTTTTATAAAGTATTAG F#FF:FFFFFFF::FFFFFFFFFFFFF:FFFF,FFFFFF,,FF::FFFFFFFFFF::F,FF, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27100:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 CTAATACTTTATAAAAAAAATCCAAACAACAAAAAAAAAACAATTATACCTTATCTACTTAA FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26178:1047_1:N:0:CCAAGTCT+TCATCCTT/1 77 * 0 0 * * 0 0 ANATTATTAATATAATTTTTTAATTATTTAATTTTTTATTATTTATAATTATATATATTTTTTTTTAATTAAATATATAAAAAAAAGTTGGATTAATTAGAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26178:1047_2:N:0:CCAAGTCT+TCATCCTT/2 141 * 0 0 * * 0 0 TTTTCTAATTAATCCAACTTTTTTTTATATATTTAATTAAAAAAAAATATATATAATTATAAATAATAAAAAATTTAATAATTATAAAATTATATTTATTATTT FFFFFFFFFFFFFF:FF:FFFFFFFFFFFF,:FFFF:FFFF:,FFF,FFF:FFFFF:FF:,FF:FF,,FFFF,FF,FFF,,FFF,FFF,FFFFFFF,FF,,FFF YT:Z:UP >>> Writing bisulfite mapping results to EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1115:24569:31078_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1132:5547:35305_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1161:31105:12242_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17149 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1161:29875:14090_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17149 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1162:8874:32925_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1162:8648:32753_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1162:9435:33677_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1207:30599:13557_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17160 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1221:21486:28432_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1243:8965:22091_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1340:16215:32831_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1362:19786:26021_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1370:2193:15280_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1377:1579:23610_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1430:28881:2440_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1460:29288:7905_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:6280:16595_1:N:0:CCAAGTCT+TCATCCTT NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1519:4851:19445_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1522:11044:15546_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1522:6732:19727_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1525:3396:14325_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1563:21721:35884_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17160 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:32136:35665_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1578:8314:26882_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17161 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1646:16821:15060_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17161 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1654:27001:32659_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1661:2899:15875_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1662:22010:11052_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17164 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1675:32208:2848_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:10845:9377_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:10619:9392_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:10276:9831_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2143:18611:31782_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2155:21395:18693_1:N:0:CCAAGTCT+TCATCCTT NC_035780.1 2 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2277:30300:24502_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2308:20835:24236_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2341:9977:6840_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2376:32895:24142_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2376:32570:23985_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2434:16875:12336_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17161 Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2442:25012:2534_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2445:19524:29982_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2463:21721:24706_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2508:13304:23688_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2508:13386:23672_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2572:2031:21104_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2612:4237:24173_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2630:26386:10645_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2661:1723:18630_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2663:2871:35775_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1115:24569:31078_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1132:5547:35305_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1161:31105:12242_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17149 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1161:29875:14090_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17149 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1162:8874:32925_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1162:8648:32753_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1162:9435:33677_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1207:30599:13557_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17160 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1221:21486:28432_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1243:8965:22091_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1340:16215:32831_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1362:19786:26021_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1370:2193:15280_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1377:1579:23610_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1430:28881:2440_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1460:29288:7905_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1461:6280:16595_1:N:0:CCAAGTCT+TCATCCTT NC_035780.1 2 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1519:4851:19445_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1522:11044:15546_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1522:6732:19727_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1525:3396:14325_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1563:21721:35884_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17160 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1570:32136:35665_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1578:8314:26882_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17161 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1646:16821:15060_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1654:27001:32659_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1661:2899:15875_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1662:22010:11052_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17164 Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1675:32208:2848_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:10845:9377_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:10619:9392_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2101:10276:9831_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2143:18611:31782_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2155:21395:18693_1:N:0:CCAAGTCT+TCATCCTT NC_035780.1 2 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2277:30300:24502_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2308:20835:24236_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2341:9977:6840_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2376:32895:24142_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2376:32570:23985_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2434:16875:12336_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17161 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2442:25012:2534_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2445:19524:29982_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17099 Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2463:21721:24706_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 74000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2508:13304:23688_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2508:13386:23672_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17167 Processed 75000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2572:2031:21104_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 2 Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2612:4237:24173_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 17171 Processed 78000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2630:26386:10645_1:N:0:CCAAGTCT+TCATCCTT NC_007175.2 1 Processed 79000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2661:1723:18630_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2663:2871:35775_1:N:0:CCAAGTCT+TCATCTTT NC_035780.1 2 Processed 80000000 sequence pairs so far Processed 80000000 sequence pairs so far 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 70909846 (88.03%) aligned concordantly 0 times 4686774 (5.82%) aligned concordantly exactly 1 time 4956638 (6.15%) aligned concordantly >1 times 11.97% overall alignment rate 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 70941058 (88.07%) aligned concordantly 0 times 4666294 (5.79%) aligned concordantly exactly 1 time 4945906 (6.14%) aligned concordantly >1 times 11.93% overall alignment rate 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 71068158 (88.23%) aligned concordantly 0 times 4618858 (5.73%) aligned concordantly exactly 1 time 4866242 (6.04%) aligned concordantly >1 times 11.77% overall alignment rate 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 71039564 (88.19%) aligned concordantly 0 times 4639069 (5.76%) aligned concordantly exactly 1 time 4874625 (6.05%) aligned concordantly >1 times 11.81% overall alignment rate Processed 80553258 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 322213032. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 322213032. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 322213032. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 322213032. Successfully deleted the temporary files EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 80553258 Final Cytosine Methylation Report ================================= Total number of C's analysed: 609527269 Total methylated C's in CpG context: 16745931 Total methylated C's in CHG context: 5488970 Total methylated C's in CHH context: 24873090 Total methylated C's in Unknown context: 1187398 Total unmethylated C's in CpG context: 61303327 Total unmethylated C's in CHG context: 114147576 Total unmethylated C's in CHH context: 386968375 Total unmethylated C's in Unknown context: 4488008 C methylated in CpG context: 21.5% C methylated in CHG context: 4.6% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 20.9% Now waiting for all child processes to complete 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 71072928 (88.23%) aligned concordantly 0 times 4622554 (5.74%) aligned concordantly exactly 1 time 4857776 (6.03%) aligned concordantly >1 times 11.77% overall alignment rate 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 70902808 (88.02%) aligned concordantly 0 times 4693810 (5.83%) aligned concordantly exactly 1 time 4956640 (6.15%) aligned concordantly >1 times 11.98% overall alignment rate 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 70936936 (88.06%) aligned concordantly 0 times 4669574 (5.80%) aligned concordantly exactly 1 time 4946748 (6.14%) aligned concordantly >1 times 11.94% overall alignment rate 80553258 reads; of these: 80553258 (100.00%) were paired; of these: 71039644 (88.19%) aligned concordantly 0 times 4642283 (5.76%) aligned concordantly exactly 1 time 4871331 (6.05%) aligned concordantly >1 times 11.81% overall alignment rate Processed 80553258 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 322213032. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 322213032. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 322213032. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 322213032. Successfully deleted the temporary files EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 80553258 Final Cytosine Methylation Report ================================= Total number of C's analysed: 609893041 Total methylated C's in CpG context: 16748837 Total methylated C's in CHG context: 5484230 Total methylated C's in CHH context: 24910188 Total methylated C's in Unknown context: 1192224 Total unmethylated C's in CpG context: 61362163 Total unmethylated C's in CHG context: 114172630 Total unmethylated C's in CHH context: 387214993 Total unmethylated C's in Unknown context: 4505020 C methylated in CpG context: 21.4% C methylated in CHG context: 4.6% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 20.9% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF06-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF06-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF06-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 161106516 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1219420310 Total methylated C's in CpG context: 33494768 Total methylated C's in CHG context: 10973200 Total methylated C's in CHH context: 49783278 Total methylated C's in Unknown context: 2379622 Total unmethylated C's in CpG context: 122665490 Total unmethylated C's in CHG context: 228320206 Total unmethylated C's in CHH context: 774183368 Total unmethylated C's in Unknown context: 8993028 C methylated in CpG context: 21.4% C methylated in CHG context: 4.6% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 20.9% Deleting temporary report files... Bismark completed in 0d 8h 32m 1s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 120674809) Using the subset file >EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz for PID: 6927 and offset 2 (sequences written out: 120674808) Using the subset file >EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 6927 and offset 2 (sequences written out: 120674808) Using the subset file >EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 120674809) Using the subset file >EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (120674809 sequences in total) Writing a C -> T converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (120674808 sequences in total) Writing a C -> T converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (120674808 sequences in total) Input files are EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.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 EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (120674809 sequences in total) Input files are EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ANTTATATAAAAATTATTTAATTTAATAATTTATTTAAAATTATTAAATTAAATTATATTTATAAATAATTTTAATAAAATTAATAATATTATTTTTAATAAATAAAAAAAATAAAAATTTTAATAATTTATTATTTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TATAAATAATAAATTATTAAAATTTTTATTTTTTTTATTTATTAAAAATAATATTATTAATTTTATTAAAATTATTTATAAATATAATTTAATTTAATAATTTTAAATAAATTATTAAATTAAATAATTTTTATATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 GNTAAATTTATAAATTTAATTTAAAAATTAAATTTTAATTAAATTATAAATAATATTTAATATAATTTTATAATAAATATAGTTTATAGTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 AACTATAAACTATATTTATTATAAAATTATATTAAATATTATTTATAATTTAATTAAAATTTAATTTTTAAATTAAATTTATAAATTTATC FFFFFFFFFFFF::FFFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ANCTATACAAAAATCACCTAACTCAACAACCTACTCAAAATCATCAAATTAAACCACACCTATAAACAATTCTAACAAAACCAATAATATCACCTTCAACAAACAAAAAAAATAAAAATCCCAATAATTCATCATCTACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TGTAGATGATGAATTATTGGGATTTTTATTTTTTTTGTTTGTTGAAGGTGATATTATTGGTTTTGTTAGAATTGTTTATAGGTGTGGTTTAATTTGATGATTTTGAGTAGGTTGTTGAGTTAGGTGATTTTTGTATAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ANCAAACTTATAAATTCAATTTAAAAATCAAATCCTAACTAAACTATAAACAATATTTAACACAACTTTATAATAAACATAATTTATAATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 AATTATAAATTATGTTTATTATAAAGTTGTGTTAAATATTGTTTATAGTTTAGTTAGGATTTGATTTTTAAATTGAATTTATAAGTTTGTT FFFFFFFFFFFF::FFFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ANCAAACTTATAAATTCAATTTAAAAATCAAATCCTAACTAAACTATAAACAATATTTAACACAACTTTATAATAAACATAATTTATAATT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 AATTATAAATTATGTTTATTATAAAGTTGTGTTAAATATTGTTTATAGTTTAGTTAGGATTTGATTTTTAAATTGAATTTATAAGTTTGTT FFFFFFFFFFFF::FFFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ANCTATACAAAAATCACCTAACTCAACAACCTACTCAAAATCATCAAATTAAACCACACCTATAAACAATTCTAACAAAACCAATAATATCACCTTCAACAAACAAAAAAAATAAAAATCCCAATAATTCATCATCTACA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TGTAGATGATGAATTATTGGGATTTTTATTTTTTTTGTTTGTTGAAGGTGATATTATTGGTTTTGTTAGAATTGTTTATAGGTGTGGTTTAATTTGATGATTTTGAGTAGGTTGTTGAGTTAGGTGATTTTTGTATAGTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: GWNJ-1012:512:GW210315000:4:1101:27407:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 ANTTATATAAAAATTATTTAATTTAATAATTTATTTAAAATTATTAAATTAAATTATATTTATAAATAATTTTAATAAAATTAATAATATTATTTTTAATAAATAAAAAAAATAAAAATTTTAATAATTTATTATTTATA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27407:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 TATAAATAATAAATTATTAAAATTTTTATTTTTTTTATTTATTAAAAATAATATTATTAATTTTATTAAAATTATTTATAAATATAATTTAATTTAATAATTTTAAATAAATTATTAAATTAAATAATTTTTATATAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25870:1047_1:N:0:GTCGGAGC+TTATAACC/1 77 * 0 0 * * 0 0 GNTAAATTTATAAATTTAATTTAAAAATTAAATTTTAATTAAATTATAAATAATATTTAATATAATTTTATAATAAATATAGTTTATAGTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25870:1047_2:N:0:GTCGGAGC+TTATAACC/2 141 * 0 0 * * 0 0 AACTATAAACTATATTTATTATAAAATTATATTAAATATTATTTATAATTTAATTAAAATTTAATTTTTAAATTAAATTTATAAATTTATC FFFFFFFFFFFF::FFFFFFFFFFFFFFF:FFFFFF,F:FFF:FFFFFFFF:FFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFF,FF:FFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1323:27254:36511_1:N:0:GTCGGAGC+TTATAACC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1324:24650:1908_1:N:0:GTCGGAGC+TTATAACC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1324:24478:3302_1:N:0:GTCGGAGC+TTATAACC NC_035781.1 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1425:5511:20369_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17196 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1464:15628:18787_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1501:21133:22091_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1501:21169:22091_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1559:24858:34554_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17163 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1564:4020:8265_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1615:26684:2707_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2162:26151:6950_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2173:32298:3505_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2238:18701:5008_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2302:29387:3537_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 1 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2319:8820:36401_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 1 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2406:11071:27806_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2409:8214:17221_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2412:14317:7686_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2465:9227:4445_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2524:6234:20588_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 1 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1102:23303:29293_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1102:18593:31532_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1129:16785:36636_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 1 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1146:32027:10927_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1153:22245:8328_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1154:23737:23719_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1159:31286:21136_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1171:21314:3583_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1171:31096:13980_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1225:15655:24815_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1237:27208:12352_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1245:9525:1047_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1245:9733:1157_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1263:29351:3881_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1307:28085:23109_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 1 Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1415:7374:16047_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1470:22092:12414_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 2 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1505:30445:25504_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1513:23204:24079_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17158 Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1526:10113:8390_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1529:27489:36918_1:N:0:GTCGGAGC+TTATAACC NC_035789.1 1 Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1559:25084:13213_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1572:29143:10755_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1601:1443:11005_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1627:14742:15186_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1628:14281:3239_1:N:0:GTCGGAGC+TTATAACG NC_035780.1 1 Processed 75000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1678:27326:1846_1:N:0:GTCGGAGC+TTATAACC NC_035781.1 2 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2106:15673:2206_1:N:0:GTCGGAGC+TTATACCC NC_007175.2 2 Processed 80000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2125:22525:20306_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17158 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2128:25120:23954_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Processed 82000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2172:3450:24439_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 86000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2202:11397:36511_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2212:10890:12712_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17158 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:17363:15217_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 92000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 95000000 sequence pairs so far Processed 96000000 sequence pairs so far Processed 96000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2336:15338:19319_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17158 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2338:32841:2065_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 97000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Processed 108000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2519:11234:6762_1:N:0:GTCGGAGC+TTATAACC NC_007175.2 17162 Processed 109000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Processed 112000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2562:24749:2926_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 113000000 sequence pairs so far Processed 113000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2573:23972:9627_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 114000000 sequence pairs so far Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Processed 115000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2622:6849:14325_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 116000000 sequence pairs so far Processed 116000000 sequence pairs so far Processed 117000000 sequence pairs so far Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 119000000 sequence pairs so far Processed 119000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2663:32307:34115_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 Processed 120000000 sequence pairs so far Processed 120000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2676:17535:19742_1:N:0:GTCGGAGC+TTATAACC NC_035780.1 2 120674808 reads; of these: 120674808 (100.00%) were paired; of these: 115020021 (95.31%) aligned concordantly 0 times 2452035 (2.03%) aligned concordantly exactly 1 time 3202752 (2.65%) aligned concordantly >1 times 4.69% overall alignment rate 120674808 reads; of these: 120674808 (100.00%) were paired; of these: 112963611 (93.61%) aligned concordantly 0 times 3419986 (2.83%) aligned concordantly exactly 1 time 4291211 (3.56%) aligned concordantly >1 times 6.39% overall alignment rate 120674808 reads; of these: 120674808 (100.00%) were paired; of these: 115044111 (95.33%) aligned concordantly 0 times 2432995 (2.02%) aligned concordantly exactly 1 time 3197702 (2.65%) aligned concordantly >1 times 4.67% overall alignment rate 120674808 reads; of these: 120674808 (100.00%) were paired; of these: 113002983 (93.64%) aligned concordantly 0 times 3388632 (2.81%) aligned concordantly exactly 1 time 4283193 (3.55%) aligned concordantly >1 times 6.36% overall alignment rate Processed 120674808 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 482699232. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 482699232. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 482699232. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 482699232. Successfully deleted the temporary files EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 120674808 Final Cytosine Methylation Report ================================= Total number of C's analysed: 330605410 Total methylated C's in CpG context: 6653517 Total methylated C's in CHG context: 1253291 Total methylated C's in CHH context: 8277065 Total methylated C's in Unknown context: 422742 Total unmethylated C's in CpG context: 35346067 Total unmethylated C's in CHG context: 61294201 Total unmethylated C's in CHH context: 217781269 Total unmethylated C's in Unknown context: 1976774 C methylated in CpG context: 15.8% C methylated in CHG context: 2.0% C methylated in CHH context: 3.7% C methylated in unknown context (CN or CHN): 17.6% Now waiting for all child processes to complete 120674809 reads; of these: 120674809 (100.00%) were paired; of these: 115043083 (95.33%) aligned concordantly 0 times 2434193 (2.02%) aligned concordantly exactly 1 time 3197533 (2.65%) aligned concordantly >1 times 4.67% overall alignment rate 120674809 reads; of these: 120674809 (100.00%) were paired; of these: 113006712 (93.65%) aligned concordantly 0 times 3388138 (2.81%) aligned concordantly exactly 1 time 4279959 (3.55%) aligned concordantly >1 times 6.35% overall alignment rate 120674809 reads; of these: 120674809 (100.00%) were paired; of these: 115017677 (95.31120674809% reads; of these:) aligned concordantly 0 times 1206748092452562 ( (2.03%) aligned concordantly exactly 1 time 100.003204570% () were paired; of these:2.66 % ) aligned concordantly >1 times112965614 (4.6993.61%% overall alignment rate) aligned concordantly 0 times 3421345 (2.84%) aligned concordantly exactly 1 time 4287850 (3.55%) aligned concordantly >1 times 6.39% overall alignment rate Processed 120674809 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 482699236. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 482699236. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 482699236. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 482699236. Successfully deleted the temporary files EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 120674809 Final Cytosine Methylation Report ================================= Total number of C's analysed: 330781567 Total methylated C's in CpG context: 6656119 Total methylated C's in CHG context: 1253739 Total methylated C's in CHH context: 8267111 Total methylated C's in Unknown context: 423934 Total unmethylated C's in CpG context: 35394638 Total unmethylated C's in CHG context: 61354863 Total unmethylated C's in CHH context: 217855097 Total unmethylated C's in Unknown context: 1973026 C methylated in CpG context: 15.8% C methylated in CHG context: 2.0% C methylated in CHH context: 3.7% C methylated in unknown context (CN or CHN): 17.7% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF07-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF07-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF07-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 241349617 Final Cytosine Methylation Report ================================= Total number of C's analysed: 661386977 Total methylated C's in CpG context: 13309636 Total methylated C's in CHG context: 2507030 Total methylated C's in CHH context: 16544176 Total methylated C's in Unknown context: 846676 Total unmethylated C's in CpG context: 70740705 Total unmethylated C's in CHG context: 122649064 Total unmethylated C's in CHH context: 435636366 Total unmethylated C's in Unknown context: 3949800 C methylated in CpG context: 15.8% C methylated in CHG context: 2.0% C methylated in CHH context: 3.7% C methylated in unknown context (CN or CHN): 17.7% Deleting temporary report files... Bismark completed in 0d 10h 22m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 64801768) Using the subset file >EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 39540 and offset 2 (sequences written out: 64801768) Using the subset file >EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 64801768) Using the subset file >EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 39540 and offset 2 (sequences written out: 64801768) Using the subset file >EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (64801768 sequences in total) Writing a C -> T converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (64801768 sequences in total) Writing a C -> T converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (64801768 sequences in total) Input files are EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ANTGGTTTGATTTGGAGGTAGTATAGAAATATTTAGAATAATTATATGTTTTGAGGGTTAAGGTTGGTATTAATTTTTAGTTTTATGAATAGGTTTGGAAGGAGTTTAAGATTTTATATGGTAGGAGAG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 CTCTCCTACCATATAAAATCTTAAACTCCTTCCAAACCTATTCATAAAACTAAAAATTAATACCAACCTTAACCCTCAAAACATATAATTATTCTAAATATTTCTATACTACCTCCAAATCAAACCACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ANTAATTTAATTTAAAAATAATATAAAAATATTTAAAATAATTATACATTTTAAAAATTAAAATTAATATTAATTTTTAATTTTACAAATAAACTTAAAAAAAATTTAAAATTTTATACAATAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 TTTTTTTATTGTATAAAATTTTAAATTTTTTTTAAGTTTATTTGTAAAATTAAAAATTAATATTAATTTTAATTTTTAAAATGTATAATTATTTTAAATATTTTTATATTATTTTTAAATTAAATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ANTAATTTAATTTAAAAATAATATAAAAATATTTAAAATAATTATACATTTTAAAAATTAAAATTAATATTAATTTTTAATTTTACAAATAAACTTAAAAAAAATTTAAAATTTTATACAATAAAAAAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 TTTTTTTATTGTATAAAATTTTAAATTTTTTTTAAGTTTATTTGTAAAATTAAAAATTAATATTAATTTTAATTTTTAAAATGTATAATTATTTTAAATATTTTTATATTATTTTTAAATTAAATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25328:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 ANTGGTTTGATTTGGAGGTAGTATAGAAATATTTAGAATAATTATATGTTTTGAGGGTTAAGGTTGGTATTAATTTTTAGTTTTATGAATAGGTTTGGAAGGAGTTTAAGATTTTATATGGTAGGAGAG F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25328:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 CTCTCCTACCATATAAAATCTTAAACTCCTTCCAAACCTATTCATAAAACTAAAAATTAATACCAACCTTAACCCTCAAAACATATAATTATTCTAAATATTTCTATACTACCTCCAAATCAAACCACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (64801768 sequences in total) Input files are EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 TNAAATGAATTTTTAATGAATTTAAAATGAATTTTAATGAATTTAAAATAAATTTTTAATGAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAATTCATTAAAAATTTATTTTAAATTCATTAAAATTCATTTTAAATTCATTAAAAATTCATTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 99 NC_035782.1_GA_converted 44517393 1 35M1D31M = 44517393 67 CNAAACAAACCCCTAACAAACTCAAAACAAACCCCAACAAACTCAAAACAAACTCCTAACAAACCC F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-9 XS:i:-9 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:1A33^A31 YS:i:-8 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 147 NC_035782.1_GA_converted 44517393 1 35M1D31M = 44517393 -67 CAAAACAAACCCCTAACAAACTCAAAACAAACCCCAACAAACTCAAAACAAACTCCTAACAAACCC FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:35^A31 YS:i:-9 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 83 NC_035780.1_CT_converted 19138695 1 29M1D37M = 19138695 -67 GGGTTTGTTAGGAGTTTGTTTTGAGTTTGTTGGGGTTTGTTTTGAGTTTGTTAGGGGTTTGTTTNG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-9 XS:i:-9 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:29^T35T1 YS:i:-8 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 163 NC_035780.1_CT_converted 19138695 1 29M1D37M = 19138695 67 GGGTTTGTTAGGAGTTTGTTTTGAGTTTGTTGGGGTTTGTTTTGAGTTTGTTAGGGGTTTGTTTTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:29^T37 YS:i:-9 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25364:1047_1:N:0:CCGTGAAG+ATCCACTG/1 77 * 0 0 * * 0 0 TNAAATGAATTTTTAATGAATTTAAAATGAATTTTAATGAATTTAAAATAAATTTTTAATGAATTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25364:1047_2:N:0:CCGTGAAG+ATCCACTG/2 141 * 0 0 * * 0 0 AAATTCATTAAAAATTTATTTTAAATTCATTAAAATTCATTTTAAATTCATTAAAAATTCATTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1144:13060:26897_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1421:32090:11036_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 3 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1419:1588:8406_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1518:16640:36135_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1518:16604:36166_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1555:2211:17159_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1578:12192:28839_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2361:11650:31313_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2624:18457:23625_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1107:2510:35180_1:N:0:CCGTGAAG+ATCCACTG NC_035781.1 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1135:10312:22514_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1155:17924:10081_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1165:21115:16329_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1164:26964:6793_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1165:21025:17738_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1174:28230:17347_1:N:0:CCGTGAAG+ATCCACTG NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1203:17888:31876_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1215:28628:33098_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1259:1181:5102_1:N:0:CCGTGAAG+ATCCACTG NC_035781.1 1 Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1344:6723:11475_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1419:29369:5134_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 65668308 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1606:10366:4319_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1609:9570:20917_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 3 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1663:27389:31735_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1674:28348:25567_1:N:0:CCGTGAAG+ATCCACTG NC_007175.2 17163 Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2115:4670:36166_1:N:0:CCGTGAAG+ATCCGCTG NC_035780.1 2 Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2145:7166:32252_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2145:7229:32268_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2147:16712:13150_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2232:2365:3521_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2312:26955:29105_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2312:27335:29387_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2332:16866:28510_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2332:16794:30514_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2343:22724:25598_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2346:10764:34695_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2471:15347:24095_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2603:12979:14700_1:N:0:CCGTGAAG+ATCCACTG NC_035780.1 2 Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54084254 (83.46%) aligned concordantly 0 times 4846485 (7.48%) aligned concordantly exactly 1 time 5871029 (9.06%) aligned concordantly >1 times 16.54% overall alignment rate 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54088388 (83.47%) aligned concordantly 0 times 4826934 (7.45%) aligned concordantly exactly 1 time 5886446 (9.08%) aligned concordantly >1 times 16.53% overall alignment rate 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54910790 (84.74%) aligned concordantly 0 times 4465986 (6.89%) aligned concordantly exactly 1 time 5424992 (8.37%) aligned concordantly >1 times 15.26% overall alignment rate 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54904089 (84.73%) aligned concordantly 0 times 4452074 (6.87%) aligned concordantly exactly 1 time 5445605 (8.40%) aligned concordantly >1 times 15.27% overall alignment rate Processed 64801768 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 259207072. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 259207072. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 259207072. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 259207072. Successfully deleted the temporary files EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 64801768 Final Cytosine Methylation Report ================================= Total number of C's analysed: 848021332 Total methylated C's in CpG context: 22027204 Total methylated C's in CHG context: 3174409 Total methylated C's in CHH context: 13242744 Total methylated C's in Unknown context: 716210 Total unmethylated C's in CpG context: 100840821 Total unmethylated C's in CHG context: 176944946 Total unmethylated C's in CHH context: 531791208 Total unmethylated C's in Unknown context: 3771894 C methylated in CpG context: 17.9% C methylated in CHG context: 1.8% C methylated in CHH context: 2.4% C methylated in unknown context (CN or CHN): 16.0% Now waiting for all child processes to complete 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54907058 (84.73%) aligned concordantly 0 times 4465922 (6.89%) aligned concordantly exactly 1 time 5428788 (8.38%) aligned concordantly >1 times 15.27% overall alignment rate 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54086841 (83.47%) aligned concordantly 0 times 4843453 (7.47%) aligned concordantly exactly 1 time 5871474 (9.06%) aligned concordantly >1 times 16.53% overall alignment rate 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54900711 (84.72%) aligned concordantly 0 times 4450294 (6.87%) aligned concordantly exactly 1 time 5450763 (8.41%) aligned concordantly >1 times 15.28% overall alignment rate 64801768 reads; of these: 64801768 (100.00%) were paired; of these: 54086314 (83.46%) aligned concordantly 0 times 4829932 (7.45%) aligned concordantly exactly 1 time 5885522 (9.08%) aligned concordantly >1 times 16.54% overall alignment rate Processed 64801768 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 259207072. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 259207072. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 259207072. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 259207072. Successfully deleted the temporary files EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 64801768 Final Cytosine Methylation Report ================================= Total number of C's analysed: 847944352 Total methylated C's in CpG context: 22025466 Total methylated C's in CHG context: 3168015 Total methylated C's in CHH context: 13224993 Total methylated C's in Unknown context: 713047 Total unmethylated C's in CpG context: 100839743 Total unmethylated C's in CHG context: 176949936 Total unmethylated C's in CHH context: 531736199 Total unmethylated C's in Unknown context: 3768078 C methylated in CpG context: 17.9% C methylated in CHG context: 1.8% C methylated in CHH context: 2.4% C methylated in unknown context (CN or CHN): 15.9% Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF07-EM03-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF07-EM03-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF07-EM03-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 129603536 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1695965684 Total methylated C's in CpG context: 44052670 Total methylated C's in CHG context: 6342424 Total methylated C's in CHH context: 26467737 Total methylated C's in Unknown context: 1429257 Total unmethylated C's in CpG context: 201680564 Total unmethylated C's in CHG context: 353894882 Total unmethylated C's in CHH context: 1063527407 Total unmethylated C's in Unknown context: 7539972 C methylated in CpG context: 17.9% C methylated in CHG context: 1.8% C methylated in CHH context: 2.4% C methylated in unknown context (CN or CHN): 15.9% Deleting temporary report files... Bismark completed in 0d 9h 46m 29s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 81761614) Using the subset file >EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 24388 and offset 2 (sequences written out: 81761613) Using the subset file >EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 81761614) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 24388 and offset 2 (sequences written out: 81761613) Using the subset file >EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Using the subset file >EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Input files are in FastQ format Writing a C -> T converted version of the input file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (81761613 sequences in total) Writing a C -> T converted version of the input file EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (81761614 sequences in total) Writing a C -> T converted version of the input file EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (81761613 sequences in total) Input files are EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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 EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (81761614 sequences in total) Input files are EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1 77 * 0 0 * * 0 0 TNATAAATTAATTAAATTTTTATTAATTTTTAAATTTTTTAAAATTTTTATTTTATATAATAATAAATTTTTTTTAATAATAATAAATTATATTATTAAATAAATAAATATATTTTTTTATTATTTTTAAATAATTAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2 141 * 0 0 * * 0 0 AAAATAATTTTAATTATTTAAAAATAATAAAAAAATATATTTATTTATTTAATAATATAATTTATTATTATTAAAAAAAATTTATTATTATATAAAATAAAAATTTTAAAAAATTTAAAAATTAATAAAAATTTAATTAATTTATTA FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFF:F:FFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27588:1047_1:N:0:AATGCCTC+TGGATCGA/1 77 * 0 0 * * 0 0 TNTATTAATGAAGATGAAATGTGGTGTATGATATGGTTTGAAAGGGTGTTTGTGATGAAATTTAGATATAGATGTGTGATGGTGGTTTGTTTTTTGA F#FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27588:1047_2:N:0:AATGCCTC+TGGATCGA/2 141 * 0 0 * * 0 0 TCAAAAAACAAACCACCATCACACATCTATATCTAAATTTCATCACAAACACCCTTTCAAACCATATCATACACCACATTTCATCTTCATTAATACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27588:1047_1:N:0:AATGCCTC+TGGATCGA/1 77 * 0 0 * * 0 0 TNTATCAATAAAAATAAAATATAATATATAATATAATTTAAAAAAATATTTATAATAAAATTTAAATATAAATATATAATAATAATTTATTTTTTAA F#FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27588:1047_2:N:0:AATGCCTC+TGGATCGA/2 141 * 0 0 * * 0 0 TTAAAAAATAAATTATTATTATATATTTATATTTAAATTTTATTATAAATATTTTTTTAAATTATATTATATATTATATTTTATTTTTATTGATATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1 99 NC_035787.1_GA_converted 40960853 0 105M1D17M1I24M = 40960853 147 CNACAAATCAACTAAACCTTTACTAATCTCTAAATTTTCTAAAACTCTTACCCCATACAATAATAAATTTTTCCTAATAATAATAAACCATATCACCAAATAAATAAATACATCCCCTTACCATTCCTAAACAACTAAAATTACCCC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-71 XN:i:0 XM:i:10 XO:i:2 XG:i:2 NM:i:12 MD:Z:1T0C42C23C0A19A0T13^A17C3C17A1 YS:i:-76 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2 147 NC_035787.1_GA_converted 40960853 0 105M1D17M1I24M = 40960853 -147 CAACAAATCAACTAAACCTTTACTAATCTCTAAATTTTCTAAAACTCTTACCCCATACAATAATAAATTTTTCCTAATAATAATAAACCATATCACCAAATAAATAAATACATCCCCTTACCATTCCTAAACAACTAAAATTACCCC FFFFFF:FFFFFFFFFFFFFFFFFFFF:F:FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF AS:i:-76 XN:i:0 XM:i:10 XO:i:2 XG:i:2 NM:i:12 MD:Z:1T0C42C23C0A19A0T13^A17C3C17A1 YS:i:-71 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27588:1047_1:N:0:AATGCCTC+TGGATCGA/1 77 * 0 0 * * 0 0 TNTATCAATAAAAATAAAATATAATATATAATATAATTTAAAAAAATATTTATAATAAAATTTAAATATAAATATATAATAATAATTTATTTTTTAA F#FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27588:1047_2:N:0:AATGCCTC+TGGATCGA/2 141 * 0 0 * * 0 0 TTAAAAAATAAATTATTATTATATATTTATATTTAAATTTTATTATAAATATTTTTTTAAATTATATTATATATTATATTTTATTTTTATTGATATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1 77 * 0 0 * * 0 0 CNACAAATCAACTAAACCTTTACTAATCTCTAAATTTTCTAAAACTCTTACCCCATACAATAATAAATTTTTCCTAATAATAATAAACCATATCACCAAATAAATAAATACATCCCCTTACCATTCCTAAACAACTAAAATTACCCC F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2 141 * 0 0 * * 0 0 GGGGTAATTTTAGTTGTTTAGGAATGGTAAGGGGATGTATTTATTTATTTGGTGATATGGTTTATTATTATTAGGAAAAATTTATTATTGTATGGGGTAAGAGTTTTAGAAAATTTAGAGATTAGTAAAGGTTTAGTTGATTTGTTG FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFF:F:FFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27588:1047_1:N:0:AATGCCTC+TGGATCGA/1 77 * 0 0 * * 0 0 TNTATTAATGAAGATGAAATGTGGTGTATGATATGGTTTGAAAGGGTGTTTGTGATGAAATTTAGATATAGATGTGTGATGGTGGTTTGTTTTTTGA F#FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27588:1047_2:N:0:AATGCCTC+TGGATCGA/2 141 * 0 0 * * 0 0 TCAAAAAACAAACCACCATCACACATCTATATCTAAATTTCATCACAAACACCCTTTCAAACCATATCATACACCACATTTCATCTTCATTAATACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1 77 * 0 0 * * 0 0 TNATAAATTAATTAAATTTTTATTAATTTTTAAATTTTTTAAAATTTTTATTTTATATAATAATAAATTTTTTTTAATAATAATAAATTATATTATTAAATAAATAAATATATTTTTTTATTATTTTTAAATAATTAAAATTATTTT F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2 141 * 0 0 * * 0 0 AAAATAATTTTAATTATTTAAAAATAATAAAAAAATATATTTATTTATTTAATAATATAATTTATTATTATTAAAAAAAATTTATTATTATATAAAATAAAAATTTTAAAAAATTTAAAAATTAATAAAAATTTAATTAATTTATTA FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFF:F:FFFFFFFFFFFFFFFFFFFF:FFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1114:18837:28416_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1171:28420:16016_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1174:4200:10802_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 3 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1464:26793:18208_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1524:8232:1407_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1662:3812:11913_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2137:8196:24862_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2148:17580:20854_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2367:2049:25081_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2401:30056:31313_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2434:2826:3223_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 21000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2602:29170:28181_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2628:31584:13510_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2652:3893:17722_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2652:3812:17832_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1105:24144:15499_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1137:5999:14387_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1137:6470:18677_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1150:10755:32800_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1149:10041:5102_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1234:32307:27289_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1246:14118:28134_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1269:23511:7388_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1310:12147:6621_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1323:2591:35352_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 3 Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1358:4101:24283_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 3 Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1474:25247:6699_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1566:29342:14356_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1610:12635:20181_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1644:16703:11851_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1655:12075:9095_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1672:28691:32518_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1672:28818:32550_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2102:11162:4445_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2108:11903:31908_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2117:27516:22999_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2136:4797:24768_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2236:31322:24799_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2236:32334:24424_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2245:8052:33098_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 61000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2251:18783:20369_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2249:21215:20541_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 62000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2301:32642:1658_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2307:15185:25473_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2309:15438:21245_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 64000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2325:4481:19210_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 3 Processed 65000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2431:22363:26976_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Processed 70000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2527:3965:10019_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2540:2781:6245_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 75000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2561:24668:13996_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2561:24252:12148_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2561:28854:34397_1:N:0:AATGCCTC+TGGATCGA NC_035781.1 2 Processed 77000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2618:11876:18239_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 3 Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2655:6479:32722_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2655:5448:36292_1:N:0:AATGCCTC+TGGATCGA NC_035780.1 2 Processed 81000000 sequence pairs so far Processed 81000000 sequence pairs so far 81761614 reads; of these: 81761614 (100.00%) were paired; of these: 66870476 (81.79%) aligned concordantly 0 times 6510136 (7.96%) aligned concordantly exactly 1 time 8381002 (10.25%) aligned concordantly >1 times 18.21% overall alignment rate 81761614 reads; of these: 81761614 (100.00%) were paired; of these: 64991911 (79.49%) aligned concordantly 0 times 7355362 (9.00%) aligned concordantly exactly 1 time 9414341 (11.51%) aligned concordantly >1 times 20.51% overall alignment rate 81761614 reads; of these: 81761614 (100.00%) were paired; of these: 66868844 (81.79%) aligned concordantly 0 times 6534893 (7.99%) aligned concordantly exactly 1 time 8357877 (10.22%) aligned concordantly >1 times 18.21% overall alignment rate 81761614 reads; of these: 81761614 (100.00%) were paired; of these: 65006365 (79.51%) aligned concordantly 0 times 7334387 (8.97%) aligned concordantly exactly 1 time 9420862 (11.52%) aligned concordantly >1 times 20.49% overall alignment rate Processed 81761614 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 327046456. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 327046456. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 327046456. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 327046456. Successfully deleted the temporary files EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 81761614 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1171685862 Total methylated C's in CpG context: 34730862 Total methylated C's in CHG context: 4217308 Total methylated C's in CHH context: 16372088 Total methylated C's in Unknown context: 952281 Total unmethylated C's in CpG context: 146173842 Total unmethylated C's in CHG context: 253105569 Total unmethylated C's in CHH context: 717086193 Total unmethylated C's in Unknown context: 4765054 C methylated in CpG context: 19.2% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in unknown context (CN or CHN): 16.7% 81761613 reads; of these: 81761613 (100.00%) were paired; of these: 66865524 (81.78%) aligned concordantly 0 times 6529507 (7.99%) aligned concordantly exactly 1 time 8366582 (10.23%) aligned concordantly >1 times 18.22% overall alignment rate 81761613 reads; of these: 81761613 (100.00%) were paired; of these: 65005927 (79.51%) aligned concordantly 0 times 7334323 (8.97%) aligned concordantly exactly 1 time 9421363 (11.52%) aligned concordantly >1 times 20.49% overall alignment rate 81761613 reads; of these: 81761613 (100.00%) were paired; of these: 66868106 (81.78%) aligned concordantly 0 times 6507737 (7.96%) aligned concordantly exactly 1 time 8385770 (10.26%) aligned concordantly >1 times 18.22% overall alignment rate 81761613 reads; of these: 81761613 (100.00%) were paired; of these: 64992387 (79.49%) aligned concordantly 0 times 7357155 (9.00%) aligned concordantly exactly 1 time 9412071 (11.51%) aligned concordantly >1 times 20.51% overall alignment rate Processed 81761613 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 327046452. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 327046452. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 327046452. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 327046452. Successfully deleted the temporary files EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 81761613 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1171599725 Total methylated C's in CpG context: 34705025 Total methylated C's in CHG context: 4216301 Total methylated C's in CHH context: 16390574 Total methylated C's in Unknown context: 953243 Total unmethylated C's in CpG context: 146170175 Total unmethylated C's in CHG context: 253110279 Total unmethylated C's in CHH context: 717007371 Total unmethylated C's in Unknown context: 4768676 C methylated in CpG context: 19.2% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in unknown context (CN or CHN): 16.7% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF08-EM03-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF08-EM03-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF08-EM03-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 163523227 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2343285587 Total methylated C's in CpG context: 69435887 Total methylated C's in CHG context: 8433609 Total methylated C's in CHH context: 32762662 Total methylated C's in Unknown context: 1905524 Total unmethylated C's in CpG context: 292344017 Total unmethylated C's in CHG context: 506215848 Total unmethylated C's in CHH context: 1434093564 Total unmethylated C's in Unknown context: 9533730 C methylated in CpG context: 19.2% C methylated in CHG context: 1.6% C methylated in CHH context: 2.2% C methylated in unknown context (CN or CHN): 16.7% Deleting temporary report files... Bismark completed in 0d 7h 14m 3s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools path provided as: '/home/shared/samtools-1.12/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 '/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs'): /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/ 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: 2 Current working directory is: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 34300 and offset 2 (sequences written out: 59336133) Using the subset file >EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 59336133) Using the subset file >EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 1 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz<) Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 34300 and offset 2 (sequences written out: 59336133) Using the subset file >EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Finished subdividing /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz for PID: 0 and offset 1 (sequences written out: 59336133) Using the subset file >EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz< as new in-file 2 (instead of >/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Writing a C -> T converted version of the input file EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz (59336133 sequences in total) Writing a C -> T converted version of the input file EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz to EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz (59336133 sequences in total) Writing a C -> T converted version of the input file EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz Writing a G -> A converted version of the input file EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz to EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Created C -> T as well as G -> A converted versions of the FastQ file EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz (59336133 sequences in total) Input files are EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created C -> T as well as G -> A converted versions of the FastQ file EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz (59336133 sequences in total) Input files are EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/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 EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27769:1047_1:N:0:AACGTTCC+AGTACTCC/1 77 * 0 0 * * 0 0 TNTTATTTAAAAAAAAATATAATATATTAAAAATTTAGATAGATAAATAAAAATAAAAGTATGGGAGATAGAATTTTTTTTTGTAAAAATTTTATGTTATTTGTAAAATTTTTTGATTAAATTTTTGTTGGTTGAATATAGGTTTTTATA F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF::FFFFFF:FFFFFFF:::F:F:,F:FFF:FFFFFFF,F:FF:FF,FFF:FFFF:F,:FF::FFF,:F:FFFFFF,:,, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27769:1047_2:N:0:AACGTTCC+AGTACTCC/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTATTTAAAAATTAAAAAAAAAAAATTAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAACAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,,FF:,,,,F,FFF,FF,FFF,,,F:,:,,,,:FFFF:,FFFF,F,::F,,FFFFFFFFFFF,,,,F:F,F,F:FFFF,FFF:FFFF:F,,:,,:FFFF:,,:,:,,,F:,,,F,,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26467:1047_1:N:0:AACGTTCC+AGTACTCC/1 77 * 0 0 * * 0 0 ANAATAATATTTATAAAAAAAATTAAAATATAATATTTAAAAAAAATAAAATATTTTTTATTTTAAAAATAATTATTATATAAATATATTATTTGTAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26467:1047_2:N:0:AACGTTCC+AGTACTCC/2 141 * 0 0 * * 0 0 TTACAAATAATATATTTATATAATAATTATTTTTAAAATAAAAAATATTTTATTTTTTTTAAATATTATATTTTAATTTTTTTTATAAATATTATTTT FFFFFFF:FFFFFF:F:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26467:1047_1:N:0:AACGTTCC+AGTACTCC/1 77 * 0 0 * * 0 0 ANAACAACATCTACAAAAAAAACTAAAACACAATACCCAAAAAAAACAAAACACTTCCCATTCCAAAAATAACCATTATACAAATATACCACCTATAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26467:1047_2:N:0:AACGTTCC+AGTACTCC/2 141 * 0 0 * * 0 0 TTATAGGTGGTATATTTGTATAATGGTTATTTTTGGAATGGGAAGTGTTTTGTTTTTTTTGGGTATTGTGTTTTAGTTTTTTTTGTAGATGTTGTTTT FFFFFFF:FFFFFF:F:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27769:1047_1:N:0:AACGTTCC+AGTACTCC/1 77 * 0 0 * * 0 0 CNCCACCTAAAAAAAAACATAACACACTAAAAACCTAAACAAACAAACAAAAATAAAAATATAAAAAATAAAATTTTTTTTTATAAAAATTTTATATTATTTATAAAATTTTTTAATTAAATTTTTATTAATTAAATATAAATTTTTATA F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF::FFFFFF:FFFFFFF:::F:F:,F:FFF:FFFFFFF,F:FF:FF,FFF:FFFF:F,:FF::FFF,:F:FFFFFF,:,, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27769:1047_2:N:0:AACGTTCC+AGTACTCC/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTATTTAAAAATTAAAAAAAAAAAATTAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAATAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,,FF:,,,,F,FFF,FF,FFF,,,F:,:,,,,:FFFF:,FFFF,F,::F,,FFFFFFFFFFF,,,,F:F,F,F:FFFF,FFF:FFFF:F,,:,,:FFFF:,,:,:,,,F:,,,F,,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:26467:1047_1:N:0:AACGTTCC+AGTACTCC/1 83 NC_035781.1_CT_converted 8258718 2 98M = 8258718 -98 TTATAGGTGGTATATTTGTATAATGGTTATTTTTGGAATGGGAAGTGTTTTGTTTTTTTTGGGTATTGTGTTTTAGTTTTTTTTGTAGATGTTGTTNT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F AS:i:-19 XS:i:-25 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:0A0A1A92A1 YS:i:-24 YT:Z:CP GWNJ-1012:512:GW210315000:4:1101:26467:1047_2:N:0:AACGTTCC+AGTACTCC/2 163 NC_035781.1_CT_converted 8258718 2 98M = 8258718 98 TTATAGGTGGTATATTTGTATAATGGTTATTTTTGGAATGGGAAGTGTTTTGTTTTTTTTGGGTATTGTGTTTTAGTTTTTTTTGTAGATGTTGTTTT FFFFFFF:FFFFFF:F:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFF AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:0A0A1A92A1 YS:i:-19 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27769:1047_1:N:0:AACGTTCC+AGTACTCC/1 77 * 0 0 * * 0 0 CNCCACCTAAAAAAAAACATAACACACTAAAAACCTAAACAAACAAACAAAAATAAAAATATAAAAAATAAAATTTTTTTTTATAAAAATTTTATATTATTTATAAAATTTTTTAATTAAATTTTTATTAATTAAATATAAATTTTTATA F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF::FFFFFF:FFFFFFF:::F:F:,F:FFF:FFFFFFF,F:FF:FF,FFF:FFFF:F,:FF::FFF,:F:FFFFFF,:,, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27769:1047_2:N:0:AACGTTCC+AGTACTCC/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTATTTAAAAATTAAAAAAAAAAAATTAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAATAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,,FF:,,,,F,FFF,FF,FFF,,,F:,:,,,,:FFFF:,FFFF,F,::F,,FFFFFFFFFFF,,,,F:F,F,F:FFFF,FFF:FFFF:F,,:,,:FFFF:,,:,:,,,F:,,,F,,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.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:GW210315000:4:1101:27769:1047_1:N:0:AACGTTCC+AGTACTCC/1 77 * 0 0 * * 0 0 TNTTATTTAAAAAAAAATATAATATATTAAAAATTTAGATAGATAAATAAAAATAAAAGTATGGGAGATAGAATTTTTTTTTGTAAAAATTTTATGTTATTTGTAAAATTTTTTGATTAAATTTTTGTTGGTTGAATATAGGTTTTTATA F#FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFF::FFFFFF:FFFFFFF:::F:F:,F:FFF:FFFFFFF,F:FF:FF,FFF:FFFF:F,:FF::FFF,:F:FFFFFF,:,, YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:27769:1047_2:N:0:AACGTTCC+AGTACTCC/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTATTTAAAAATTAAAAAAAAAAAATTAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAACAAAAAAAAAAAAAAAAAAAA FFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,,FF:,,,,F,FFF,FF,FFF,,,F:,:,,,,:FFFF:,FFFF,F,::F,,FFFFFFFFFFF,,,,F:F,F,F:FFFF,FFF:FFFF:F,,:,,:FFFF:,,:,:,,,F:,,,F,,FFFF YT:Z:UP Found first alignment: GWNJ-1012:512:GW210315000:4:1101:26467:1047_1:N:0:AACGTTCC+AGTACTCC/1 77 * 0 0 * * 0 0 ANAATAATATTTATAAAAAAAATTAAAATATAATATTTAAAAAAAATAAAATATTTTTTATTTTAAAAATAATTATTATATAAATATATTATTTGTAA F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP GWNJ-1012:512:GW210315000:4:1101:26467:1047_2:N:0:AACGTTCC+AGTACTCC/2 141 * 0 0 * * 0 0 TTACAAATAATATATTTATATAATAATTATTTTTAAAATAAAAAATATTTTATTTTTTTTAAATATTATATTTTAATTTTTTTTATAAATATTATTTT FFFFFFF:FFFFFF:F:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam <<< Reading in the sequence files EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz Reading in the sequence files EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1119:2546:30545_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1120:21486:30812_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1138:23764:27868_1:N:0:AACGTTCC+AGTACTCC NC_007175.2 2 Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1212:8784:2550_1:N:0:AACGTTCC+AGTACTCC NC_007175.2 2 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1254:18774:18850_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1260:1570:6277_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 5000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1272:10321:34773_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 6000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1360:23592:28823_1:N:0:AACGTTCC+AGTACTCC NC_007175.2 2 Processed 8000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1401:17969:25911_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 3 Processed 9000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:1615:17933:30326_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2233:10104:11068_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Processed 20000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2241:17309:8234_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2275:6560:26193_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2321:20283:22686_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2323:3242:34882_1:N:0:AACGTTCC+GGTACTCC NC_007175.2 17106 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2321:19497:20353_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2323:2853:33646_1:N:0:AACGTTCC+GGTACTCC NC_007175.2 17106 Processed 23000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2455:2926:1861_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Processed 26000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2514:10872:21198_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2537:12048:35289_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 28000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2551:17083:31172_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1012:512:GW210315000:4:2553:12753:34663_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 29000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1213:9543:11193_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 35000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1236:17164:28025_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1242:7102:25911_1:N:0:AACGTTCC+AGTACTCC NC_035782.1 3 Processed 36000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1339:23194:9189_1:N:0:AACGTTCC+GGTACTCC NC_035780.1 2 Processed 38000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1443:14678:33927_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1461:29369:19069_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 41000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1520:31846:1094_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1520:31792:1376_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Processed 42000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1619:3251:4398_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:1620:6090:7467_1:N:0:GACGTTCC+AGTACTCC NC_035780.1 2 Processed 44000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2112:13747:27899_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:14262:19179_1:N:0:AACGTTCC+AGTACTCC NC_007175.2 1 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2262:13829:26068_1:N:0:AACGTTCC+AGTACTCC NC_007175.2 1 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2269:16432:23750_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2345:24921:21355_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 65668299 Processed 52000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2606:28094:12821_1:N:0:AACGTTCC+AGTACTCC NC_035781.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2617:4463:35806_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Chromosomal sequence could not be extracted for GWNJ-1013:195:GW2105211192nd:2:2627:8287:6167_1:N:0:AACGTTCC+AGTACTCC NC_035780.1 2 Processed 58000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 59000000 sequence pairs so far 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48838582 (82.31%) aligned concordantly 0 times 4667741 (7.87%) aligned concordantly exactly 1 time 5829810 (9.83%) aligned concordantly >1 times 17.69% overall alignment rate 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48853945 (82.33%) aligned concordantly 0 times 4680647 (7.89%) aligned concordantly exactly 1 time 5801541 (9.78%) aligned concordantly >1 times 17.67% overall alignment rate 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48502566 (81.74%) aligned concordantly 0 times 4826436 (8.13%) aligned concordantly exactly 1 time 6007131 (10.12%) aligned concordantly >1 times 18.26% overall alignment rate 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48501109 (81.74%) aligned concordantly 0 times 4803572 (8.10%) aligned concordantly exactly 1 time 6031452 (10.16%) aligned concordantly >1 times 18.26% overall alignment rate Processed 59336133 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 237344532. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 237344532. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 237344532. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 237344532. Successfully deleted the temporary files EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz, EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz, EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.1.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 59336133 Final Cytosine Methylation Report ================================= Total number of C's analysed: 740246189 Total methylated C's in CpG context: 22363499 Total methylated C's in CHG context: 4465417 Total methylated C's in CHH context: 17529411 Total methylated C's in Unknown context: 1029829 Total unmethylated C's in CpG context: 90668688 Total unmethylated C's in CHG context: 159450502 Total unmethylated C's in CHH context: 445768672 Total unmethylated C's in Unknown context: 3683139 C methylated in CpG context: 19.8% C methylated in CHG context: 2.7% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 21.9% 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48505064 (81.75%) aligned concordantly 0 times 4824365 (8.13%) aligned concordantly exactly 1 time 6006704 (10.12%) aligned concordantly >1 times 18.25% overall alignment rate 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48837103 (82.31%) aligned concordantly 0 times 4666739 (7.86%) aligned concordantly exactly 1 time 5832291 (9.83%) aligned concordantly >1 times 17.69% overall alignment rate 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48850781 (82.33%) aligned concordantly 0 times 4684396 (7.89%) aligned concordantly exactly 1 time 5800956 (9.78%) aligned concordantly >1 times 17.67% overall alignment rate 59336133 reads; of these: 59336133 (100.00%) were paired; of these: 48504179 (81.74%) aligned concordantly 0 times 4805617 (8.10%) aligned concordantly exactly 1 time 6026337 (10.16%) aligned concordantly >1 times 18.26% overall alignment rate Processed 59336133 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 237344532. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 237344532. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 237344532. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 237344532. Successfully deleted the temporary files EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz, EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz, EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_C_to_T.fastq.gz and EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz.temp.2.gz_G_to_A.fastq.gz Final Alignment report ====================== Sequence pairs analysed in total: 59336133 Final Cytosine Methylation Report ================================= Total number of C's analysed: 740211437 Total methylated C's in CpG context: 22346356 Total methylated C's in CHG context: 4470955 Total methylated C's in CHH context: 17531196 Total methylated C's in Unknown context: 1031487 Total unmethylated C's in CpG context: 90688746 Total unmethylated C's in CHG context: 159479969 Total unmethylated C's in CHH context: 445694215 Total unmethylated C's in Unknown context: 3686169 C methylated in CpG context: 19.8% C methylated in CHG context: 2.7% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 21.9% Now waiting for all child processes to complete Right, cleaning up now... Deleting temporary sequence files... Now merging BAM files EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam into >>> EF08-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam <<< Merging from file >> EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam << Merging from file >> EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_pe.bam << Deleting temporary BAM files... Writing report to /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF08-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt Now merging temporary reports EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt into >>> /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/EF08-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_PE_report.txt <<< Merging from file >> EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt << Merging from file >> EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 118672266 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1480457626 Total methylated C's in CpG context: 44709855 Total methylated C's in CHG context: 8936372 Total methylated C's in CHH context: 35060607 Total methylated C's in Unknown context: 2061316 Total unmethylated C's in CpG context: 181357434 Total unmethylated C's in CHG context: 318930471 Total unmethylated C's in CHH context: 891462887 Total unmethylated C's in Unknown context: 7369308 C methylated in CpG context: 19.8% C methylated in CHG context: 2.7% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 21.9% Deleting temporary report files... Bismark completed in 0d 5h 0m 7s ==================== Bismark run complete ====================