[Fri Oct 9 11:29:23 PDT 2026] Pum2 (Pum/Pumalin) Detecting adapter sequence for read1... >Illumina TruSeq Adapter Read 1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA Detecting adapter sequence for read2... >Illumina TruSeq Adapter Read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Read1 before filtering: total reads: 37572534 total bases: 5673452634 Q20 bases: 5607736979(98.8417%) Q30 bases: 5435657447(95.8086%) Q40 bases: 5435657447(95.8086%) Read2 before filtering: total reads: 37572534 total bases: 5673452634 Q20 bases: 5598902319(98.686%) Q30 bases: 5416918338(95.4783%) Q40 bases: 5416918338(95.4783%) Read1 after filtering: total reads: 36956713 total bases: 5116820447 Q20 bases: 5072754128(99.1388%) Q30 bases: 4940125345(96.5468%) Q40 bases: 4940125345(96.5468%) Read2 after filtering: total reads: 36956713 total bases: 5118550090 Q20 bases: 5070808889(99.0673%) Q30 bases: 4925046193(96.2196%) Q40 bases: 4925046193(96.2196%) Filtering result: reads passed filter: 73913426 reads failed due to low quality: 590648 reads failed due to too many N: 1460 reads failed due to too short: 639534 reads with adapter trimmed: 7206981 bases trimmed due to adapters: 162652945 Duplication rate: 5.61252% Insert size peak (evaluated by paired-end reads): 221 JSON report: output/13-wgbs/fastp/Pum2.fastp.json HTML report: output/13-wgbs/fastp/Pum2.fastp.html fastp -i /mmfs1/gscratch/scrubbed/sr320/chil-wgbs/PUM2 (paired)_R1.fastq.gz -I /mmfs1/gscratch/scrubbed/sr320/chil-wgbs/PUM2 (paired)_R2.fastq.gz -o output/13-wgbs/trimmed/Pum2_R1.fq.gz -O output/13-wgbs/trimmed/Pum2_R2.fq.gz --detect_adapter_for_pe --trim_poly_g --trim_front1 10 --trim_front2 10 --length_required 50 --thread 16 --json output/13-wgbs/fastp/Pum2.fastp.json --html output/13-wgbs/fastp/Pum2.fastp.html fastp v1.0.1, time used: 96 seconds Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools' Reference genome folder provided is data/13-wgbs-genome/ (absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 2 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil'): output/13-wgbs/trimmed/Pum2_R1.fq.gz output/13-wgbs/trimmed/Pum2_R2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/ Using temp directory: /tmp/13-wgbs-Pum2-1046737 Temporary files will be written into the directory: /tmp/13-wgbs-Pum2-1046737/ Summary of all aligner options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Running Bismark Parallel version. Number of parallel instances to be spawned: 8 Current working directory is: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ chr Chromosome_10A (41401248 bp) chr Chromosome_2A (98156180 bp) chr Chromosome_4A (93973257 bp) chr Chromosome_6A (76092957 bp) chr Chromosome_1B (231619483 bp) chr Chromosome_5B (125625032 bp) chr Chromosome_6B (129267145 bp) chr Chromosome_7B (183991082 bp) chr Chromosome_8B (108828118 bp) chr Chromosome_9B (91966420 bp) Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz Paired-end alignments will be performed ======================================= Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz The provided filenames for paired-end alignments are output/13-wgbs/trimmed/Pum2_R1.fq.gz and output/13-wgbs/trimmed/Pum2_R2.fq.gz Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 0 and offset 2 (sequences written out: 4619589) Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 0 and offset 7 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.2< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.7< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 0 and offset 1 (sequences written out: 4619590) Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 0 and offset 3 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.1< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 0 and offset 4 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.3< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.4< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 0 and offset 6 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.6< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 0 and offset 5 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.5< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum2_R1.fq.gz for PID: 1048111 and offset 8 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.8< as new in-file 1 (instead of >output/13-wgbs/trimmed/Pum2_R1.fq.gz<) Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 0 and offset 6 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.6< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.6 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.6_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 0 and offset 4 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.4< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.4 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.4_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 0 and offset 2 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.2< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.2 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.2_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 0 and offset 3 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.3< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.3 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.3_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 0 and offset 1 (sequences written out: 4619590) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.1< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.1 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.1_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 0 and offset 7 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.7< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.7 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.7_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 0 and offset 5 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.5< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.5 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.5_C_to_T.fastq Finished subdividing output/13-wgbs/trimmed/Pum2_R2.fq.gz for PID: 1048111 and offset 8 (sequences written out: 4619589) Using the subset file >/tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.8< as new in-file 2 (instead of >output/13-wgbs/trimmed/Pum2_R2.fq.gz<) Input files are in FastQ format Writing a C -> T converted version of the input file Pum2_R1.fq.gz.temp.8 to /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.8_C_to_T.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.6 (4619589 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.6 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.6_G_to_A.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.4 (4619589 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.4 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.4_G_to_A.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.2 (4619589 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.2 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.2_G_to_A.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.3 (4619589 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.3 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.3_G_to_A.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.1 (4619590 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.1 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.1_G_to_A.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.7 (4619589 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.7 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.7_G_to_A.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.5 (4619589 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.5 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.5_G_to_A.fastq Created C -> T converted version of the FastQ file Pum2_R1.fq.gz.temp.8 (4619589 sequences in total) Writing a G -> A converted version of the input file Pum2_R2.fq.gz.temp.8 to /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.8_G_to_A.fastq Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.6 (4619589 sequences in total) Input files are Pum2_R1.fq.gz.temp.6_C_to_T.fastq and Pum2_R2.fq.gz.temp.6_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.6_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.6_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.2 (4619589 sequences in total) Input files are Pum2_R1.fq.gz.temp.2_C_to_T.fastq and Pum2_R2.fq.gz.temp.2_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.2_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.2_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.4 (4619589 sequences in total) Input files are Pum2_R1.fq.gz.temp.4_C_to_T.fastq and Pum2_R2.fq.gz.temp.4_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.4_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.4_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.3 (4619589 sequences in total) Input files are Pum2_R1.fq.gz.temp.3_C_to_T.fastq and Pum2_R2.fq.gz.temp.3_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.3_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.3_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.1 (4619590 sequences in total) Input files are Pum2_R1.fq.gz.temp.1_C_to_T.fastq and Pum2_R2.fq.gz.temp.1_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.1_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.1_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.7 (4619589 sequences in total) Input files are Pum2_R1.fq.gz.temp.7_C_to_T.fastq and Pum2_R2.fq.gz.temp.7_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.7_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.7_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.8 (4619589 sequences in total) Input files are Pum2_R1.fq.gz.temp.8_C_to_T.fastq and Pum2_R2.fq.gz.temp.8_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.8_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.8_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Created G -> A converted version of the FastQ file Pum2_R2.fq.gz.temp.5 (4619589 sequences in total) Input files are Pum2_R1.fq.gz.temp.5_C_to_T.fastq and Pum2_R2.fq.gz.temp.5_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ with the specified options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.5_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.5_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00129:489:23JFWNLT4:8:1229:7974:4559_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_7B_CT_converted 183439824 0 80M3D61M = 183439883 200 TGTGGTAAGTTTGGTTGAAATTGGTTTAGTGGTTTTTGAGAAGAAGTTGAAAATGTGAAAAGTTTATGATGTTGTTGTTGATGATGATAGGTAATAGATATATTTTGATTAGAATAGTTTATTTGAGTTTTTGGTTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-56 XN:i:0 XM:i:7 XO:i:1 XG:i:3 NM:i:10 MD:Z:40G36A2^ATA5A7G1G20T23T0 YS:i:-69 YT:Z:CP LH00129:489:23JFWNLT4:8:1229:7974:4559_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_7B_CT_converted 183439883 0 21M3D66M1I43M2I8M = 183439824 -200 AAGTTTATGATGTTGTTGTTGATGATGATAGGTAATAGATATATTTTGATTAGAATAGTTTATTTGAGTTTTTGGTTTAGGAAAGTTAAAAAAAGTATAAATAAAATATGGAATAGAAAATGGAATAGAATAAAAAAAAAA IIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIIII9IIIIIIIII9IIIIII99IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII AS:i:-69 XS:i:-69 XN:i:0 XM:i:6 XO:i:3 XG:i:6 NM:i:12 MD:Z:18A2^ATA5A7G1G20T23T56 YS:i:-56 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.6_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.6_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1223:11687:14382_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_8B_CT_converted 47121083 23 141M = 47121288 335 AGGGAGTTTGATAGTGGGTTATTGGAAAATATTTATGTTGGAAAAGATATAATTTAAAATAAGTAGAATGATGTGGGAATGTTTGATAAAGAAATTAAATAATAGATAAATATTTAAAAAAGAATTTAATTTATGATATTG IIIII9IIIIIIIII9IIIIII9IIIIII9IIIIIIIII9IIIIIIII*IIIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIII9I9IIIIIIII9IIII9II9III AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:99A15T25 YS:i:-62 YT:Z:CP LH00129:489:23JFWNLT4:8:1223:11687:14382_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_8B_CT_converted 47121288 23 125M11I5M = 47121083 -335 TTGTTTTATTAAGGAGATGAGGGAGGAATATGTAATAGATGGGGGTTAGTTGAAATATAGTAATATTTTTTAGTAATATAGTGAAAGGTTAAGATAATGAAAAGTGATTAAATTAATAGTTTTTATTTTTTTTTTTTTTTT II999III*9I99IIIIIIIIIII99IIIIII9IIII9I9I9II9I9IIIIIIIIIIIIIIIIIII9*IIIIIIIIIIIIIIIIIIIII*IIIIIIIIIIIIII9III9IIIIIIIIIIIII9I9II9III9IIII*9I9I AS:i:-62 XN:i:0 XM:i:4 XO:i:1 XG:i:11 NM:i:15 MD:Z:83G42A0A0G1 YS:i:-12 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:1149:7189:8833_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_4A_CT_converted 57143809 42 141M = 57144072 404 AGGTGTTTTAATAGTTTGAGTTATTTGGTTATTTGTGATTAAATTTAGTTGATTGTTATATTTTGTTTTTATATTGTTTTTGGTATATTGTATTTGATAATGGATAATTTTGTTTATTTGATTAAGATATAGGGTTTATGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:-6 YT:Z:CP LH00129:489:23JFWNLT4:8:1149:7189:8833_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_4A_CT_converted 57144072 42 141M = 57143809 -404 TAGGAATGGTTGGAAATTAATTATTATTTAGGTATAAAGATTAGTTTAGAAAAAAAGATAAATTTTTAATTAGGTTTAGGTTTTAAATAAATTAATGAATTATGAAATGTTTGTGATTATGAATAATTTAGTTATATTGTT IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:49G91 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.2_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.2_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.8_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.8_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1380:5344:26741_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_1B_CT_converted 191434079 42 141M = 191434264 326 TTGTTTAATTATTTATTTTGTATTGTTTATAGGAGTTATGAGATTGATTATTGTTTGTTATTTTTATTTTTTATGTATATGTTATTGTAGAGGTTTTATGATTTTTAAAAAAGTGGAAGAAGTGGGAGAATAAGAAGTGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1380:5344:26741_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_1B_CT_converted 191434264 42 141M = 191434079 -326 ATTATAGATATTTAATGGATAGATATTTGTGATATATTATAGGTGATTATTGGATAATTTGATGATTTTATATTTATATGTATGTTGATGATATGGATAGTGATTAATTGTATAAATTTTATAAGTAATATAAAATAGATA IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.1_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.1_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1258:12553:23392_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_9B_CT_converted 81701784 1 123M6I11M = 81701774 -144 ATAAAATGATGGTAAAATTTGTAGATTTTTTTTGTTGAATTTAAGTAAAAATATATTTAAATTTGTATTTAAATTATAAATTTTATGTAAAAAGTATTGAAAAGTGTGTTTTTATAAGTAATGTTTTTTTTTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-35 XS:i:-35 XN:i:0 XM:i:2 XO:i:1 XG:i:6 NM:i:8 MD:Z:130A1A1 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1258:12553:23392_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_9B_CT_converted 81701774 1 140M = 81701784 144 ATATTTTAATATAAAATGATGGTAAAATTTGTAGATTTTTTTTGTTGAATTTAAGTAAAAATATATTTAAATTTGTATTTAAATTATAAATTTTATGTAAAAAGTATTGAAAAGTGTGTTTTTATAAGTAATGTTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:140 YS:i:-35 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:2485:43602:22383_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 TTTTAATTTTTATTTGAATGAAAAATGTTGATTAGATATTGTGATTTTATTTAAAGGGTTATTATAAAGTTAGATTTGATATTAAATATTTAATGTTAATTTGATTAATATGAATTTGTTGTTTTGGAAAAGGTTAAGGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00129:489:23JFWNLT4:8:2485:43602:22383_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 TTAACCTATTCAATATCTCATAAACTATATAAAATAAAATTTTCATATCTAATATTTAAATTTCTTATAACAAACCTTTCATTTCATACTATAACTTTATAACCTTAACCTTTTCCAAAACAACAAATTCATATTAATCAA IIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII*IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.7_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.7_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1149:8370:12644_1:N:0:TGAGTACT+GACAATAA/1 99 Chromosome_4A_CT_converted 17315978 1 141M = 17316244 407 TTTAGTAAAGAGAGTTATTGTTTAGTAAAGAAAGTTATTGTTTAGTAAAGAGAGTTATTGTTTAGTATAGAAAGTTATTGTTTAGTAAAGAGAGTTATTGTTTAGTATAGAAAGTTATTGTTTAGTAAAGAGAGTTATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII*IIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9I AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:-6 YT:Z:CP LH00129:489:23JFWNLT4:8:1149:8370:12644_2:N:0:TGAGTACT+GACAATAA/2 147 Chromosome_4A_CT_converted 17316244 1 141M = 17315978 -407 AAAGAGAGTTATTGTTTAGTAGATAAAGGTGTTGTTTAGTAAAGAGAGTTGTTGTTTAGTAAAGAGAGTTATTGTTTAGTAAAGAGAGTTATTGTTTAGTAAAGAGAGTTATTGTTTAGTAAAGAGAGTTATTGTTTAGTA IIIIIII9IIIIIIIIII9IIII*IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:50A90 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.4_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.4_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.5_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.5_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:2429:16023:25507_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 AAAAAAAAAATATGTGTGTTTTTTATTATATGAGATTTTAAAATAGGGTAGGTATTTTAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAAAGGTGGGGGGTGGGTTTTTATTATTTTTTTTTTAAATT I9IIIIIII*99I99II*II9III*I9I9II9I9IIIIIII9*9III*9II99II*99*99I9I99II999III*IIIIIIIIIIIIIII9I99II9I*999I****9***9I*9*9*9******9**999999999***9 YT:Z:UP LH00129:489:23JFWNLT4:8:2429:16023:25507_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 TTATAACATACCACCACTACCATTTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCAACCCCCCCCCCCTCTTCCAAAACCCCCCACAAACAAAAAACACCACCTTTTTTTTTCCCCCCAAAAAAAACC IIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII999III99I*9I99III*II**III99***9I*999I*9*9*99*9***999**********9*9****9**99*99999*9**9*****9I9**** YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.3_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.3_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 2 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00129:489:23JFWNLT4:8:1229:7974:4559_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_7B_GA_converted 958979 0 52M3D89M = 958923 -200 TCCTAAACCAAAAACTCAAATAAACTATTCTAATCAAAATATATCTATTACCTATCATCATCAACAACAACATCATAAACTTTTCACATTTTCAACTTCTTCTCAAAAACCACTAAACCAATTTCAACCAAACTTACCACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-56 XN:i:0 XM:i:7 XO:i:1 XG:i:3 NM:i:10 MD:Z:0A23A20C1C4^TAT6T4T36C40 YS:i:-69 YT:Z:CP LH00129:489:23JFWNLT4:8:1229:7974:4559_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_7B_GA_converted 958923 0 1M2I44M1I63M3D30M = 958979 200 TTTTTTTTTTATTCTATTCCATTTTCTATTCCATATTTTATTTATACTTTTTTTAACTTTCCTAAACCAAAAACTCAAATAAACTATTCTAATCAAAATATATCTATTACCTATCATCATCAACAACAACATCATAAACTT IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII99IIIIII9IIIIIIIII9IIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIII AS:i:-69 XS:i:-69 XN:i:0 XM:i:6 XO:i:3 XG:i:6 NM:i:12 MD:Z:56A23A20C1C4^TAT6T4T18 YS:i:-56 YT:Z:CP >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.6_bismark_bt2_pe.bam <<< Found first alignment: LH00129:489:23JFWNLT4:8:1149:8370:12644_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 TTTAGTAAAGAGAGTTATTGTTTAGTAAAGAAAGTTATTGTTTAGTAAAGAGAGTTATTGTTTAGTATAGAAAGTTATTGTTTAGTAAAGAGAGTTATTGTTTAGTATAGAAAGTTATTGTTTAGTAAAGAGAGTTATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII*IIIIIIIIIIIII9IIIIIII9IIIIIIIIIII9I YT:Z:UP LH00129:489:23JFWNLT4:8:1149:8370:12644_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 TACTAAACAATAACTCTCTTTACTAAACAATAACTCTCTTTACTAAACAATAACTCTCTTTACTAAACAATAACTCTCTTTACTAAACAACAACTCTCTTTACTAAACAACACCTTTATCTACTAAACAATAACTCTCTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII*IIII9IIIIIIIIII9IIIIIII YT:Z:UP Found first alignment: LH00129:489:23JFWNLT4:8:2485:43602:22383_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_5B_GA_converted 83283187 42 141M = 83283087 -241 AACCTTAACCTTTTCCAAAACAACAAATTCATATTAATCAAATTAACATTAAATATTTAATATCAAATCTAACTTTATAATAACCCTTTAAATAAAATCACAATATCTAATCAACATTTTTCATTCAAATAAAAATTAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:68T72 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:2485:43602:22383_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_5B_GA_converted 83283087 42 141M = 83283187 241 TTAACCTATTCAATATCTCATAAACTATATAAAATAAAATTTTCATATCTAATATTTAAATTTCTTATAACAAACCTTTCATTTCATACTATAACTTTATAACCTTAACCTTTTCCAAAACAACAAATTCATATTAATCAA IIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII*IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:-6 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:2429:16023:25507_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 AAAAAAAAAATATGTGTGTTTTTTATTATATGAGATTTTAAAATAGGGTAGGTATTTTAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAAAGGTGGGGGGTGGGTTTTTATTATTTTTTTTTTAAATT I9IIIIIII*99I99II*II9III*I9I9II9I9IIIIIII9*9III*9II99II*99*99I9I99II999III*IIIIIIIIIIIIIII9I99II9I*999I****9***9I*9*9*9******9**999999999***9 YT:Z:UP LH00129:489:23JFWNLT4:8:2429:16023:25507_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 TTATAACATACCACCACTACCATTTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCAACCCCCCCCCCCTCTTCCAAAACCCCCCACAAACAAAAAACACCACCTTTTTTTTTCCCCCCAAAAAAAACC IIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII999III99I*9I99III*II**III99***9I*999I*9*9*99*9***999**********9*9****9**99*99999*9**9*****9I9**** YT:Z:UP >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.5_bismark_bt2_pe.bam <<< Found first alignment: LH00129:489:23JFWNLT4:8:1258:12553:23392_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_5B_GA_converted 114681729 1 4M6I130M = 114681733 144 AAAAAAAAAAAAAAAAACATTACTTATAAAAACACACTTTTCAATACTTTTTACATAAAATTTATAATTTAAATACAAATTTAAATATATTTTTACTTAAATTCAACAAAAAAAATCTACAAATTTTACCATCATTTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-35 XS:i:-35 XN:i:0 XM:i:2 XO:i:1 XG:i:6 NM:i:8 MD:Z:1T1T130 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1258:12553:23392_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_5B_GA_converted 114681733 1 140M = 114681729 -144 AAAAAAACATTACTTATAAAAACACACTTTTCAATACTTTTTACATAAAATTTATAATTTAAATACAAATTTAAATATATTTTTACTTAAATTCAACAAAAAAAATCTACAAATTTTACCATCATTTTATATTAAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:140 YS:i:-35 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:1223:11687:14382_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_8B_GA_converted 24568135 24 141M = 24567941 -335 CAATATCATAAATTAAATTCTTTTTTAAATATTTATCTATTATTTAATTTCTTTATCAAACATTCCCACATCATTCTACTTATTTTAAATTATATCTTTTCCAACATAAATATTTTCCAATAACCCACTATCAAACTCCCT III9II9IIII9IIIIIIII9I9IIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIII*IIIIIIII9IIIIIIIII9IIIIII9IIIIII9IIIIIIIII9IIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:-56 YT:Z:CP LH00129:489:23JFWNLT4:8:1223:11687:14382_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_8B_GA_converted 24567941 24 4M11I126M = 24568135 335 AAAAAAAAAAAAAAAATAAAAACTATTAATTTAATCACTTTTCATTATCTTAACCTTTCACTATATTACTAAAAAATATTACTATATTTCAACTAACCCCCATCTATTACATATTCCTCCCTCATCTCCTTAATAAAACAA I9I9*IIII9III9II9I9IIIIIIIIIIIII9III9IIIIIIIIIIIIII*IIIIIIIIIIIIIIIIIIIII*9IIIIIIIIIIIIIIIIIII9I9II9I9I9IIII9IIIIII99IIIIIIIIIII99I9*III999II AS:i:-56 XN:i:0 XM:i:3 XO:i:1 XG:i:11 NM:i:14 MD:Z:1C0T0T126 YS:i:0 YT:Z:CP Found first alignment: LH00129:489:23JFWNLT4:8:1149:7189:8833_1:N:0:TGAGTACT+GACAATAA/1 77 * 0 0 * * 0 0 AGGTGTTTTAATAGTTTGAGTTATTTGGTTATTTGTGATTAAATTTAGTTGATTGTTATATTTTGTTTTTATATTGTTTTTGGTATATTGTATTTGATAATGGATAATTTTGTTTATTTGATTAAGATATAGGGTTTATGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00129:489:23JFWNLT4:8:1149:7189:8833_2:N:0:TGAGTACT+GACAATAA/2 141 * 0 0 * * 0 0 AACAATATAACTAAATTATTCATAATCACAAACATTTCATAATTCATTAATTTATTTAAAACCTAAACCTAATTAAAAATTTATCTTTTTTTCTAAACTAATCTTTATACCTAAATAATAATTAATTTCCAACCATTCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII YT:Z:UP >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.3_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.2_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.4_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.8_bismark_bt2_pe.bam <<< >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.7_bismark_bt2_pe.bam <<< Found first alignment: LH00129:489:23JFWNLT4:8:1380:5344:26741_1:N:0:TGAGTACT+GACAATAA/1 83 Chromosome_1B_GA_converted 54264319 42 141M = 54264134 -326 TTCACTTCTTATTCTCCCACTTCTTCCACTTTTTTAAAAATCATAAAACCTCTACAATAACATATACATAAAAAATAAAAATAACAAACAATAATCAATCTCATAACTCCTATAAACAATACAAAATAAATAATTAAACAA 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP LH00129:489:23JFWNLT4:8:1380:5344:26741_2:N:0:TGAGTACT+GACAATAA/2 163 Chromosome_1B_GA_converted 54264134 42 141M = 54264319 326 TATCTATTTTATATTACTTATAAAATTTATACAATTAATCACTATCCATATCATCAACATACATATAAATATAAAATCATCAAATTATCCAATAATCACCTATAATATATCACAAATATCTATCCATTAAATATCTATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:141 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to Pum2_R1.fq.gz.temp.1_bismark_bt2_pe.bam <<< Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.6 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.6 Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.5 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.5 Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.3 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.3 Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.2 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.2 Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.4 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.4 Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.8 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.8 Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.7 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.7 Reading in the sequence files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.1 and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.1 Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00129:489:23JFWNLT4:8:2358:38165:8931_1:N:0:TGAGTACT+GACAATAA Chromosome_9B 91966292 Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00129:489:23JFWNLT4:8:2252:8119:10388_1:N:0:TGAGTACT+GACAATAA Chromosome_9B 91966292 Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 4000000 sequence pairs so far 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1626556 (35.21%) aligned concordantly 0 times 1060692 (22.96%) aligned concordantly exactly 1 time 1932341 (41.83%) aligned concordantly >1 times 64.79% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1628908 (35.26%) aligned concordantly 0 times 1058934 (22.92%) aligned concordantly exactly 1 time 1931747 (41.82%) aligned concordantly >1 times 64.74% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1626996 (35.22%) aligned concordantly 0 times 1060069 (22.95%) aligned concordantly exactly 1 time 1932524 (41.83%) aligned concordantly >1 times 64.78% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1628791 (35.26%) aligned concordantly 0 times 1060111 (22.95%) aligned concordantly exactly 1 time 1930687 (41.79%) aligned concordantly >1 times 64.74% overall alignment rate Processed 4619589 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.4_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.4_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619589 Number of paired-end alignments with a unique best hit: 2586765 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 591048 Sequence pairs did not map uniquely: 1441776 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1294023 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1292742 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114262454 Total methylated C's in CpG context: 2705163 Total methylated C's in CHG context: 116457 Total methylated C's in CHH context: 518703 Total methylated C's in Unknown context: 13992 Total unmethylated C's in CpG context: 11188644 Total unmethylated C's in CHG context: 19385145 Total unmethylated C's in CHH context: 80348342 Total unmethylated C's in Unknown context: 123159 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.2% Processed 4619589 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.3_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.3_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619589 Number of paired-end alignments with a unique best hit: 2585148 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 591401 Sequence pairs did not map uniquely: 1443040 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1293625 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1291523 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114203457 Total methylated C's in CpG context: 2699002 Total methylated C's in CHG context: 116712 Total methylated C's in CHH context: 517244 Total methylated C's in Unknown context: 13727 Total unmethylated C's in CpG context: 11199853 Total unmethylated C's in CHG context: 19373407 Total unmethylated C's in CHH context: 80297239 Total unmethylated C's in Unknown context: 123961 C methylated in CpG context: 19.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.0% 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1628402 (35.25%) aligned concordantly 0 times 1059322 (22.93%) aligned concordantly exactly 1 time 1931865 (41.82%) aligned concordantly >1 times 64.75% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1627077 (35.22%) aligned concordantly 0 times 1060621 (22.96%) aligned concordantly exactly 1 time 1931891 (41.82%) aligned concordantly >1 times 64.78% overall alignment rate Processed 4619589 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.8_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.8_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619589 Number of paired-end alignments with a unique best hit: 2585678 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 591351 Sequence pairs did not map uniquely: 1442560 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1294361 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1291315 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114192576 Total methylated C's in CpG context: 2711049 Total methylated C's in CHG context: 117509 Total methylated C's in CHH context: 518807 Total methylated C's in Unknown context: 13641 Total unmethylated C's in CpG context: 11184924 Total unmethylated C's in CHG context: 19385028 Total unmethylated C's in CHH context: 80275259 Total unmethylated C's in Unknown context: 122643 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.0% Now waiting for all child processes to complete 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1629352 (35.27%) aligned concordantly 0 times 1059468 (22.93%) aligned concordantly exactly 1 time 1930769 (41.80%) aligned concordantly >1 times 64.73% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1628654 (35.26%) aligned concordantly 0 times 1058224 (22.91%) aligned concordantly exactly 1 time 1932711 (41.84%) aligned concordantly >1 times 64.74% overall alignment rate Processed 4619589 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.7_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.7_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619589 Number of paired-end alignments with a unique best hit: 2583805 Mapping efficiency: 55.9% Sequence pairs with no alignments under any condition: 592192 Sequence pairs did not map uniquely: 1443592 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1293170 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1290635 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114146156 Total methylated C's in CpG context: 2705115 Total methylated C's in CHG context: 116540 Total methylated C's in CHH context: 516712 Total methylated C's in Unknown context: 13609 Total unmethylated C's in CpG context: 11174045 Total unmethylated C's in CHG context: 19381117 Total unmethylated C's in CHH context: 80252627 Total unmethylated C's in Unknown context: 123669 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 9.9% 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1626278 (35.20%) aligned concordantly 0 times 1059773 (22.94%) aligned concordantly exactly 1 time 1933538 (41.86%) aligned concordantly >1 times 64.80% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1628637 (35.26%) aligned concordantly 0 times 1059549 (22.94%) aligned concordantly exactly 1 time 1931403 (41.81%) aligned concordantly >1 times 64.74% overall alignment rate Processed 4619589 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.2_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.2_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619589 Number of paired-end alignments with a unique best hit: 2587145 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 590079 Sequence pairs did not map uniquely: 1442365 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1295813 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1291332 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114328715 Total methylated C's in CpG context: 2712220 Total methylated C's in CHG context: 117277 Total methylated C's in CHH context: 519173 Total methylated C's in Unknown context: 13701 Total unmethylated C's in CpG context: 11198596 Total unmethylated C's in CHG context: 19402591 Total unmethylated C's in CHH context: 80378858 Total unmethylated C's in Unknown context: 123482 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.0% 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1628219 (35.25%) aligned concordantly 0 times 1059315 (22.93%) aligned concordantly exactly 1 time 1932055 (41.82%) aligned concordantly >1 times 64.75% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1630023 (35.29%) aligned concordantly 0 times 1059779 (22.94%) aligned concordantly exactly 1 time 1929787 (41.77%) aligned concordantly >1 times 64.71% overall alignment rate Processed 4619589 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.6_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.6_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619589 Number of paired-end alignments with a unique best hit: 2584969 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 592153 Sequence pairs did not map uniquely: 1442467 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1294127 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1290842 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114186463 Total methylated C's in CpG context: 2707771 Total methylated C's in CHG context: 116576 Total methylated C's in CHH context: 518784 Total methylated C's in Unknown context: 13687 Total unmethylated C's in CpG context: 11197712 Total unmethylated C's in CHG context: 19384066 Total unmethylated C's in CHH context: 80261554 Total unmethylated C's in Unknown context: 124114 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 9.9% 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1626385 (35.21%) aligned concordantly 0 times 1061023 (22.97%) aligned concordantly exactly 1 time 1932181 (41.83%) aligned concordantly >1 times 64.79% overall alignment rate 4619589 reads; of these: 4619589 (100.00%) were paired; of these: 1631704 (35.32%) aligned concordantly 0 times 1057186 (22.88%) aligned concordantly exactly 1 time 1930699 (41.79%) aligned concordantly >1 times 64.68% overall alignment rate Processed 4619589 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.5_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.5_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619589 Number of paired-end alignments with a unique best hit: 2585938 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 592482 Sequence pairs did not map uniquely: 1441169 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1296536 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1289402 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114243983 Total methylated C's in CpG context: 2713679 Total methylated C's in CHG context: 117394 Total methylated C's in CHH context: 518066 Total methylated C's in Unknown context: 13677 Total unmethylated C's in CpG context: 11191688 Total unmethylated C's in CHG context: 19396971 Total unmethylated C's in CHH context: 80306185 Total unmethylated C's in Unknown context: 122832 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.0% 4619590 reads; of these: 4619590 (100.00%) were paired; of these: 1630557 (35.30%) aligned concordantly 0 times 1058748 (22.92%) aligned concordantly exactly 1 time 1930285 (41.78%) aligned concordantly >1 times 64.70% overall alignment rate 4619590 reads; of these: 4619590 (100.00%) were paired; of these: 1629411 (35.27%) aligned concordantly 0 times 1059933 (22.94%) aligned concordantly exactly 1 time 1930246 (41.78%) aligned concordantly >1 times 64.73% overall alignment rate Processed 4619590 sequences in total Successfully deleted the temporary files /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.1_C_to_T.fastq and /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.1_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 4619590 Number of paired-end alignments with a unique best hit: 2584991 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 592506 Sequence pairs did not map uniquely: 1442093 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1293934 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 1291057 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 114207441 Total methylated C's in CpG context: 2703395 Total methylated C's in CHG context: 117186 Total methylated C's in CHH context: 517961 Total methylated C's in Unknown context: 13547 Total unmethylated C's in CpG context: 11194016 Total unmethylated C's in CHG context: 19373675 Total unmethylated C's in CHH context: 80301208 Total unmethylated C's in Unknown context: 124361 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 9.8% All child processes successfully finished. at /mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/bismark line 599, line 18478356. Right, cleaning up now... Deleting temporary sequence files... /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.1 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.1 /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.2 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.2 /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.3 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.3 /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.4 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.4 /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.5 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.5 /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.6 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.6 /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.7 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.7 /tmp/13-wgbs-Pum2-1046737/Pum2_R1.fq.gz.temp.8 /tmp/13-wgbs-Pum2-1046737/Pum2_R2.fq.gz.temp.8 Now merging BAM files Pum2_R1.fq.gz.temp.1_bismark_bt2_pe.bam Pum2_R1.fq.gz.temp.2_bismark_bt2_pe.bam Pum2_R1.fq.gz.temp.3_bismark_bt2_pe.bam Pum2_R1.fq.gz.temp.4_bismark_bt2_pe.bam Pum2_R1.fq.gz.temp.5_bismark_bt2_pe.bam Pum2_R1.fq.gz.temp.6_bismark_bt2_pe.bam Pum2_R1.fq.gz.temp.7_bismark_bt2_pe.bam Pum2_R1.fq.gz.temp.8_bismark_bt2_pe.bam into >>> Pum2_R1_bismark_bt2_pe.bam <<< (using --threads 4) Merging from file >> Pum2_R1.fq.gz.temp.1_bismark_bt2_pe.bam << Merging from file >> Pum2_R1.fq.gz.temp.2_bismark_bt2_pe.bam << Merging from file >> Pum2_R1.fq.gz.temp.3_bismark_bt2_pe.bam << Merging from file >> Pum2_R1.fq.gz.temp.4_bismark_bt2_pe.bam << Merging from file >> Pum2_R1.fq.gz.temp.5_bismark_bt2_pe.bam << Merging from file >> Pum2_R1.fq.gz.temp.6_bismark_bt2_pe.bam << Merging from file >> Pum2_R1.fq.gz.temp.7_bismark_bt2_pe.bam << Merging from file >> Pum2_R1.fq.gz.temp.8_bismark_bt2_pe.bam << Deleting temporary BAM files... /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.1_bismark_bt2_pe.bam /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.2_bismark_bt2_pe.bam /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.3_bismark_bt2_pe.bam /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.4_bismark_bt2_pe.bam /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.5_bismark_bt2_pe.bam /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.6_bismark_bt2_pe.bam /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.7_bismark_bt2_pe.bam /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.8_bismark_bt2_pe.bam Writing report to /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1_bismark_bt2_PE_report.txt Now merging temporary reports Pum2_R1.fq.gz.temp.1_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.2_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.3_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.4_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.5_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.6_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.7_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.8_bismark_bt2_PE_report.txt into >>> /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1_bismark_bt2_PE_report.txt <<< Merging from file >> Pum2_R1.fq.gz.temp.1_bismark_bt2_PE_report.txt << Merging from file >> Pum2_R1.fq.gz.temp.2_bismark_bt2_PE_report.txt << Merging from file >> Pum2_R1.fq.gz.temp.3_bismark_bt2_PE_report.txt << Merging from file >> Pum2_R1.fq.gz.temp.4_bismark_bt2_PE_report.txt << Merging from file >> Pum2_R1.fq.gz.temp.5_bismark_bt2_PE_report.txt << Merging from file >> Pum2_R1.fq.gz.temp.6_bismark_bt2_PE_report.txt << Merging from file >> Pum2_R1.fq.gz.temp.7_bismark_bt2_PE_report.txt << Merging from file >> Pum2_R1.fq.gz.temp.8_bismark_bt2_PE_report.txt << Printing a final merged alignment report for all individual sub-reports Final Alignment report ====================== Sequence pairs analysed in total: 36956713 Number of paired-end alignments with a unique best hit: 20684439 Mapping efficiency: 56.0% Sequence pairs with no alignments under any condition: 4733212 Sequence pairs did not map uniquely: 11539062 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 10355589 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 10328848 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 913771245 Total methylated C's in CpG context: 21657394 Total methylated C's in CHG context: 935651 Total methylated C's in CHH context: 4145450 Total methylated C's in Unknown context: 109581 Total unmethylated C's in CpG context: 89529478 Total unmethylated C's in CHG context: 155082000 Total unmethylated C's in CHH context: 642421272 Total unmethylated C's in Unknown context: 988221 C methylated in CpG context: 19.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in Unknown context (CN or CHN): 10.0% Deleting temporary report files... Pum2_R1.fq.gz.temp.1_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.2_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.3_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.4_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.5_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.6_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.7_bismark_bt2_PE_report.txt Pum2_R1.fq.gz.temp.8_bismark_bt2_PE_report.txt Bismark completed in 0d 0h 54m 9s ==================== Bismark run complete ==================== Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/dedup/ Processing paired-end Bismark output file(s) (SAM format): output/13-wgbs/bismark/Pum2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>output/13-wgbs/bismark/Pum2_pe.bam<< for signs of file truncation... Now testing Bismark result file output/13-wgbs/bismark/Pum2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: Pum2_pe.deduplicated.bam Total number of alignments analysed in output/13-wgbs/bismark/Pum2_pe.bam: 20684437 Total number duplicated alignments removed: 1397378 (6.76%) Duplicated alignments were found at: 1302581 different position(s) Total count of deduplicated leftover sequences: 19287059 (93.24% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:Chromosome_10A LN:41401248 skipping header line: @SQ SN:Chromosome_2A LN:98156180 skipping header line: @SQ SN:Chromosome_4A LN:93973257 skipping header line: @SQ SN:Chromosome_6A LN:76092957 skipping header line: @SQ SN:Chromosome_1B LN:231619483 skipping header line: @SQ SN:Chromosome_5B LN:125625032 skipping header line: @SQ SN:Chromosome_6B LN:129267145 skipping header line: @SQ SN:Chromosome_7B LN:183991082 skipping header line: @SQ SN:Chromosome_8B LN:108828118 skipping header line: @SQ SN:Chromosome_9B LN:91966420 skipping header line: @PG ID:Bismark VN:v0.25.1 CL:"bismark --genome data/13-wgbs-genome -1 output/13-wgbs/trimmed/Pum2_R1.fq.gz -2 output/13-wgbs/trimmed/Pum2_R2.fq.gz --score_min L,0,-0.6 --parallel 8 -p 2 --temp_dir /tmp/13-wgbs-Pum2-1046737 --output_dir output/13-wgbs/bismark" skipping header line: @PG ID:samtools PN:samtools PP:Bismark VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -bSh - skipping header line: @PG ID:samtools.1 PN:samtools PP:samtools VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.1_bismark_bt2_pe.bam skipping header line: @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view --threads 4 -bSh - skipping header line: @PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h --threads 1 output/13-wgbs/bismark/Pum2_pe.bam *** Bismark methylation extractor version v0.25.1 *** Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/ Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 8 First 5 bp will be disregarded when processing the methylation call string of Read 2 Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated Merge CHG and CHH context to non-CpG context specified Output path specified as: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/ Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '40G'. Temporary directory used for sorting is the output directory Checking file >>output/13-wgbs/dedup/Pum2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >output/13-wgbs/dedup/Pum2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context to /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/CpG_context_Pum2_pe.deduplicated.txt.gz Writing result file containing methylation information for C in any other context to /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Non_CpG_context_Pum2_pe.deduplicated.txt.gz Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Now reading in Bismark result file output/13-wgbs/dedup/Pum2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:Chromosome_10A LN:41401248 skipping SAM header line: @SQ SN:Chromosome_2A LN:98156180 skipping SAM header line: @SQ SN:Chromosome_4A LN:93973257 skipping SAM header line: @SQ SN:Chromosome_6A LN:76092957 skipping SAM header line: @SQ SN:Chromosome_1B LN:231619483 skipping SAM header line: @SQ SN:Chromosome_5B LN:125625032 skipping SAM header line: @SQ SN:Chromosome_6B LN:129267145 skipping SAM header line: @SQ SN:Chromosome_7B LN:183991082 skipping SAM header line: @SQ SN:Chromosome_8B LN:108828118 skipping SAM header line: @SQ SN:Chromosome_9B LN:91966420 skipping SAM header line: @PG ID:Bismark VN:v0.25.1 CL:"bismark --genome data/13-wgbs-genome -1 output/13-wgbs/trimmed/Pum2_R1.fq.gz -2 output/13-wgbs/trimmed/Pum2_R2.fq.gz --score_min L,0,-0.6 --parallel 8 -p 2 --temp_dir /tmp/13-wgbs-Pum2-1046737 --output_dir output/13-wgbs/bismark" skipping SAM header line: @PG ID:samtools PN:samtools PP:Bismark VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -bSh - skipping SAM header line: @PG ID:samtools.1 PN:samtools PP:samtools VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark/Pum2_R1.fq.gz.temp.1_bismark_bt2_pe.bam skipping SAM header line: @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view --threads 4 -bSh - skipping SAM header line: @PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h --threads 1 output/13-wgbs/bismark/Pum2_pe.bam skipping SAM header line: @PG ID:samtools.4 PN:samtools PP:samtools.3 VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -bS --threads 1 - skipping SAM header line: @PG ID:samtools.5 PN:samtools PP:samtools.4 VN:1.22.1 CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h output/13-wgbs/dedup/Pum2_pe.deduplicated.bam Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed 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Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. All child process successfully finished. Merging individual splitting reports into overall report: '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt' Merging from these individual files: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.1 /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.2 /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.3 /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.4 /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.5 /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.6 /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.7 /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.8 Processed 19287059 lines in total Total number of methylation call strings processed: 38574118 Final Cytosine Methylation Report ================================= Total number of C's analysed: 682454947 Total methylated C's in CpG context: 16122733 Total methylated C's in CHG context: 567568 Total methylated C's in CHH context: 2550268 Total C to T conversions in CpG context: 67059765 Total C to T conversions in CHG context: 115917390 Total C to T conversions in CHH context: 480237223 C methylated in CpG context: 19.4% C methylated in non-CpG context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 8 individual files: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.1.mbias /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.2.mbias /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.3.mbias /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.4.mbias /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.5.mbias /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.6.mbias /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.7.mbias /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Pum2_pe.deduplicated_splitting_report.txt.8.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 141 Maximum read length of Read 2: 136 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 141 Maximum read length of Read 2: 136 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/CpG_context_Pum2_pe.deduplicated.txt.gz contains data -> kept /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Non_CpG_context_Pum2_pe.deduplicated.txt.gz contains data -> kept Using these input files: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/CpG_context_Pum2_pe.deduplicated.txt.gz /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/Non_CpG_context_Pum2_pe.deduplicated.txt.gz Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: Pum2_pe.deduplicated.bedGraph.gz output directory: >/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 40G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/CpG_context_Pum2_pe.deduplicated.txt.gz Writing bedGraph to file: Pum2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: Pum2_pe.deduplicated.bismark.cov.gz Changed directory to /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/ Now writing methylation information for file >>CpG_context_Pum2_pe.deduplicated.txt.gz<< to individual files for each chromosome Finished writing out individual chromosome files for CpG_context_Pum2_pe.deduplicated.txt.gz Collecting temporary chromosome file information... Processing the following input file(s): CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_2A.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_6A.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_8B.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_1B.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_6B.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_4A.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_9B.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_5B.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_7B.methXtractor.temp CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_10A.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_10A.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_10A.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_1B.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_1B.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_2A.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_2A.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_4A.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_4A.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_5B.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_5B.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_6A.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_6A.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_6B.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_6B.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_7B.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_7B.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_8B.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_8B.methXtractor.temp Sorting input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_9B.methXtractor.temp by positions (using -S of 40G) Successfully deleted the temporary input file CpG_context_Pum2_pe.deduplicated.txt.gz.chrChromosome_9B.methXtractor.temp Finished BedGraph conversion ... Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/ Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: output/13-wgbs/methylation/Pum2_pe.deduplicated.bismark.cov.gz Output directory: >/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/< Parent directory: >/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/< Genome directory: >/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/< Coverage threshold 0 (all positions will be reported, default) CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 1-based (default) GZIP compression: yes Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/data/13-wgbs-genome/ Couldn't find files ending in .fa, trying .fa.gz instead chr Chromosome_10A (41401248 bp) chr Chromosome_2A (98156180 bp) chr Chromosome_4A (93973257 bp) chr Chromosome_6A (76092957 bp) chr Chromosome_1B (231619483 bp) chr Chromosome_5B (125625032 bp) chr Chromosome_6B (129267145 bp) chr Chromosome_7B (183991082 bp) chr Chromosome_8B (108828118 bp) chr Chromosome_9B (91966420 bp) Stored sequence information of 10 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== Adding context-specific methylation summaries >>> Writing genome-wide cytosine report to: Pum2.CpG_report.txt.gz <<< >>> Writing all cytosine context summary file to: Pum2.cytosine_context_summary.txt <<< Storing all covered cytosine positions for chromosome: Chromosome_10A Writing cytosine report for chromosome Chromosome_10A (stored 1393014 different covered positions) Writing cytosine report for chromosome Chromosome_1B (stored 1778819 different covered positions) Writing cytosine report for chromosome Chromosome_2A (stored 3066843 different covered positions) Writing cytosine report for chromosome Chromosome_4A (stored 2973400 different covered positions) Writing cytosine report for chromosome Chromosome_5B (stored 2908589 different covered positions) Writing cytosine report for chromosome Chromosome_6A (stored 2548484 different covered positions) Writing cytosine report for chromosome Chromosome_6B (stored 2826228 different covered positions) Writing cytosine report for chromosome Chromosome_7B (stored 1454743 different covered positions) Writing cytosine report for chromosome Chromosome_8B (stored 2838761 different covered positions) Writing cytosine report for last chromosome Chromosome_9B (stored 2692428 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 10 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>Pum2.CpG_report.txt.gz<<, in output directory '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation/') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Pum2.CpG_report.merged_CpG_evidence.cov.gz <<< CpG merging complete. Good luck finding DMRs with bsseq! [bam_sort_core] merging from 1 files and 8 in-memory blocks... Summary of parameters for nucleotide coverage report: ===================================================== Output directory: >output/13-wgbs/dedup/< Parent directory: >/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/< Genome directory: >data/13-wgbs-genome/< Samtools installation: >/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools< Now reading in and storing sequence information of the genome specified in: data/13-wgbs-genome/ chr Chromosome_10A (41401248 bp) chr Chromosome_2A (98156180 bp) chr Chromosome_4A (93973257 bp) chr Chromosome_6A (76092957 bp) chr Chromosome_1B (231619483 bp) chr Chromosome_5B (125625032 bp) chr Chromosome_6B (129267145 bp) chr Chromosome_7B (183991082 bp) chr Chromosome_8B (108828118 bp) chr Chromosome_9B (91966420 bp) Stored sequence information of 10 chromosomes/scaffolds in total ================================================================== Mono- and di-nucleotide coverage will now be written into a report ================================================================== Detected file 'genomic_nucleotide_frequencies.txt' in the genome folder data/13-wgbs-genome/ already. Using nucleotide frequencies contained therein ... ============================================================================================================================================================================================ Calculating read frequencies from file 'output/13-wgbs/dedup/Pum2_pe.deduplicated.bam' ========================================================================================== Determined the file to be paired-end Processed 500000 lines Processed 1000000 lines Processed 1500000 lines Processed 2000000 lines Processed 2500000 lines Processed 3000000 lines Processed 3500000 lines Processed 4000000 lines Processed 4500000 lines Processed 5000000 lines Processed 5500000 lines Processed 6000000 lines Processed 6500000 lines Processed 7000000 lines Processed 7500000 lines Processed 8000000 lines Processed 8500000 lines Processed 9000000 lines Processed 9500000 lines Processed 10000000 lines Processed 10500000 lines Processed 11000000 lines Processed 11500000 lines Processed 12000000 lines Processed 12500000 lines Processed 13000000 lines Processed 13500000 lines Processed 14000000 lines Processed 14500000 lines Processed 15000000 lines Processed 15500000 lines Processed 16000000 lines Processed 16500000 lines Processed 17000000 lines Processed 17500000 lines Processed 18000000 lines Processed 18500000 lines Processed 19000000 lines Processed 19500000 lines Processed 20000000 lines Processed 20500000 lines Processed 21000000 lines Processed 21500000 lines Processed 22000000 lines Processed 22500000 lines Processed 23000000 lines Processed 23500000 lines Processed 24000000 lines Processed 24500000 lines Processed 25000000 lines Processed 25500000 lines Processed 26000000 lines Processed 26500000 lines Processed 27000000 lines Processed 27500000 lines Processed 28000000 lines Processed 28500000 lines Processed 29000000 lines Processed 29500000 lines Processed 30000000 lines Processed 30500000 lines Processed 31000000 lines Processed 31500000 lines Processed 32000000 lines Processed 32500000 lines Processed 33000000 lines Processed 33500000 lines Processed 34000000 lines Processed 34500000 lines Processed 35000000 lines Processed 35500000 lines Processed 36000000 lines Processed 36500000 lines Processed 37000000 lines Processed 37500000 lines Processed 38000000 lines Processed 38500000 lines Printing nucleotide stats to >> output/13-wgbs/dedup/Pum2_pe.deduplicated.nucleotide_stats.txt << Final Stage: Calculating averages ================================= (di-)nucleotide count sample percent sample count genomic percent genomic coverage A 1616945953 34.52 378413849 32.06 4.273 C 746499364 15.94 211781786 17.94 3.525 G 827897105 17.67 211810957 17.95 3.909 T 1493013717 31.87 378309330 32.05 3.947 AA 589958119 12.69 128492079 10.89 4.591 AC 256060252 5.51 68264877 5.78 3.751 AG 259197148 5.57 62424886 5.29 4.152 AT 500554229 10.76 119230832 10.10 4.198 CA 308417467 6.63 80836853 6.85 3.815 CC 129277401 2.78 42358709 3.59 3.052 CG 90464293 1.95 26104181 2.21 3.466 CT 212647816 4.57 62481783 5.29 3.403 GA 284001152 6.11 67679435 5.73 4.196 GC 120557178 2.59 33452245 2.83 3.604 GG 150439010 3.23 42378301 3.59 3.550 GT 267011456 5.74 68300800 5.79 3.909 TA 422771627 9.09 101400983 8.59 4.169 TC 235224232 5.06 67705770 5.74 3.474 TG 321876159 6.92 80903356 6.85 3.979 TT 502360487 10.80 128294772 10.87 3.916 [Fri Oct 9 13:25:19 PDT 2026] Pum2 done