[2026-10-09 17:19:10,904] root [DEBUG ] Logging to file: /tmp/tmp08m0kagi/multiqc.log [2026-10-09 17:19:10,905] multiqc.core.update_config [DEBUG ] This is MultiQC v1.30 [2026-10-09 17:19:10,905] multiqc.core.update_config [DEBUG ] Running Python 3.13.5 | packaged by conda-forge | (main, Jun 16 2025, 08:27:50) [GCC 13.3.0] [2026-10-09 17:19:10,924] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443 [2026-10-09 17:19:11,401] urllib3.connectionpool [DEBUG ] https://api.multiqc.info:443 "GET /version?version_multiqc=1.30&version_python=3.13.5&operating_system=Linux&is_docker=False&is_singularity=True&is_conda=True&is_ci=False&is_notebook=False&ai_summary=False&ai_summary_full=False HTTP/1.1" 200 178 [2026-10-09 17:19:11,401] multiqc.core.version_check [WARNING] MultiQC Version v1.35 now available! [2026-10-09 17:19:11,401] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.35, released 2026-05-13 [2026-10-09 17:19:11,402] multiqc.multiqc [DEBUG ] Working dir : /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil [2026-10-09 17:19:11,402] multiqc.multiqc [DEBUG ] Template : default [2026-10-09 17:19:11,402] multiqc.multiqc [DEBUG ] Command used: /mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/multiqc --force --filename multiqc_13-wgbs --outdir output/13-wgbs/reports output/13-wgbs/fastp output/13-wgbs/bismark output/13-wgbs/dedup output/13-wgbs/methylation [2026-10-09 17:19:11,402] multiqc.core.file_search [INFO ] Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/fastp [2026-10-09 17:19:11,402] multiqc.core.file_search [INFO ] Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark [2026-10-09 17:19:11,402] multiqc.core.file_search [INFO ] Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/dedup [2026-10-09 17:19:11,402] multiqc.core.file_search [INFO ] Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation [2026-10-09 17:19:11,403] multiqc.core.file_search [DEBUG ] Analysing modules: bases2fastq, cellranger_arc, cells2stats, custom_content, ccs, ngsderive, purple, conpair, isoseq, lima, peddy, percolator, haplocheck, somalier, methylqa, mosdepth, phantompeakqualtools, qualimap, bamdst, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, checkm, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, glimpse, gopeaks, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featurecounts, fgbio, dragen, dragen_fastqc, dedup, pbmarkdup, damageprofiler, mapdamage, biobambam2, jcvi, mtnucratio, picard, vep, bakta, prokka, checkm2, qc3C, nanoq, nanostat, samblaster, samtools, bamtools, sambamba, ngsbits, pairtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umicollapse, umitools, truvari, megahit, ganon, gtdbtk, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, hostile, cellranger, snpsplit, odgi, vg, pangolin, nextclade, freyja, humid, kat, leehom, librarian, nonpareil, adapterremoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, sequali, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, spaceranger, xenome, xengsort, metaphlan, seqwho, telseq, ataqv, mgikit, mosaicatcher, software_versions [2026-10-09 17:19:11,403] multiqc.core.file_search [DEBUG ] Search keys: adapterremoval, afterqc, anglerfish, ataqv, bakta, bamdst, bamtools, bases2fastq, bbduk, bbmap, bcftools, bcl2fastq, bclconvert, biobambam2, biobloomtools, biscuit, bismark, bowtie1, bowtie2, busco, bustools, ccs, cellranger, cellranger_arc, cells2stats, checkm, checkm2, checkqc, clipandmerge, clusterflow, conpair, custom_content, cutadapt, damageprofiler, dedup, deeptools, diamond, disambiguate, dragen, dragen_fastqc, eigenstratdatabasetools, fastp, fastq_screen, fastqc, featurecounts, fgbio, filtlong, flash, flexbar, freyja, ganon, gatk, gffcompare, glimpse, goleft_indexcov, gopeaks, gtdbtk, haplocheck, happy, hicexplorer, hicpro, hicup, hifiasm, hisat2, homer, hops, hostile, htseq, humid, interop, isoseq, ivar, jcvi, jellyfish, kaiju, kallisto, kat, kraken, leehom, librarian, lima, longranger, macs2, malt, mapdamage, megahit, metaphlan, methylqa, mgikit, minionqc, mirtop, mirtrace, mosaicatcher, mosdepth, motus, mtnucratio, multiqc_data, multivcfanalyzer, nanoq, nanostat, nextclade, ngsbits, ngsderive, nonpareil, odgi, optitype, pairtools, pangolin, pbmarkdup, peddy, percolator, phantompeakqualtools, picard, porechop, preseq, prinseqplusplus, prokka, purple, pychopper, pycoqc, qc3C, qorts, qualimap, quast, rna_seqc, rockhopper, rsem, rseqc, salmon, sambamba, samblaster, samtools, sargasso, seqera_cli, sequali, seqwho, seqyclean, sexdeterrmine, sickle, skewer, slamdunk, snippy, snpeff, snpsplit, software_versions, somalier, sortmerna, sourmash, spaceranger, stacks, star, supernova, telseq, theta2, tophat, trimmomatic, truvari, umicollapse, umitools, varscan2, vcftools, vep, verifybamid, vg, whatshap, xengsort, xenome [2026-10-09 17:19:13,801] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_ignore_pattern: 15|, |skipped_filesize_limit: 120|, |skipped_module_specific_max_filesize: 60|, |skipped_no_match: 165| [2026-10-09 17:19:13,803] multiqc.core.exec_modules [DEBUG ] Running module: custom_content [2026-10-09 17:19:13,824] multiqc.core.exec_modules [DEBUG ] No samples found: custom_content [2026-10-09 17:19:13,824] multiqc.core.exec_modules [DEBUG ] Running module: bismark [2026-10-09 17:19:13,876] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_alignment.txt [2026-10-09 17:19:13,877] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_alignment.json [2026-10-09 17:19:13,877] multiqc.modules.bismark.bismark [INFO ] Found 15 alignment reports [2026-10-09 17:19:13,877] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_alignment: found old_data = False [2026-10-09 17:19:13,877] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_alignment: no old data or empty, using new data only [2026-10-09 17:19:15,053] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_dedup.txt [2026-10-09 17:19:15,053] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_dedup.json [2026-10-09 17:19:15,053] multiqc.modules.bismark.bismark [INFO ] Found 15 dedup reports [2026-10-09 17:19:15,053] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_deduplication: found old_data = False [2026-10-09 17:19:15,053] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_deduplication: no old data or empty, using new data only [2026-10-09 17:19:15,067] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_strand_alignment: found old_data = False [2026-10-09 17:19:15,067] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_strand_alignment: no old data or empty, using new data only [2026-10-09 17:19:15,073] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_methextract.txt [2026-10-09 17:19:15,073] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_methextract.json [2026-10-09 17:19:15,074] multiqc.modules.bismark.bismark [INFO ] Found 15 methextract reports [2026-10-09 17:19:15,074] multiqc.plots.table_object [DEBUG ] Table key 'percent_chg_meth' not found in data for 'bismark-methylation-dp'. Skipping. Check for possible typos between data keys and header keys [2026-10-09 17:19:15,074] multiqc.plots.table_object [DEBUG ] Table key 'percent_chh_meth' not found in data for 'bismark-methylation-dp'. Skipping. Check for possible typos between data keys and header keys [2026-10-09 17:19:15,074] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark-methylation-dp: found old_data = False [2026-10-09 17:19:15,074] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark-methylation-dp: no old data or empty, using new data only [2026-10-09 17:19:15,120] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_mbias: found old_data = False [2026-10-09 17:19:15,120] multiqc.plots.plot [DEBUG ] merge_with_previous for bismark_mbias: no old data or empty, using new data only [2026-10-09 17:19:15,192] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_bam2nuc.txt [2026-10-09 17:19:15,193] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_bam2nuc.json [2026-10-09 17:19:15,194] multiqc.modules.bismark.bismark [INFO ] Found 15 bismark bam2nuc reports [2026-10-09 17:19:15,194] multiqc.base_module [DEBUG ] bismark: deleting attribute self.bismark_data [2026-10-09 17:19:15,194] multiqc.base_module [DEBUG ] bismark: deleting attribute self.bismark_mbias_data [2026-10-09 17:19:15,194] multiqc.core.exec_modules [DEBUG ] Running module: fastp [2026-10-09 17:19:15,243] multiqc.modules.fastp.fastp [INFO ] Found 15 reports [2026-10-09 17:19:15,243] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: PUM1 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: PUM1 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: PUM1 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: PUM1 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: PUM2 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: PUM2 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: PUM2 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: PUM2 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: PUM3 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: PUM3 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: PUM3 (paired)_R1 [2026-10-09 17:19:15,244] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: PUM3 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: PUM4 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: PUM4 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: PUM4 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: PUM4 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: PUM5 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: PUM5 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: PUM5 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: PUM5 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: Qui1 (paired)_R1 [2026-10-09 17:19:15,245] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: Qui1 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: Qui1 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: Qui1 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: Qui2 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: Qui2 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: Qui2 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: Qui2 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: Qui3 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: Qui3 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: Qui3 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: Qui3 (paired)_R1 [2026-10-09 17:19:15,246] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: Qui4 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: Qui4 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: Qui4 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: Qui4 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: Qui5 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: Qui5 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: Qui5 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: Qui5 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RP1 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: RP1 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: RP1 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: RP1 (paired)_R1 [2026-10-09 17:19:15,247] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RP2 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: RP2 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: RP2 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: RP2 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RP3 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: RP3 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: RP3 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: RP3 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RP4 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: RP4 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: RP4 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: RP4 (paired)_R1 [2026-10-09 17:19:15,248] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RP5 (paired)_R1 [2026-10-09 17:19:15,249] multiqc.modules.fastp.fastp [DEBUG ] Read quality merged_and_filtered not found: RP5 (paired)_R1 [2026-10-09 17:19:15,249] multiqc.modules.fastp.fastp [DEBUG ] Content curve data merged_and_filtered not found: RP5 (paired)_R1 [2026-10-09 17:19:15,249] multiqc.modules.fastp.fastp [DEBUG ] Overrepresented sequences data merged_and_filtered not found: RP5 (paired)_R1 [2026-10-09 17:19:15,275] multiqc.report [DEBUG ] Wrote data file multiqc_fastp.txt [2026-10-09 17:19:15,393] multiqc.report [DEBUG ] Wrote data file multiqc_fastp.json [2026-10-09 17:19:15,393] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp_filtered_reads_plot: found old_data = False [2026-10-09 17:19:15,393] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp_filtered_reads_plot: no old data or empty, using new data only [2026-10-09 17:19:15,405] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-duprates-plot: found old_data = False [2026-10-09 17:19:15,405] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-duprates-plot: no old data or empty, using new data only [2026-10-09 17:19:15,408] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-insert-size-plot: found old_data = False [2026-10-09 17:19:15,408] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-insert-size-plot: no old data or empty, using new data only [2026-10-09 17:19:15,433] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-seq-quality-plot: found old_data = False [2026-10-09 17:19:15,433] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-seq-quality-plot: no old data or empty, using new data only [2026-10-09 17:19:15,467] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-seq-content-gc-plot: found old_data = False [2026-10-09 17:19:15,467] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-seq-content-gc-plot: no old data or empty, using new data only [2026-10-09 17:19:15,505] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-seq-content-n-plot: found old_data = False [2026-10-09 17:19:15,505] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp-seq-content-n-plot: no old data or empty, using new data only [2026-10-09 17:19:15,537] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp_overrepresented_sequences_plot: found old_data = False [2026-10-09 17:19:15,537] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp_overrepresented_sequences_plot: no old data or empty, using new data only [2026-10-09 17:19:15,538] multiqc.plots.table_object [DEBUG ] Table key 'samples' not found in data for 'fastp_top_overrepresented_sequences_table'. Skipping. Check for possible typos between data keys and header keys [2026-10-09 17:19:15,538] multiqc.plots.table_object [DEBUG ] Table key 'total_count' not found in data for 'fastp_top_overrepresented_sequences_table'. Skipping. Check for possible typos between data keys and header keys [2026-10-09 17:19:15,538] multiqc.plots.table_object [DEBUG ] Table key 'total_percent' not found in data for 'fastp_top_overrepresented_sequences_table'. Skipping. Check for possible typos between data keys and header keys [2026-10-09 17:19:15,538] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp_top_overrepresented_sequences_table: found old_data = False [2026-10-09 17:19:15,538] multiqc.plots.plot [DEBUG ] merge_with_previous for fastp_top_overrepresented_sequences_table: no old data or empty, using new data only [2026-10-09 17:19:15,538] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_data [2026-10-09 17:19:15,538] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_duplication_plotdata [2026-10-09 17:19:15,538] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_insert_size_data [2026-10-09 17:19:15,538] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_all_data [2026-10-09 17:19:15,540] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_qual_plotdata [2026-10-09 17:19:15,540] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_gc_content_data [2026-10-09 17:19:15,540] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_n_content_data [2026-10-09 17:19:15,540] multiqc.base_module [DEBUG ] fastp: deleting attribute self.fastp_overrepresented_sequences [2026-10-09 17:19:15,540] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions [2026-10-09 17:19:15,593] multiqc.report [DEBUG ] Wrote data file multiqc_software_versions.txt [2026-10-09 17:19:15,593] multiqc.core.write_results [DEBUG ] Rendering plots [2026-10-09 17:19:15,606] multiqc.plots.table_object [DEBUG ] Table key 'percent_chg_meth' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys [2026-10-09 17:19:15,606] multiqc.plots.table_object [DEBUG ] Table key 'percent_chh_meth' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys [2026-10-09 17:19:15,609] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: found old_data = False [2026-10-09 17:19:15,609] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: no old data or empty, using new data only [2026-10-09 17:19:15,661] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.txt [2026-10-09 17:19:15,661] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.json [2026-10-09 17:19:15,685] multiqc.core.ai [DEBUG ] Saved AI prompt to multiqc_data/llms-full.txt [2026-10-09 17:19:15,894] multiqc.core.write_results [DEBUG ] Exporting plot data to files [2026-10-09 17:19:15,895] multiqc.report [DEBUG ] Wrote data file bismark_alignment.txt [2026-10-09 17:19:15,895] multiqc.report [DEBUG ] Wrote data file bismark_deduplication.txt [2026-10-09 17:19:15,895] multiqc.report [DEBUG ] Wrote data file bismark_strand_alignment.txt [2026-10-09 17:19:15,895] multiqc.report [DEBUG ] Wrote data file bismark-methylation-dp.txt [2026-10-09 17:19:15,897] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CpG_R1.txt [2026-10-09 17:19:15,898] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHG_R1.txt [2026-10-09 17:19:15,900] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHH_R1.txt [2026-10-09 17:19:15,901] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CpG_R2.txt [2026-10-09 17:19:15,903] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHG_R2.txt [2026-10-09 17:19:15,904] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHH_R2.txt [2026-10-09 17:19:15,905] multiqc.report [DEBUG ] Wrote data file fastp_filtered_reads_plot.txt [2026-10-09 17:19:15,908] multiqc.report [DEBUG ] Wrote data file fastp-insert-size-plot.txt [2026-10-09 17:19:15,910] multiqc.report [DEBUG ] Wrote data file fastp-seq-quality-plot_Read_1_Before_filtering.txt [2026-10-09 17:19:15,911] multiqc.report [DEBUG ] Wrote data file fastp-seq-quality-plot_Read_1_After_filtering.txt [2026-10-09 17:19:15,913] multiqc.report [DEBUG ] Wrote data file fastp-seq-quality-plot_Read_2_Before_filtering.txt [2026-10-09 17:19:15,915] multiqc.report [DEBUG ] Wrote data file fastp-seq-quality-plot_Read_2_After_filtering.txt [2026-10-09 17:19:15,917] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-gc-plot_Read_1_Before_filtering.txt [2026-10-09 17:19:15,919] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-gc-plot_Read_1_After_filtering.txt [2026-10-09 17:19:15,920] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-gc-plot_Read_2_Before_filtering.txt [2026-10-09 17:19:15,922] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-gc-plot_Read_2_After_filtering.txt [2026-10-09 17:19:15,924] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-n-plot_Read_1_Before_filtering.txt [2026-10-09 17:19:15,925] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-n-plot_Read_1_After_filtering.txt [2026-10-09 17:19:15,927] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-n-plot_Read_2_Before_filtering.txt [2026-10-09 17:19:15,929] multiqc.report [DEBUG ] Wrote data file fastp-seq-content-n-plot_Read_2_After_filtering.txt [2026-10-09 17:19:15,929] multiqc.core.write_results [DEBUG ] Moving data file from '/tmp/tmp08m0kagi/multiqc_data' to '/mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/reports/multiqc_13-wgbs_data' [2026-10-09 17:19:16,356] multiqc.core.write_results [INFO ] Data : output/13-wgbs/reports/multiqc_13-wgbs_data (overwritten) [2026-10-09 17:19:18,936] multiqc.core.write_results [DEBUG ] Compressing plot data [2026-10-09 17:19:19,155] multiqc.core.write_results [INFO ] Report : output/13-wgbs/reports/multiqc_13-wgbs.html (overwritten) [2026-10-09 17:19:19,155] multiqc.core.write_results [DEBUG ] Report HTML written to /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/reports/multiqc_13-wgbs.html