[2025-08-29 17:10:48,253] root [DEBUG ] Logging to file: /tmp/tmpnkivb2i6/multiqc.log
[2025-08-29 17:10:48,254] multiqc.core.update_config [DEBUG ] This is MultiQC v1.29
[2025-08-29 17:10:48,254] multiqc.core.update_config [DEBUG ] Running Python 3.13.3 | packaged by conda-forge | (main, Apr 14 2025, 20:44:03) [GCC 13.3.0]
[2025-08-29 17:10:48,383] multiqc.config [INFO ] Loading config settings from: multiqc_config.yml
[2025-08-29 17:10:48,383] multiqc.config [DEBUG ] New config: {'report_comment': 'This report has been generated by the nf-core/methylseq analysis pipeline. For information about how to interpret these results, please see the documentation.\n', 'report_section_order': {'nf-core-methylseq-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-methylseq-summary': {'order': -1002}}, 'export_plots': True, 'disable_version_detection': True, 'table_columns_visible': {'QualiMap': {'avg_gc': False, '30_x_pc': False, 'percentage_aligned': False}}, 'top_modules': ['bismark']}
[2025-08-29 17:10:48,388] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443
[2025-08-29 17:10:48,986] urllib3.connectionpool [DEBUG ] https://api.multiqc.info:443 "GET /version?version_multiqc=1.29&version_python=3.13.3&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&ai_provider=seqera HTTP/1.1" 200 178
[2025-08-29 17:10:48,986] multiqc.core.version_check [WARNING] MultiQC Version v1.30 now available!
[2025-08-29 17:10:48,986] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.30, released 2025-07-09
[2025-08-29 17:10:48,987] multiqc.multiqc [DEBUG ] Working dir : /gscratch/scrubbed/srlab/nxf.3iIJDtp8PY
[2025-08-29 17:10:48,987] multiqc.multiqc [DEBUG ] Template : default
[2025-08-29 17:10:48,987] multiqc.multiqc [DEBUG ] Command used: /usr/local/bin/multiqc --force --config multiqc_config.yml .
[2025-08-29 17:10:48,987] multiqc.core.file_search [INFO ] Search path: /gscratch/scrubbed/srlab/nxf.3iIJDtp8PY
[2025-08-29 17:10:48,987] multiqc.core.file_search [DEBUG ] Analysing modules: bismark, 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, 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
[2025-08-29 17:10:48,987] 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
[2025-08-29 17:11:11,126] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_no_match: 46|, |skipped_module_specific_max_filesize: 42|
[2025-08-29 17:11:11,127] multiqc.core.exec_modules [DEBUG ] Running module: bismark
[2025-08-29 17:11:11,383] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_alignment.txt
[2025-08-29 17:11:11,384] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_alignment.json
[2025-08-29 17:11:11,384] multiqc.modules.bismark.bismark [INFO ] Found 40 alignment reports
[2025-08-29 17:11:12,930] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_dedup.txt
[2025-08-29 17:11:12,930] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_dedup.json
[2025-08-29 17:11:12,930] multiqc.modules.bismark.bismark [INFO ] Found 40 dedup reports
[2025-08-29 17:11:12,991] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_methextract.txt
[2025-08-29 17:11:12,992] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_methextract.json
[2025-08-29 17:11:12,992] multiqc.modules.bismark.bismark [INFO ] Found 40 methextract reports
[2025-08-29 17:11:12,992] 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
[2025-08-29 17:11:12,992] 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
[2025-08-29 17:11:13,143] multiqc.base_module [DEBUG ] bismark: deleting attribute self.bismark_data
[2025-08-29 17:11:13,143] multiqc.base_module [DEBUG ] bismark: deleting attribute self.bismark_mbias_data
[2025-08-29 17:11:13,144] multiqc.core.exec_modules [DEBUG ] Running module: custom_content
[2025-08-29 17:11:13,198] multiqc.core.special_case_modules.custom_content [INFO ] nf-core-methylseq-methods-description: Found 1 sample (html)
[2025-08-29 17:11:13,198] multiqc.core.special_case_modules.custom_content [INFO ] nf-core-methylseq-summary: Found 1 sample (html)
[2025-08-29 17:11:13,198] multiqc.core.exec_modules [DEBUG ] Running module: fastqc
[2025-08-29 17:11:13,385] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP1_1_fastqc.zip' as already parsed 'ACR-139-TP1_1'
[2025-08-29 17:11:13,450] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP1_2_fastqc.zip' as already parsed 'ACR-139-TP1_2'
[2025-08-29 17:11:13,646] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP2_1_fastqc.zip' as already parsed 'ACR-139-TP2_1'
[2025-08-29 17:11:13,743] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP2_2_fastqc.zip' as already parsed 'ACR-139-TP2_2'
[2025-08-29 17:11:13,960] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP3_1_fastqc.zip' as already parsed 'ACR-139-TP3_1'
[2025-08-29 17:11:14,055] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP3_2_fastqc.zip' as already parsed 'ACR-139-TP3_2'
[2025-08-29 17:11:14,342] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP4_1_fastqc.zip' as already parsed 'ACR-139-TP4_1'
[2025-08-29 17:11:14,431] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-139-TP4_2_fastqc.zip' as already parsed 'ACR-139-TP4_2'
[2025-08-29 17:11:14,442] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP1_1_fastqc.zip' as already parsed 'ACR-145-TP1_1'
[2025-08-29 17:11:14,691] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP1_2_fastqc.zip' as already parsed 'ACR-145-TP1_2'
[2025-08-29 17:11:14,837] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP2_1_fastqc.zip' as already parsed 'ACR-145-TP2_1'
[2025-08-29 17:11:14,919] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP2_2_fastqc.zip' as already parsed 'ACR-145-TP2_2'
[2025-08-29 17:11:15,214] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP3_1_fastqc.zip' as already parsed 'ACR-145-TP3_1'
[2025-08-29 17:11:15,291] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP3_2_fastqc.zip' as already parsed 'ACR-145-TP3_2'
[2025-08-29 17:11:15,382] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP4_1_fastqc.zip' as already parsed 'ACR-145-TP4_1'
[2025-08-29 17:11:15,393] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-145-TP4_2_fastqc.zip' as already parsed 'ACR-145-TP4_2'
[2025-08-29 17:11:15,579] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP1_1_fastqc.zip' as already parsed 'ACR-150-TP1_1'
[2025-08-29 17:11:15,719] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP1_2_fastqc.zip' as already parsed 'ACR-150-TP1_2'
[2025-08-29 17:11:15,806] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP2_1_fastqc.zip' as already parsed 'ACR-150-TP2_1'
[2025-08-29 17:11:15,951] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP2_2_fastqc.zip' as already parsed 'ACR-150-TP2_2'
[2025-08-29 17:11:16,204] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP3_1_fastqc.zip' as already parsed 'ACR-150-TP3_1'
[2025-08-29 17:11:16,260] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP3_2_fastqc.zip' as already parsed 'ACR-150-TP3_2'
[2025-08-29 17:11:16,314] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP4_1_fastqc.zip' as already parsed 'ACR-150-TP4_1'
[2025-08-29 17:11:16,527] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-150-TP4_2_fastqc.zip' as already parsed 'ACR-150-TP4_2'
[2025-08-29 17:11:16,638] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP1_1_fastqc.zip' as already parsed 'ACR-173-TP1_1'
[2025-08-29 17:11:16,933] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP1_2_fastqc.zip' as already parsed 'ACR-173-TP1_2'
[2025-08-29 17:11:17,005] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP2_1_fastqc.zip' as already parsed 'ACR-173-TP2_1'
[2025-08-29 17:11:17,085] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP2_2_fastqc.zip' as already parsed 'ACR-173-TP2_2'
[2025-08-29 17:11:17,176] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP3_1_fastqc.zip' as already parsed 'ACR-173-TP3_1'
[2025-08-29 17:11:17,231] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP3_2_fastqc.zip' as already parsed 'ACR-173-TP3_2'
[2025-08-29 17:11:17,371] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP4_1_fastqc.zip' as already parsed 'ACR-173-TP4_1'
[2025-08-29 17:11:17,412] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-173-TP4_2_fastqc.zip' as already parsed 'ACR-173-TP4_2'
[2025-08-29 17:11:17,546] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP1_1_fastqc.zip' as already parsed 'ACR-186-TP1_1'
[2025-08-29 17:11:17,615] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP1_2_fastqc.zip' as already parsed 'ACR-186-TP1_2'
[2025-08-29 17:11:17,742] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP2_1_fastqc.zip' as already parsed 'ACR-186-TP2_1'
[2025-08-29 17:11:17,873] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP2_2_fastqc.zip' as already parsed 'ACR-186-TP2_2'
[2025-08-29 17:11:17,884] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP3_1_fastqc.zip' as already parsed 'ACR-186-TP3_1'
[2025-08-29 17:11:18,041] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP3_2_fastqc.zip' as already parsed 'ACR-186-TP3_2'
[2025-08-29 17:11:18,241] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP4_1_fastqc.zip' as already parsed 'ACR-186-TP4_1'
[2025-08-29 17:11:18,382] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-186-TP4_2_fastqc.zip' as already parsed 'ACR-186-TP4_2'
[2025-08-29 17:11:18,742] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP1_1_fastqc.zip' as already parsed 'ACR-225-TP1_1'
[2025-08-29 17:11:18,752] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP1_2_fastqc.zip' as already parsed 'ACR-225-TP1_2'
[2025-08-29 17:11:18,763] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP2_1_fastqc.zip' as already parsed 'ACR-225-TP2_1'
[2025-08-29 17:11:18,834] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP2_2_fastqc.zip' as already parsed 'ACR-225-TP2_2'
[2025-08-29 17:11:18,845] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP3_1_fastqc.zip' as already parsed 'ACR-225-TP3_1'
[2025-08-29 17:11:18,856] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP3_2_fastqc.zip' as already parsed 'ACR-225-TP3_2'
[2025-08-29 17:11:19,000] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP4_1_fastqc.zip' as already parsed 'ACR-225-TP4_1'
[2025-08-29 17:11:19,172] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-225-TP4_2_fastqc.zip' as already parsed 'ACR-225-TP4_2'
[2025-08-29 17:11:19,626] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP1_1_fastqc.zip' as already parsed 'ACR-229-TP1_1'
[2025-08-29 17:11:19,788] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP1_2_fastqc.zip' as already parsed 'ACR-229-TP1_2'
[2025-08-29 17:11:19,799] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP2_1_fastqc.zip' as already parsed 'ACR-229-TP2_1'
[2025-08-29 17:11:19,882] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP2_2_fastqc.zip' as already parsed 'ACR-229-TP2_2'
[2025-08-29 17:11:20,012] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP3_1_fastqc.zip' as already parsed 'ACR-229-TP3_1'
[2025-08-29 17:11:20,101] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP3_2_fastqc.zip' as already parsed 'ACR-229-TP3_2'
[2025-08-29 17:11:20,183] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP4_1_fastqc.zip' as already parsed 'ACR-229-TP4_1'
[2025-08-29 17:11:20,290] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-229-TP4_2_fastqc.zip' as already parsed 'ACR-229-TP4_2'
[2025-08-29 17:11:20,441] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP1_1_fastqc.zip' as already parsed 'ACR-237-TP1_1'
[2025-08-29 17:11:20,513] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP1_2_fastqc.zip' as already parsed 'ACR-237-TP1_2'
[2025-08-29 17:11:20,589] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP2_1_fastqc.zip' as already parsed 'ACR-237-TP2_1'
[2025-08-29 17:11:20,664] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP2_2_fastqc.zip' as already parsed 'ACR-237-TP2_2'
[2025-08-29 17:11:20,789] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP3_1_fastqc.zip' as already parsed 'ACR-237-TP3_1'
[2025-08-29 17:11:20,942] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP3_2_fastqc.zip' as already parsed 'ACR-237-TP3_2'
[2025-08-29 17:11:21,035] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP4_1_fastqc.zip' as already parsed 'ACR-237-TP4_1'
[2025-08-29 17:11:21,209] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-237-TP4_2_fastqc.zip' as already parsed 'ACR-237-TP4_2'
[2025-08-29 17:11:21,282] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP1_1_fastqc.zip' as already parsed 'ACR-244-TP1_1'
[2025-08-29 17:11:21,501] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP1_2_fastqc.zip' as already parsed 'ACR-244-TP1_2'
[2025-08-29 17:11:21,512] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP2_1_fastqc.zip' as already parsed 'ACR-244-TP2_1'
[2025-08-29 17:11:21,614] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP2_2_fastqc.zip' as already parsed 'ACR-244-TP2_2'
[2025-08-29 17:11:21,835] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP3_1_fastqc.zip' as already parsed 'ACR-244-TP3_1'
[2025-08-29 17:11:21,944] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP3_2_fastqc.zip' as already parsed 'ACR-244-TP3_2'
[2025-08-29 17:11:22,019] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP4_1_fastqc.zip' as already parsed 'ACR-244-TP4_1'
[2025-08-29 17:11:22,119] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-244-TP4_2_fastqc.zip' as already parsed 'ACR-244-TP4_2'
[2025-08-29 17:11:22,271] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP1_1_fastqc.zip' as already parsed 'ACR-265-TP1_1'
[2025-08-29 17:11:22,336] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP1_2_fastqc.zip' as already parsed 'ACR-265-TP1_2'
[2025-08-29 17:11:22,402] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP2_1_fastqc.zip' as already parsed 'ACR-265-TP2_1'
[2025-08-29 17:11:22,664] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP2_2_fastqc.zip' as already parsed 'ACR-265-TP2_2'
[2025-08-29 17:11:22,872] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP3_1_fastqc.zip' as already parsed 'ACR-265-TP3_1'
[2025-08-29 17:11:23,439] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP3_2_fastqc.zip' as already parsed 'ACR-265-TP3_2'
[2025-08-29 17:11:23,523] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP4_1_fastqc.zip' as already parsed 'ACR-265-TP4_1'
[2025-08-29 17:11:23,680] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ACR-265-TP4_2_fastqc.zip' as already parsed 'ACR-265-TP4_2'
[2025-08-29 17:11:23,680] multiqc.modules.fastqc.fastqc [INFO ] Found 80 reports
[2025-08-29 17:11:24,374] multiqc.plots.plot [DEBUG ] Plot fastqc_adapter_content_plot has 126 samples > config.plots_defer_loading_numseries=100, will defer render
[2025-08-29 17:11:24,600] multiqc.report [DEBUG ] Wrote data file multiqc_fastqc.txt
[2025-08-29 17:11:24,602] multiqc.report [DEBUG ] Wrote data file multiqc_fastqc.json
[2025-08-29 17:11:24,605] multiqc.base_module [DEBUG ] fastqc: deleting attribute self.order_of_duplication_levels
[2025-08-29 17:11:24,605] multiqc.base_module [DEBUG ] fastqc: deleting attribute self.status_colours
[2025-08-29 17:11:24,605] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions
[2025-08-29 17:11:24,605] multiqc.core.software_versions [DEBUG ] Reading software versions settings from: 365/nf_core_methylseq_software_mqc_versions.yml
[2025-08-29 17:11:24,609] multiqc.report [DEBUG ] Wrote data file multiqc_software_versions.txt
[2025-08-29 17:11:24,609] multiqc.core.order_modules_and_sections [DEBUG ] config.report_section_order: module 'software_versions' not found.
[2025-08-29 17:11:24,609] multiqc.core.write_results [INFO ] Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag
[2025-08-29 17:11:38,517] 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
[2025-08-29 17:11:38,517] 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
[2025-08-29 17:11:38,704] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.txt
[2025-08-29 17:11:38,705] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.json
[2025-08-29 17:11:39,106] multiqc.core.write_results [DEBUG ] Exporting plot data to files
[2025-08-29 17:11:39,106] multiqc.report [DEBUG ] Wrote data file bismark_alignment.txt
[2025-08-29 17:11:39,106] multiqc.report [DEBUG ] Wrote data file bismark_deduplication.txt
[2025-08-29 17:11:39,106] multiqc.report [DEBUG ] Wrote data file bismark_strand_alignment.txt
[2025-08-29 17:11:39,107] multiqc.report [DEBUG ] Wrote data file bismark-methylation-dp.txt
[2025-08-29 17:11:39,111] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CpG_R1.txt
[2025-08-29 17:11:39,115] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHG_R1.txt
[2025-08-29 17:11:39,119] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHH_R1.txt
[2025-08-29 17:11:39,123] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CpG_R2.txt
[2025-08-29 17:11:39,127] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHG_R2.txt
[2025-08-29 17:11:39,131] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHH_R2.txt
[2025-08-29 17:11:39,131] multiqc.report [DEBUG ] Wrote data file fastqc_sequence_counts_plot.txt
[2025-08-29 17:11:39,136] multiqc.report [DEBUG ] Wrote data file fastqc_per_base_sequence_quality_plot.txt
[2025-08-29 17:11:39,138] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_quality_scores_plot.txt
[2025-08-29 17:11:39,147] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_gc_content_plot_Percentages.txt
[2025-08-29 17:11:39,153] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_gc_content_plot_Counts.txt
[2025-08-29 17:11:39,158] multiqc.report [DEBUG ] Wrote data file fastqc_per_base_n_content_plot.txt
[2025-08-29 17:11:39,160] multiqc.report [DEBUG ] Wrote data file fastqc_sequence_length_distribution_plot.txt
[2025-08-29 17:11:39,161] multiqc.report [DEBUG ] Wrote data file fastqc_sequence_duplication_levels_plot.txt
[2025-08-29 17:11:39,161] multiqc.report [DEBUG ] Wrote data file fastqc_top_overrepresented_sequences_table.txt
[2025-08-29 17:11:39,169] multiqc.report [DEBUG ] Wrote data file fastqc_adapter_content_plot.txt
[2025-08-29 17:11:39,169] multiqc.report [DEBUG ] Wrote data file fastqc-status-check-heatmap.txt
[2025-08-29 17:11:39,169] multiqc.core.write_results [DEBUG ] Moving data file from '/tmp/tmpnkivb2i6/multiqc_data' to '/gscratch/scrubbed/srlab/nxf.3iIJDtp8PY/multiqc_data'
[2025-08-29 17:11:39,797] multiqc.core.write_results [INFO ] Data : multiqc_data
[2025-08-29 17:11:40,091] multiqc.core.write_results [DEBUG ] Compressing plot data
[2025-08-29 17:11:40,450] multiqc.core.write_results [INFO ] Report : multiqc_report.html
[2025-08-29 17:11:40,450] multiqc.core.write_results [DEBUG ] Moving plots directory from '/tmp/tmpnkivb2i6/multiqc_plots' to '/gscratch/scrubbed/srlab/nxf.3iIJDtp8PY/multiqc_plots'
[2025-08-29 17:11:40,506] multiqc.core.write_results [INFO ] Plots : multiqc_plots
[2025-08-29 17:11:40,506] multiqc.core.write_results [DEBUG ] Report HTML written to /gscratch/scrubbed/srlab/nxf.3iIJDtp8PY/multiqc_report.html