[2025-08-06 12:05:37,564] root [DEBUG ] Logging to file: /tmp/tmpfgttgokn/multiqc.log [2025-08-06 12:05:37,564] multiqc.core.update_config [DEBUG ] This is MultiQC v1.29 [2025-08-06 12:05:37,564] 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] [2025-08-06 12:05:37,703] multiqc.config [INFO ] Loading config settings from: multiqc_config.yml [2025-08-06 12:05:37,703] 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']} [2025-08-06 12:05:37,707] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443 [2025-08-06 12:05:38,133] 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 [2025-08-06 12:05:38,134] multiqc.core.version_check [WARNING] MultiQC Version v1.30 now available! [2025-08-06 12:05:38,134] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.30, released 2025-07-09 [2025-08-06 12:05:38,134] multiqc.multiqc [DEBUG ] Working dir : /gscratch/scrubbed/srlab/nxf.HTpPwf7YWN [2025-08-06 12:05:38,134] multiqc.multiqc [DEBUG ] Template : default [2025-08-06 12:05:38,134] multiqc.multiqc [DEBUG ] Command used: /usr/local/bin/multiqc --force --config multiqc_config.yml . [2025-08-06 12:05:38,134] multiqc.core.file_search [INFO ] Search path: /gscratch/scrubbed/srlab/nxf.HTpPwf7YWN [2025-08-06 12:05:38,135] 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 [2025-08-06 12:05:38,135] 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 [2025-08-06 12:05:40,488] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_module_specific_max_filesize: 20|, |skipped_no_match: 12| [2025-08-06 12:05:40,489] multiqc.core.exec_modules [DEBUG ] Running module: bismark [2025-08-06 12:05:40,505] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_alignment.txt [2025-08-06 12:05:40,505] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_alignment.json [2025-08-06 12:05:40,505] multiqc.modules.bismark.bismark [INFO ] Found 6 alignment reports [2025-08-06 12:05:40,839] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_dedup.txt [2025-08-06 12:05:40,840] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_dedup.json [2025-08-06 12:05:40,840] multiqc.modules.bismark.bismark [INFO ] Found 6 dedup reports [2025-08-06 12:05:40,898] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_methextract.txt [2025-08-06 12:05:40,898] multiqc.report [DEBUG ] Wrote data file multiqc_bismark_methextract.json [2025-08-06 12:05:40,898] multiqc.modules.bismark.bismark [INFO ] Found 6 methextract reports [2025-08-06 12:05:40,898] 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 [2025-08-06 12:05:40,898] 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 [2025-08-06 12:05:40,938] multiqc.base_module [DEBUG ] bismark: deleting attribute self.bismark_data [2025-08-06 12:05:40,938] multiqc.base_module [DEBUG ] bismark: deleting attribute self.bismark_mbias_data [2025-08-06 12:05:40,938] multiqc.core.exec_modules [DEBUG ] Running module: custom_content [2025-08-06 12:05:40,948] multiqc.core.special_case_modules.custom_content [INFO ] nf-core-methylseq-methods-description: Found 1 sample (html) [2025-08-06 12:05:40,948] multiqc.core.special_case_modules.custom_content [INFO ] nf-core-methylseq-summary: Found 1 sample (html) [2025-08-06 12:05:40,948] multiqc.core.exec_modules [DEBUG ] Running module: cutadapt [2025-08-06 12:05:40,966] multiqc.modules.cutadapt.cutadapt [INFO ] Found 12 reports [2025-08-06 12:05:40,966] multiqc.report [DEBUG ] Wrote data file multiqc_cutadapt.txt [2025-08-06 12:05:40,966] multiqc.report [DEBUG ] Wrote data file multiqc_cutadapt.json [2025-08-06 12:05:40,988] multiqc.base_module [DEBUG ] cutadapt: deleting attribute self.cutadapt_data [2025-08-06 12:05:40,988] multiqc.base_module [DEBUG ] cutadapt: deleting attribute self.cutadapt_length_counts [2025-08-06 12:05:40,988] multiqc.base_module [DEBUG ] cutadapt: deleting attribute self.cutadapt_length_exp [2025-08-06 12:05:40,988] multiqc.base_module [DEBUG ] cutadapt: deleting attribute self.cutadapt_length_obsexp [2025-08-06 12:05:40,988] multiqc.core.exec_modules [DEBUG ] Running module: fastqc [2025-08-06 12:05:41,005] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LCo_BSr1_1_fastqc.zip' as already parsed 'LCo_BSr1_1' [2025-08-06 12:05:41,014] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LCo_BSr1_2_fastqc.zip' as already parsed 'LCo_BSr1_2' [2025-08-06 12:05:41,022] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LCo_BSr2_1_fastqc.zip' as already parsed 'LCo_BSr2_1' [2025-08-06 12:05:41,029] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LCo_BSr2_2_fastqc.zip' as already parsed 'LCo_BSr2_2' [2025-08-06 12:05:41,037] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LCo_BSr3_1_fastqc.zip' as already parsed 'LCo_BSr3_1' [2025-08-06 12:05:41,044] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LCo_BSr3_2_fastqc.zip' as already parsed 'LCo_BSr3_2' [2025-08-06 12:05:41,052] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LYa_BSr1_1_fastqc.zip' as already parsed 'LYa_BSr1_1' [2025-08-06 12:05:41,060] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LYa_BSr1_2_fastqc.zip' as already parsed 'LYa_BSr1_2' [2025-08-06 12:05:41,067] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LYa_BSr2_1_fastqc.zip' as already parsed 'LYa_BSr2_1' [2025-08-06 12:05:41,075] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LYa_BSr2_2_fastqc.zip' as already parsed 'LYa_BSr2_2' [2025-08-06 12:05:41,082] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LYa_BSr3_1_fastqc.zip' as already parsed 'LYa_BSr3_1' [2025-08-06 12:05:41,090] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'LYa_BSr3_2_fastqc.zip' as already parsed 'LYa_BSr3_2' [2025-08-06 12:05:41,090] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2025-08-06 12:05:41,215] multiqc.plots.table_object [DEBUG ] Table key 'samples' not found in data for 'fastqc_top_overrepresented_sequences_table'. Skipping. Check for possible typos between data keys and header keys [2025-08-06 12:05:41,215] multiqc.plots.table_object [DEBUG ] Table key 'total_count' not found in data for 'fastqc_top_overrepresented_sequences_table'. Skipping. Check for possible typos between data keys and header keys [2025-08-06 12:05:41,215] multiqc.plots.table_object [DEBUG ] Table key 'total_percent' not found in data for 'fastqc_top_overrepresented_sequences_table'. Skipping. Check for possible typos between data keys and header keys [2025-08-06 12:05:41,251] multiqc.report [DEBUG ] Wrote data file multiqc_fastqc.txt [2025-08-06 12:05:41,251] multiqc.report [DEBUG ] Wrote data file multiqc_fastqc.json [2025-08-06 12:05:41,252] multiqc.base_module [DEBUG ] fastqc: deleting attribute self.order_of_duplication_levels [2025-08-06 12:05:41,252] multiqc.base_module [DEBUG ] fastqc: deleting attribute self.status_colours [2025-08-06 12:05:41,252] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions [2025-08-06 12:05:41,252] multiqc.core.software_versions [DEBUG ] Reading software versions settings from: 71/nf_core_methylseq_software_mqc_versions.yml [2025-08-06 12:05:41,256] multiqc.report [DEBUG ] Wrote data file multiqc_software_versions.txt [2025-08-06 12:05:41,256] multiqc.core.order_modules_and_sections [DEBUG ] config.report_section_order: module 'software_versions' not found. [2025-08-06 12:05:41,256] 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 [2025-08-06 12:06:01,817] 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 [2025-08-06 12:06:01,817] 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 [2025-08-06 12:06:01,885] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.txt [2025-08-06 12:06:01,886] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.json [2025-08-06 12:06:01,928] multiqc.core.write_results [DEBUG ] Exporting plot data to files [2025-08-06 12:06:01,928] multiqc.report [DEBUG ] Wrote data file bismark_alignment.txt [2025-08-06 12:06:01,929] multiqc.report [DEBUG ] Wrote data file bismark_deduplication.txt [2025-08-06 12:06:01,929] multiqc.report [DEBUG ] Wrote data file bismark_strand_alignment.txt [2025-08-06 12:06:01,929] multiqc.report [DEBUG ] Wrote data file bismark-methylation-dp.txt [2025-08-06 12:06:01,930] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CpG_R1.txt [2025-08-06 12:06:01,930] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHG_R1.txt [2025-08-06 12:06:01,931] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHH_R1.txt [2025-08-06 12:06:01,932] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CpG_R2.txt [2025-08-06 12:06:01,932] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHG_R2.txt [2025-08-06 12:06:01,933] multiqc.report [DEBUG ] Wrote data file bismark_mbias_CHH_R2.txt [2025-08-06 12:06:01,933] multiqc.report [DEBUG ] Wrote data file cutadapt_filtered_reads_plot.txt [2025-08-06 12:06:01,935] multiqc.report [DEBUG ] Wrote data file cutadapt_trimmed_sequences_plot_3_Counts.txt [2025-08-06 12:06:01,936] multiqc.report [DEBUG ] Wrote data file cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt [2025-08-06 12:06:01,936] multiqc.report [DEBUG ] Wrote data file fastqc_sequence_counts_plot.txt [2025-08-06 12:06:01,937] multiqc.report [DEBUG ] Wrote data file fastqc_per_base_sequence_quality_plot.txt [2025-08-06 12:06:01,937] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_quality_scores_plot.txt [2025-08-06 12:06:01,939] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_gc_content_plot_Percentages.txt [2025-08-06 12:06:01,940] multiqc.report [DEBUG ] Wrote data file fastqc_per_sequence_gc_content_plot_Counts.txt [2025-08-06 12:06:01,940] multiqc.report [DEBUG ] Wrote data file fastqc_per_base_n_content_plot.txt [2025-08-06 12:06:01,941] multiqc.report [DEBUG ] Wrote data file fastqc_sequence_duplication_levels_plot.txt [2025-08-06 12:06:01,942] multiqc.report [DEBUG ] Wrote data file fastqc_adapter_content_plot.txt [2025-08-06 12:06:01,942] multiqc.report [DEBUG ] Wrote data file fastqc-status-check-heatmap.txt [2025-08-06 12:06:01,942] multiqc.core.write_results [DEBUG ] Moving data file from '/tmp/tmpfgttgokn/multiqc_data' to '/gscratch/scrubbed/srlab/nxf.HTpPwf7YWN/multiqc_data' [2025-08-06 12:06:02,073] multiqc.core.write_results [INFO ] Data : multiqc_data [2025-08-06 12:06:02,131] multiqc.core.write_results [DEBUG ] Compressing plot data [2025-08-06 12:06:02,250] multiqc.core.write_results [INFO ] Report : multiqc_report.html [2025-08-06 12:06:02,250] multiqc.core.write_results [DEBUG ] Moving plots directory from '/tmp/tmpfgttgokn/multiqc_plots' to '/gscratch/scrubbed/srlab/nxf.HTpPwf7YWN/multiqc_plots' [2025-08-06 12:06:02,311] multiqc.core.write_results [INFO ] Plots : multiqc_plots [2025-08-06 12:06:02,311] multiqc.core.write_results [DEBUG ] Report HTML written to /gscratch/scrubbed/srlab/nxf.HTpPwf7YWN/multiqc_report.html