[2026-06-04 17:08:51,638] root [DEBUG ] Logging to file: /tmp/tmpwcxhzucp/multiqc.log
[2026-06-04 17:08:51,640] multiqc.core.update_config [DEBUG ] This is MultiQC v1.33
[2026-06-04 17:08:51,640] multiqc.core.update_config [DEBUG ] Running Python 3.14.4 | packaged by conda-forge | (main, Apr 8 2026, 01:59:35) [GCC 14.3.0]
[2026-06-04 17:08:51,750] multiqc.config [INFO ] Loading config settings from: multiqc_config.yml
[2026-06-04 17:08:51,750] multiqc.config [ERROR ] Config 'custom_logo' path not found, skipping (nf-core-sarek_logo_light.png)
[2026-06-04 17:08:51,750] multiqc.config [DEBUG ] New config: {'custom_logo_url': 'https://github.com/nf-core/sarek/', 'custom_logo_title': 'nf-core/sarek', 'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.5.0" target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/sarek/3.5.0/docs/output" target="_blank">documentation</a>.\n', 'report_section_order': {'nf-core-sarek-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-sarek-summary': {'order': -1002}}, 'export_plots': True, 'disable_version_detection': True, 'run_modules': ['custom_content', 'fastqc', 'fastp', 'picard', 'samtools', 'mosdepth', 'gatk', 'bcftools', 'vcftools', 'snpeff', 'vep'], 'module_order': [{'fastqc': {'name': 'FastQC (raw)', 'path_filters_exclude': ['*_val_*.zip']}}, {'fastp': {'name': 'FastP (Read preprocessing)'}}, {'picard': {'name': 'GATK4 MarkDuplicates', 'info': ' metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark).'}}, {'samtools': {'name': 'Samtools Flagstat'}}, {'mosdepth': {'name': 'Mosdepth'}}, {'gatk': {'name': 'GATK4 BQSR'}}, {'bcftools': {'name': 'Bcftools'}}, {'vcftools': {'name': 'Vcftools'}}, {'snpeff': {'name': 'SNPeff'}}, {'vep': {'name': 'VEP'}}], 'sample_names_replace_regex': True, 'sample_names_replace': {'\\.[0-9]{4}$': '.md', 'module': 'picard'}, 'custom_data': {'dedup_metrics': {'id': 'dedup_metrics', 'section_name': 'Sentieon Dedup Metrics', 'plot_type': 'table', 'pconfig': {'id': 'dedup_metrics', 'namespace': 'Sentieon Dedup Metrics'}, 'headers': {'LIBRARY': {'description': 'LIBRARY'}, 'UNPAIRED_READS_EXAMINED': {'description': 'UNPAIRED_READS_EXAMINE'}, 'READ_PAIRS_EXAMINED': {'description': 'READ_PAIRS_EXAMINED'}, 'SECONDARY_OR_SUPPLEMENTARY_RDS': {'description': 'SECONDARY_OR_SUPPLEMENTARY_RDS'}, 'UNMAPPED_READS': {'description': 'UNMAPPED_READS'}, 'UNPAIRED_READ_DUPLICATES': {'description': 'UNPAIRED_READ_DUPLICATES'}, 'READ_PAIR_DUPLICATES': {'description': 'READ_PAIR_DUPLICATES'}, 'READ_PAIR_OPTICAL_DUPLICATES': {'description': 'READ_PAIR_OPTICAL_DUPLICATES'}, 'PERCENT_DUPLICATION': {'description': 'PERCENT_DUPLICATION'}, 'ESTIMATED_LIBRARY_SIZE': {'description': 'ESTIMATED_LIBRARY_SIZE'}}}}}
[2026-06-04 17:08:51,750] multiqc.config [DEBUG ] Added to filename patterns: [{'snpeff': {'contents': 'SnpEff_version', 'max_filesize': 5000000}, 'dedup_metrics': {'fn': '*.metrics.multiqc.tsv'}}]
[2026-06-04 17:08:51,750] multiqc.config [DEBUG ] Added to filename clean extensions: [['_val', {'type': 'regex_keep', 'pattern': '^.*.(md|recal).mosdepth.(global|region).dist', 'module': 'mosdepth'}]]
[2026-06-04 17:08:51,751] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443
[2026-06-04 17:08:52,175] urllib3.connectionpool [DEBUG ] https://api.multiqc.info:443 "GET /version?version_multiqc=1.33&version_python=3.14.4&operating_system=Linux&is_docker=False&is_singularity=False&is_conda=True&is_uv=False&is_ci=False&is_notebook=False&ai_summary=False&ai_summary_full=False&ai_provider=seqera HTTP/1.1" 200 178
[2026-06-04 17:08:52,175] multiqc.core.version_check [WARNING] MultiQC Version v1.35 now available!
[2026-06-04 17:08:52,175] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.35, released 2026-05-13
[2026-06-04 17:08:52,176] multiqc.multiqc [DEBUG ] Working dir : /tmp/nxf.6RJhfc3liy
[2026-06-04 17:08:52,176] multiqc.multiqc [DEBUG ] Template : default
[2026-06-04 17:08:52,177] multiqc.multiqc [DEBUG ] Command used: /opt/conda/bin/multiqc --force --config multiqc_config.yml .
[2026-06-04 17:08:52,177] multiqc.core.file_search [INFO ] Search path: /tmp/nxf.6RJhfc3liy
[2026-06-04 17:08:52,177] multiqc.core.file_search [INFO ] Only using modules: custom_content, fastqc, fastp, picard, samtools, mosdepth, gatk, bcftools, vcftools, snpeff, vep
[2026-06-04 17:08:52,177] multiqc.core.file_search [DEBUG ] Analysing modules: custom_content, fastqc, fastp, picard, samtools, mosdepth, gatk, bcftools, vcftools, snpeff, vep
[2026-06-04 17:08:52,177] multiqc.core.file_search [DEBUG ] Search keys: bcftools, custom_content, dedup_metrics, fastp, fastqc, gatk, mosdepth, multiqc_data, picard, samtools, snpeff, software_versions, vcftools, vep
[2026-06-04 17:08:52,178] multiqc.report [DEBUG ] Ignored 326 search patterns that didn't match running modules
[2026-06-04 17:08:52,217] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_module_specific_max_filesize: 4|, |skipped_no_match: 47|
[2026-06-04 17:08:52,218] multiqc.core.exec_modules [DEBUG ] Running module: custom_content
[2026-06-04 17:08:52,224] multiqc.core.special_case_modules.custom_content [INFO ] nf-core-sarek-methods-description: Found 1 sample (html)
[2026-06-04 17:08:52,224] multiqc.core.special_case_modules.custom_content [INFO ] altera-sarek-summary: Found 1 sample (html)
[2026-06-04 17:08:52,225] multiqc.core.exec_modules [DEBUG ] Running module: samtools
[2026-06-04 17:08:52,246] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools_alignment_plot: found old_data = False
[2026-06-04 17:08:52,246] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools_alignment_plot: no old data or empty, using new data only
[2026-06-04 17:08:52,302] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools-stats-dp: found old_data = False
[2026-06-04 17:08:52,302] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools-stats-dp: no old data or empty, using new data only
[2026-06-04 17:08:52,310] multiqc.report [DEBUG ] Wrote data file multiqc_samtools_stats.txt
[2026-06-04 17:08:52,311] multiqc.report [DEBUG ] Wrote data file multiqc_samtools_stats.json
[2026-06-04 17:08:52,311] multiqc.modules.samtools.samtools [INFO ] Found 4 stats reports
[2026-06-04 17:08:52,311] multiqc.base_module [DEBUG ] samtools: deleting attribute self.samtools_idxstats
[2026-06-04 17:08:52,311] multiqc.core.exec_modules [DEBUG ] Running module: mosdepth
[2026-06-04 17:08:52,312] multiqc.config [DEBUG ] Using default coverage thresholds: 1, 5, 10, 30, 50
[2026-06-04 17:08:52,316] multiqc.config [DEBUG ] Using default coverage thresholds: 1, 5, 10, 30, 50
[2026-06-04 17:08:52,323] multiqc.modules.mosdepth.mosdepth [INFO ] Found reports for 4 samples
[2026-06-04 17:08:52,324] multiqc.report [DEBUG ] Wrote data file mosdepth_cumcov_dist.txt
[2026-06-04 17:08:52,326] multiqc.report [DEBUG ] Wrote data file mosdepth_cumcov_dist.json
[2026-06-04 17:08:52,327] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-cumcoverage-dist-id: found old_data = False
[2026-06-04 17:08:52,327] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-cumcoverage-dist-id: no old data or empty, using new data only
[2026-06-04 17:08:52,334] multiqc.report [DEBUG ] Wrote data file mosdepth_cov_dist.txt
[2026-06-04 17:08:52,335] multiqc.report [DEBUG ] Wrote data file mosdepth_cov_dist.json
[2026-06-04 17:08:52,335] multiqc.report [DEBUG ] Wrote data file mosdepth_perchrom.txt
[2026-06-04 17:08:52,336] multiqc.report [DEBUG ] Wrote data file mosdepth_perchrom.json
[2026-06-04 17:08:52,362] multiqc.validation [WARNING] mosdepth/mosdepth.py: warnings while parsing barplot.pconfig[id='mosdepth-coverage-per-contig-single'] {id: mosdepth-coverage-per-contig-single, title: Mosdepth: Coverage per contig, xlab: Sample, ylab: Average Coverage, tt_suffix: x, hide_zero_cats: False, categories: True}:
• 'categories': unrecognized field. Available fields: id, title, subtitle, anchor, height, width, square, logswitch, logswitch_active, logswitch_label, cpswitch, cpswitch_c_active, cpswitch_counts_label, cpswitch_percent_label, xlog, ylog, data_labels, xlab, ylab, xsuffix, ysuffix, tt_suffix, xlab_format, ylab_format, tt_label, x_decimals, y_decimals, tt_decimals, xmin, xmax, ymin, ymax, x_clipmin, x_clipmax, y_clipmin, y_clipmax, save_data_file, showlegend, x_minrange, y_minrange, x_bands, y_bands, x_lines, y_lines, series_label, flat_if_very_large, stacking, hide_zero_cats, sort_samples, cluster_samples, cluster_method, cluster_switch_clustered_active, use_legend, suffix, lab_format, sample_groups
[2026-06-04 17:08:52,363] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-coverage-per-contig-single: found old_data = False
[2026-06-04 17:08:52,363] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-coverage-per-contig-single: no old data or empty, using new data only
[2026-06-04 17:08:52,367] multiqc.config [DEBUG ] Using default coverage thresholds: 1, 5, 10, 30, 50
[2026-06-04 17:08:52,368] multiqc.base_module [DEBUG ] mosdepth: deleting attribute self.cfg
[2026-06-04 17:08:52,368] multiqc.core.exec_modules [DEBUG ] Running module: snpeff
[2026-06-04 17:08:52,369] multiqc.core.exec_modules [DEBUG ] No samples found: snpeff
[2026-06-04 17:08:52,369] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions
[2026-06-04 17:08:52,369] multiqc.core.software_versions [DEBUG ] Reading software versions settings from: 17/nf_core_sarek_software_mqc_versions.yml
[2026-06-04 17:08:52,370] multiqc.core.file_search [INFO ] Only using modules: samtools, mosdepth, nf-core-sarek-methods-description, altera-sarek-summary
[2026-06-04 17:08:52,371] multiqc.report [DEBUG ] Wrote data file multiqc_software_versions.txt
[2026-06-04 17:08:52,371] multiqc.core.order_modules_and_sections [DEBUG ] config.report_section_order: module 'software_versions' not found.
[2026-06-04 17:08:52,371] multiqc.core.order_modules_and_sections [DEBUG ] config.report_section_order: module 'nf-core-sarek-summary' not found.
[2026-06-04 17:08:52,371] 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
[2026-06-04 17:08:55,531] multiqc.plots.table_object [DEBUG ] Table key 'mean_coverage' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys
[2026-06-04 17:08:55,531] multiqc.plots.table_object [DEBUG ] Table key 'min_coverage' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys
[2026-06-04 17:08:55,531] multiqc.plots.table_object [DEBUG ] Table key 'max_coverage' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys
[2026-06-04 17:08:55,531] multiqc.plots.table_object [DEBUG ] Table key 'coverage_bases' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys
[2026-06-04 17:08:55,531] multiqc.plots.table_object [DEBUG ] Table key 'length' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys
[2026-06-04 17:08:55,532] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: found old_data = False
[2026-06-04 17:08:55,532] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: no old data or empty, using new data only
[2026-06-04 17:08:55,542] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.txt
[2026-06-04 17:08:55,542] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.json
[2026-06-04 17:08:55,547] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,548] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,548] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,549] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,550] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,551] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,552] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-04 17:08:55,553] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-04 17:08:55,555] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,556] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,557] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,557] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,559] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,559] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,561] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,561] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,562] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,562] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,564] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,564] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-04 17:08:55,565] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-04 17:08:55,566] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-04 17:08:55,567] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-04 17:08:55,567] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-04 17:08:55,598] multiqc.core.ai [DEBUG ] Saved AI prompt to multiqc_data/llms-full.txt
[2026-06-04 17:08:55,598] multiqc.core.write_results [DEBUG ] Exporting plot data to files
[2026-06-04 17:08:55,598] multiqc.report [DEBUG ] Wrote data file samtools_alignment_plot.txt
[2026-06-04 17:08:55,598] multiqc.report [DEBUG ] Wrote data file samtools-stats-dp.txt
[2026-06-04 17:08:55,600] multiqc.report [DEBUG ] Wrote data file mosdepth-cumcoverage-dist-id.txt
[2026-06-04 17:08:55,600] multiqc.report [DEBUG ] Wrote data file mosdepth-coverage-per-contig-single.txt
[2026-06-04 17:08:55,600] multiqc.core.write_results [DEBUG ] Moving data file from '/tmp/tmpwcxhzucp/multiqc_data' to '/tmp/nxf.6RJhfc3liy/multiqc_data'
[2026-06-04 17:08:55,652] multiqc.core.write_results [INFO ] Data : multiqc_data
[2026-06-04 17:08:55,659] multiqc.core.write_results [DEBUG ] Compressing plot data
[2026-06-04 17:08:55,727] multiqc.core.write_results [INFO ] Report : multiqc_report.html
[2026-06-04 17:08:55,727] multiqc.core.write_results [DEBUG ] Moving plots directory from '/tmp/tmpwcxhzucp/multiqc_plots' to '/tmp/nxf.6RJhfc3liy/multiqc_plots'
[2026-06-04 17:08:55,729] multiqc.core.write_results [INFO ] Plots : multiqc_plots