[2026-06-05 03:16:24,426] root [DEBUG ] Logging to file: /tmp/tmpugt_ms97/multiqc.log
[2026-06-05 03:16:24,429] multiqc.core.update_config [DEBUG ] This is MultiQC v1.33
[2026-06-05 03:16:24,429] 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]
[2026-06-05 03:16:24,590] multiqc.config [INFO ] Loading config settings from: multiqc_config.yml
[2026-06-05 03:16:24,590] multiqc.config [ERROR ] Config 'custom_logo' path not found, skipping (nf-core-sarek_logo_light.png)
[2026-06-05 03:16:24,591] 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 nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation.\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'}}}}}
[2026-06-05 03:16:24,591] multiqc.config [DEBUG ] Added to filename patterns: [{'snpeff': {'contents': 'SnpEff_version', 'max_filesize': 5000000}, 'dedup_metrics': {'fn': '*.metrics.multiqc.tsv'}}]
[2026-06-05 03:16:24,591] multiqc.config [DEBUG ] Added to filename clean extensions: [['_val', {'type': 'regex_keep', 'pattern': '^.*.(md|recal).mosdepth.(global|region).dist', 'module': 'mosdepth'}]]
[2026-06-05 03:16:24,592] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443
[2026-06-05 03:16:25,040] 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
[2026-06-05 03:16:25,040] multiqc.core.version_check [WARNING] MultiQC Version v1.35 now available!
[2026-06-05 03:16:25,040] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.35, released 2026-05-13
[2026-06-05 03:16:25,041] multiqc.multiqc [DEBUG ] Working dir : /tmp/nxf.uMOsqH3Syc
[2026-06-05 03:16:25,041] multiqc.multiqc [DEBUG ] Template : default
[2026-06-05 03:16:25,041] multiqc.multiqc [DEBUG ] Command used: /opt/conda/bin/multiqc --force --config multiqc_config.yml .
[2026-06-05 03:16:25,041] multiqc.core.file_search [INFO ] Search path: /tmp/nxf.uMOsqH3Syc
[2026-06-05 03:16:25,042] multiqc.core.file_search [INFO ] Only using modules: custom_content, fastqc, fastp, picard, samtools, mosdepth, gatk, bcftools, vcftools, snpeff, vep
[2026-06-05 03:16:25,042] multiqc.core.file_search [DEBUG ] Analysing modules: custom_content, fastqc, fastp, picard, samtools, mosdepth, gatk, bcftools, vcftools, snpeff, vep
[2026-06-05 03:16:25,042] 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
[2026-06-05 03:16:25,044] multiqc.report [DEBUG ] Ignored 326 search patterns that didn't match running modules
[2026-06-05 03:16:25,107] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_module_specific_max_filesize: 4|, |skipped_no_match: 61|
[2026-06-05 03:16:25,109] multiqc.core.exec_modules [DEBUG ] Running module: custom_content
[2026-06-05 03:16:25,117] multiqc.core.special_case_modules.custom_content [INFO ] nf-core-sarek-methods-description: Found 1 sample (html)
[2026-06-05 03:16:25,117] multiqc.core.special_case_modules.custom_content [INFO ] altera-sarek-summary: Found 1 sample (html)
[2026-06-05 03:16:25,118] multiqc.core.exec_modules [DEBUG ] Running module: samtools
[2026-06-05 03:16:25,146] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools_alignment_plot: found old_data = False
[2026-06-05 03:16:25,146] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools_alignment_plot: no old data or empty, using new data only
[2026-06-05 03:16:25,188] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools-stats-dp: found old_data = False
[2026-06-05 03:16:25,188] multiqc.plots.plot [DEBUG ] merge_with_previous for samtools-stats-dp: no old data or empty, using new data only
[2026-06-05 03:16:25,197] multiqc.report [DEBUG ] Wrote data file multiqc_samtools_stats.txt
[2026-06-05 03:16:25,198] multiqc.report [DEBUG ] Wrote data file multiqc_samtools_stats.json
[2026-06-05 03:16:25,198] multiqc.modules.samtools.samtools [INFO ] Found 4 stats reports
[2026-06-05 03:16:25,198] multiqc.base_module [DEBUG ] samtools: deleting attribute self.samtools_idxstats
[2026-06-05 03:16:25,198] multiqc.core.exec_modules [DEBUG ] Running module: mosdepth
[2026-06-05 03:16:25,200] multiqc.config [DEBUG ] Using default coverage thresholds: 1, 5, 10, 30, 50
[2026-06-05 03:16:25,210] multiqc.config [DEBUG ] Using default coverage thresholds: 1, 5, 10, 30, 50
[2026-06-05 03:16:25,222] multiqc.modules.mosdepth.mosdepth [INFO ] Found reports for 4 samples
[2026-06-05 03:16:25,223] multiqc.report [DEBUG ] Wrote data file mosdepth_cumcov_dist.txt
[2026-06-05 03:16:25,225] multiqc.report [DEBUG ] Wrote data file mosdepth_cumcov_dist.json
[2026-06-05 03:16:25,228] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-cumcoverage-dist-id: found old_data = False
[2026-06-05 03:16:25,228] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-cumcoverage-dist-id: no old data or empty, using new data only
[2026-06-05 03:16:25,237] multiqc.report [DEBUG ] Wrote data file mosdepth_cov_dist.txt
[2026-06-05 03:16:25,239] multiqc.report [DEBUG ] Wrote data file mosdepth_cov_dist.json
[2026-06-05 03:16:25,239] multiqc.report [DEBUG ] Wrote data file mosdepth_perchrom.txt
[2026-06-05 03:16:25,239] multiqc.report [DEBUG ] Wrote data file mosdepth_perchrom.json
[2026-06-05 03:16:25,270] 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
[2026-06-05 03:16:25,270] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-coverage-per-contig-single: found old_data = False
[2026-06-05 03:16:25,270] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-coverage-per-contig-single: no old data or empty, using new data only
[2026-06-05 03:16:25,277] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-xy-coverage-plot: found old_data = False
[2026-06-05 03:16:25,277] multiqc.plots.plot [DEBUG ] merge_with_previous for mosdepth-xy-coverage-plot: no old data or empty, using new data only
[2026-06-05 03:16:25,282] multiqc.config [DEBUG ] Using default coverage thresholds: 1, 5, 10, 30, 50
[2026-06-05 03:16:25,283] multiqc.base_module [DEBUG ] mosdepth: deleting attribute self.cfg
[2026-06-05 03:16:25,283] multiqc.core.exec_modules [DEBUG ] Running module: bcftools
[2026-06-05 03:16:25,289] multiqc.report [DEBUG ] Wrote data file multiqc_bcftools_stats.txt
[2026-06-05 03:16:25,290] multiqc.report [DEBUG ] Wrote data file multiqc_bcftools_stats.json
[2026-06-05 03:16:25,290] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools-stats-subtypes: found old_data = False
[2026-06-05 03:16:25,290] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools-stats-subtypes: no old data or empty, using new data only
[2026-06-05 03:16:25,301] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools_stats_vqc: found old_data = False
[2026-06-05 03:16:25,301] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools_stats_vqc: no old data or empty, using new data only
[2026-06-05 03:16:25,311] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools_stats_indel-lengths: found old_data = False
[2026-06-05 03:16:25,311] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools_stats_indel-lengths: no old data or empty, using new data only
[2026-06-05 03:16:25,317] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools_stats_variant_depths: found old_data = False
[2026-06-05 03:16:25,317] multiqc.plots.plot [DEBUG ] merge_with_previous for bcftools_stats_variant_depths: no old data or empty, using new data only
[2026-06-05 03:16:25,323] multiqc.modules.bcftools.bcftools [INFO ] Found 12 stats reports
[2026-06-05 03:16:25,323] multiqc.base_module [DEBUG ] bcftools: deleting attribute self.general_stats_headers
[2026-06-05 03:16:25,323] multiqc.base_module [DEBUG ] bcftools: deleting attribute self.general_stats_data
[2026-06-05 03:16:25,323] multiqc.core.exec_modules [DEBUG ] Running module: vcftools
[2026-06-05 03:16:25,327] multiqc.report [DEBUG ] Wrote data file vcftools_tstv_by_count.txt
[2026-06-05 03:16:25,328] multiqc.report [DEBUG ] Wrote data file vcftools_tstv_by_count.json
[2026-06-05 03:16:25,329] multiqc.plots.plot [DEBUG ] merge_with_previous for vcftools_tstv_by_count: found old_data = False
[2026-06-05 03:16:25,329] multiqc.plots.plot [DEBUG ] merge_with_previous for vcftools_tstv_by_count: no old data or empty, using new data only
[2026-06-05 03:16:25,334] multiqc.modules.vcftools.vcftools [INFO ] Found 12 TsTv.count reports
[2026-06-05 03:16:25,337] multiqc.report [DEBUG ] Wrote data file vcftools_tstv_by_qual.txt
[2026-06-05 03:16:25,339] multiqc.report [DEBUG ] Wrote data file vcftools_tstv_by_qual.json
[2026-06-05 03:16:25,340] multiqc.plots.plot [DEBUG ] merge_with_previous for vcftools_tstv_by_qual: found old_data = False
[2026-06-05 03:16:25,340] multiqc.plots.plot [DEBUG ] merge_with_previous for vcftools_tstv_by_qual: no old data or empty, using new data only
[2026-06-05 03:16:25,346] multiqc.modules.vcftools.vcftools [INFO ] Found 12 TsTv.qual reports
[2026-06-05 03:16:25,346] multiqc.base_module [DEBUG ] vcftools: deleting attribute self.vcftools_tstv_by_count
[2026-06-05 03:16:25,346] multiqc.base_module [DEBUG ] vcftools: deleting attribute self.vcftools_tstv_by_qual
[2026-06-05 03:16:25,346] multiqc.base_module [DEBUG ] vcftools: deleting attribute self.vcftools_tstv_summary
[2026-06-05 03:16:25,346] multiqc.core.exec_modules [DEBUG ] Running module: snpeff
[2026-06-05 03:16:25,353] multiqc.modules.snpeff.snpeff [INFO ] Found 12 reports
[2026-06-05 03:16:25,354] multiqc.report [DEBUG ] Wrote data file multiqc_snpeff.txt
[2026-06-05 03:16:25,354] multiqc.report [DEBUG ] Wrote data file multiqc_snpeff.json
[2026-06-05 03:16:25,355] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_variant_effects_region: found old_data = False
[2026-06-05 03:16:25,355] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_variant_effects_region: no old data or empty, using new data only
[2026-06-05 03:16:25,362] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_variant_effects_impact: found old_data = False
[2026-06-05 03:16:25,362] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_variant_effects_impact: no old data or empty, using new data only
[2026-06-05 03:16:25,369] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_effects: found old_data = False
[2026-06-05 03:16:25,369] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_effects: no old data or empty, using new data only
[2026-06-05 03:16:25,376] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_variant_effects_class: found old_data = False
[2026-06-05 03:16:25,376] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_variant_effects_class: no old data or empty, using new data only
[2026-06-05 03:16:25,383] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_qualities: found old_data = False
[2026-06-05 03:16:25,383] multiqc.plots.plot [DEBUG ] merge_with_previous for snpeff_qualities: no old data or empty, using new data only
[2026-06-05 03:16:25,387] multiqc.base_module [DEBUG ] snpeff: deleting attribute self.snpeff_data
[2026-06-05 03:16:25,387] multiqc.base_module [DEBUG ] snpeff: deleting attribute self.snpeff_section_totals
[2026-06-05 03:16:25,387] multiqc.base_module [DEBUG ] snpeff: deleting attribute self.snpeff_qualities
[2026-06-05 03:16:25,387] multiqc.core.exec_modules [DEBUG ] Running module: vep
[2026-06-05 03:16:25,395] multiqc.modules.vep.vep [INFO ] Found 12 VEP summaries
[2026-06-05 03:16:25,396] multiqc.report [DEBUG ] Wrote data file vep.txt
[2026-06-05 03:16:25,397] multiqc.report [DEBUG ] Wrote data file vep.json
[2026-06-05 03:16:25,398] multiqc.plots.plot [DEBUG ] merge_with_previous for vep-general-stats: found old_data = False
[2026-06-05 03:16:25,398] multiqc.plots.plot [DEBUG ] merge_with_previous for vep-general-stats: no old data or empty, using new data only
[2026-06-05 03:16:25,406] multiqc.plots.plot [DEBUG ] merge_with_previous for variant_classes_plot: found old_data = False
[2026-06-05 03:16:25,407] multiqc.plots.plot [DEBUG ] merge_with_previous for variant_classes_plot: no old data or empty, using new data only
[2026-06-05 03:16:25,414] multiqc.plots.plot [DEBUG ] merge_with_previous for consequences_all__plot: found old_data = False
[2026-06-05 03:16:25,414] multiqc.plots.plot [DEBUG ] merge_with_previous for consequences_all__plot: no old data or empty, using new data only
[2026-06-05 03:16:25,422] multiqc.plots.plot [DEBUG ] merge_with_previous for sift_summary_plot: found old_data = False
[2026-06-05 03:16:25,422] multiqc.plots.plot [DEBUG ] merge_with_previous for sift_summary_plot: no old data or empty, using new data only
[2026-06-05 03:16:25,428] multiqc.plots.plot [DEBUG ] merge_with_previous for polyphen_summary_plot: found old_data = False
[2026-06-05 03:16:25,428] multiqc.plots.plot [DEBUG ] merge_with_previous for polyphen_summary_plot: no old data or empty, using new data only
[2026-06-05 03:16:25,434] multiqc.plots.plot [DEBUG ] merge_with_previous for variants_by_chromosome_plot: found old_data = False
[2026-06-05 03:16:25,435] multiqc.plots.plot [DEBUG ] merge_with_previous for variants_by_chromosome_plot: no old data or empty, using new data only
[2026-06-05 03:16:25,441] multiqc.plots.plot [DEBUG ] merge_with_previous for position_in_protein_plot: found old_data = False
[2026-06-05 03:16:25,442] multiqc.plots.plot [DEBUG ] merge_with_previous for position_in_protein_plot: no old data or empty, using new data only
[2026-06-05 03:16:25,447] multiqc.base_module [DEBUG ] vep: deleting attribute self.vep_data
[2026-06-05 03:16:25,448] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions
[2026-06-05 03:16:25,448] multiqc.core.software_versions [DEBUG ] Reading software versions settings from: 91/nf_core_sarek_software_mqc_versions.yml
[2026-06-05 03:16:25,455] multiqc.core.file_search [INFO ] Only using modules: samtools, mosdepth, bcftools, vcftools, snpeff, vep, nf-core-sarek-methods-description, altera-sarek-summary
[2026-06-05 03:16:25,456] multiqc.report [DEBUG ] Wrote data file multiqc_software_versions.txt
[2026-06-05 03:16:25,456] multiqc.core.order_modules_and_sections [DEBUG ] config.report_section_order: module 'software_versions' not found.
[2026-06-05 03:16:25,456] multiqc.core.order_modules_and_sections [DEBUG ] config.report_section_order: module 'nf-core-sarek-summary' not found.
[2026-06-05 03:16:25,456] 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
[2026-06-05 03:16:40,821] 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
[2026-06-05 03:16:40,821] 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
[2026-06-05 03:16:40,821] 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
[2026-06-05 03:16:40,821] 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
[2026-06-05 03:16:40,821] 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
[2026-06-05 03:16:40,822] multiqc.plots.table_object [DEBUG ] Table key 'variations_hom' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys
[2026-06-05 03:16:40,822] multiqc.plots.table_object [DEBUG ] Table key 'variations_het' not found in data for 'general_stats_table'. Skipping. Check for possible typos between data keys and header keys
[2026-06-05 03:16:40,824] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: found old_data = False
[2026-06-05 03:16:40,824] multiqc.plots.plot [DEBUG ] merge_with_previous for general_stats_table: no old data or empty, using new data only
[2026-06-05 03:16:40,844] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.txt
[2026-06-05 03:16:40,844] multiqc.report [DEBUG ] Wrote data file multiqc_general_stats.json
[2026-06-05 03:16:40,851] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,852] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,853] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,855] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,856] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,857] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,858] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-05 03:16:40,859] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-05 03:16:40,860] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,862] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,863] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,864] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,865] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,866] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,868] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,874] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,874] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,876] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,876] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,878] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,878] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,880] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,881] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,883] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,883] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,885] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,885] multiqc.utils.mqc_colour [WARNING] Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
[2026-06-05 03:16:40,887] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-05 03:16:40,887] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-05 03:16:40,889] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-05 03:16:40,889] multiqc.utils.mqc_colour [WARNING] Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
[2026-06-05 03:16:40,891] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,891] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,897] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,897] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,902] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,903] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,908] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,908] multiqc.utils.mqc_colour [WARNING] Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
[2026-06-05 03:16:40,914] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,914] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,919] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,919] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,925] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:40,925] multiqc.utils.mqc_colour [WARNING] Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
[2026-06-05 03:16:41,037] multiqc.core.ai [DEBUG ] Saved AI prompt to multiqc_data/llms-full.txt
[2026-06-05 03:16:41,037] multiqc.core.write_results [DEBUG ] Exporting plot data to files
[2026-06-05 03:16:41,037] multiqc.report [DEBUG ] Wrote data file samtools_alignment_plot.txt
[2026-06-05 03:16:41,037] multiqc.report [DEBUG ] Wrote data file samtools-stats-dp.txt
[2026-06-05 03:16:41,039] multiqc.report [DEBUG ] Wrote data file mosdepth-cumcoverage-dist-id.txt
[2026-06-05 03:16:41,039] multiqc.report [DEBUG ] Wrote data file mosdepth-coverage-per-contig-single.txt
[2026-06-05 03:16:41,039] multiqc.report [DEBUG ] Wrote data file mosdepth-xy-coverage-plot.txt
[2026-06-05 03:16:41,040] multiqc.report [DEBUG ] Wrote data file bcftools-stats-subtypes.txt
[2026-06-05 03:16:41,041] multiqc.report [DEBUG ] Wrote data file bcftools_stats_vqc_Count_SNP.txt
[2026-06-05 03:16:41,042] multiqc.report [DEBUG ] Wrote data file bcftools_stats_vqc_Count_Transitions.txt
[2026-06-05 03:16:41,043] multiqc.report [DEBUG ] Wrote data file bcftools_stats_vqc_Count_Transversions.txt
[2026-06-05 03:16:41,043] multiqc.report [DEBUG ] Wrote data file bcftools_stats_vqc_Count_Indels.txt
[2026-06-05 03:16:41,044] multiqc.report [DEBUG ] Wrote data file bcftools_stats_indel-lengths.txt
[2026-06-05 03:16:41,045] multiqc.report [DEBUG ] Wrote data file bcftools_stats_variant_depths.txt
[2026-06-05 03:16:41,045] multiqc.report [DEBUG ] Wrote data file vcftools_tstv_by_count.txt
[2026-06-05 03:16:41,047] multiqc.report [DEBUG ] Wrote data file vcftools_tstv_by_qual.txt
[2026-06-05 03:16:41,047] multiqc.report [DEBUG ] Wrote data file snpeff_variant_effects_region.txt
[2026-06-05 03:16:41,047] multiqc.report [DEBUG ] Wrote data file snpeff_variant_effects_impact.txt
[2026-06-05 03:16:41,047] multiqc.report [DEBUG ] Wrote data file snpeff_effects.txt
[2026-06-05 03:16:41,047] multiqc.report [DEBUG ] Wrote data file snpeff_variant_effects_class.txt
[2026-06-05 03:16:41,048] multiqc.report [DEBUG ] Wrote data file snpeff_qualities.txt
[2026-06-05 03:16:41,048] multiqc.report [DEBUG ] Wrote data file vep-general-stats.txt
[2026-06-05 03:16:41,048] multiqc.report [DEBUG ] Wrote data file variant_classes_plot.txt
[2026-06-05 03:16:41,048] multiqc.report [DEBUG ] Wrote data file consequences_all__plot_Consequences_most_severe_.txt
[2026-06-05 03:16:41,049] multiqc.report [DEBUG ] Wrote data file consequences_all__plot_Coding_consequences.txt
[2026-06-05 03:16:41,049] multiqc.report [DEBUG ] Wrote data file consequences_all__plot_Consequences_all_.txt
[2026-06-05 03:16:41,049] multiqc.report [DEBUG ] Wrote data file sift_summary_plot.txt
[2026-06-05 03:16:41,049] multiqc.report [DEBUG ] Wrote data file polyphen_summary_plot.txt
[2026-06-05 03:16:41,049] multiqc.report [DEBUG ] Wrote data file variants_by_chromosome_plot.txt
[2026-06-05 03:16:41,049] multiqc.report [DEBUG ] Wrote data file position_in_protein_plot.txt
[2026-06-05 03:16:41,049] multiqc.core.write_results [DEBUG ] Moving data file from '/tmp/tmpugt_ms97/multiqc_data' to '/tmp/nxf.uMOsqH3Syc/multiqc_data'
[2026-06-05 03:16:41,154] multiqc.core.write_results [INFO ] Data : multiqc_data
[2026-06-05 03:16:41,164] multiqc.core.write_results [DEBUG ] Compressing plot data
[2026-06-05 03:16:41,292] multiqc.core.write_results [INFO ] Report : multiqc_report.html
[2026-06-05 03:16:41,292] multiqc.core.write_results [DEBUG ] Moving plots directory from '/tmp/tmpugt_ms97/multiqc_plots' to '/tmp/nxf.uMOsqH3Syc/multiqc_plots'
[2026-06-05 03:16:41,303] multiqc.core.write_results [INFO ] Plots : multiqc_plots