[2026-06-02 15:10:38,402] multiqc [DEBUG ] This is MultiQC v1.21
[2026-06-02 15:10:38,404] multiqc [DEBUG ] Loading config settings from: multiqc_config.yml
[2026-06-02 15:10:38,404] multiqc [DEBUG ] New config: {'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/rnafusion/releases/tag/3.0.2" target="_blank">nf-core/rnafusion</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnafusion/3.0.2/docs/output" target="_blank">documentation</a>.\n', 'report_section_order': {'nf-core-rnafusion-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-rnafusion-summary': {'order': -1002}}, 'export_plots': True, 'disable_version_detection': True, 'run_modules': ['custom_content', 'fastqc', 'fastp', 'star', 'samtools', 'picard', 'arriba', 'kallisto', 'rseqc', 'preseq'], 'module_order': ['fastp', {'fastqc': {'name': 'FastQC (raw)', 'info': 'This section of the report shows FastQC results before adapter trimming.', 'path_filters': ['*.zip']}}, {'fastqc': {'name': 'FastQC (trimmed)', 'info': 'This section of the report shows FastQC results after adapter trimming.', 'path_filters': ['*_trimmed*.zip']}}]}
[2026-06-02 15:10:38,405] multiqc [DEBUG ] Loading config settings from: multiqc_config.yml
[2026-06-02 15:10:38,405] multiqc [DEBUG ] New config: {'report_comment': 'This report has been generated by the <a href="https://github.com/nf-core/rnafusion/releases/tag/3.0.2" target="_blank">nf-core/rnafusion</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnafusion/3.0.2/docs/output" target="_blank">documentation</a>.\n', 'report_section_order': {'nf-core-rnafusion-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-rnafusion-summary': {'order': -1002}}, 'export_plots': True, 'disable_version_detection': True, 'run_modules': ['custom_content', 'fastqc', 'fastp', 'star', 'samtools', 'picard', 'arriba', 'kallisto', 'rseqc', 'preseq'], 'module_order': ['fastp', {'fastqc': {'name': 'FastQC (raw)', 'info': 'This section of the report shows FastQC results before adapter trimming.', 'path_filters': ['*.zip']}}, {'fastqc': {'name': 'FastQC (trimmed)', 'info': 'This section of the report shows FastQC results after adapter trimming.', 'path_filters': ['*_trimmed*.zip']}}]}
[2026-06-02 15:10:38,405] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc --force --config multiqc_config.yml .
[2026-06-02 15:10:38,852] multiqc [WARNING] MultiQC Version v1.35 now available!
[2026-06-02 15:10:38,852] multiqc [DEBUG ] Latest MultiQC version is v1.35, released 2026-05-13
[2026-06-02 15:10:38,852] multiqc [DEBUG ] Working dir : /tmp/nxf.zmjcXr5f3s
[2026-06-02 15:10:38,852] multiqc [DEBUG ] Template : default
[2026-06-02 15:10:38,852] multiqc [DEBUG ] Running Python 3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:53:32) [GCC 12.3.0]
[2026-06-02 15:10:38,852] multiqc [ERROR ] Module(s) in config.run_modules are unknown: arriba
[2026-06-02 15:10:38,852] multiqc [INFO ] Only using modules: custom_content, fastqc, fastp, star, samtools, picard, kallisto, rseqc, preseq
[2026-06-02 15:10:38,852] multiqc [DEBUG ] Analysing modules: custom_content, kallisto, picard, preseq, rseqc, samtools, star, fastp, fastqc, fastqc
[2026-06-02 15:10:38,852] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp2qc50he1
[2026-06-02 15:10:38,852] multiqc [INFO ] Search path : /tmp/nxf.zmjcXr5f3s
[2026-06-02 15:10:38,853] multiqc [DEBUG ] Ignored 284 search patterns as didn't match running modules.
[2026-06-02 15:10:38,914] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_no_match: 43] // [skipped_ignore_pattern: 2]
[2026-06-02 15:10:38,947] multiqc.modules.custom_content.custom_content [INFO ] rna_contamination: Found 2 General Statistics columns
[2026-06-02 15:10:38,947] multiqc.modules.custom_content.custom_content [INFO ] rseqc_extra_metrics: Found 2 General Statistics columns
[2026-06-02 15:10:38,947] multiqc.modules.custom_content.custom_content [INFO ] seqtools_metrics: Found 2 General Statistics columns
[2026-06-02 15:10:38,948] multiqc.modules.custom_content.custom_content [INFO ] nf-core-rnafusion-summary: Found 1 sample (html)
[2026-06-02 15:10:38,948] multiqc.modules.custom_content.custom_content [INFO ] kallisto_qc_metrics: Found 2 General Statistics columns
[2026-06-02 15:10:38,948] multiqc.modules.custom_content.custom_content [INFO ] nf-core-rnafusion-methods-description: Found 1 sample (html)
[2026-06-02 15:10:38,948] multiqc.modules.custom_content.custom_content [INFO ] preseq_metrics: Found 2 General Statistics columns
[2026-06-02 15:10:38,948] multiqc.modules.kallisto.kallisto [INFO ] Found 2 reports
[2026-06-02 15:10:38,949] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_kallisto.txt
[2026-06-02 15:10:38,980] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_picard_insertSize.txt
[2026-06-02 15:10:39,011] multiqc.modules.picard.picard [INFO ] Found 2 InsertSizeMetrics reports
[2026-06-02 15:10:39,011] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_picard_dups.txt
[2026-06-02 15:10:39,015] multiqc.modules.picard.picard [INFO ] Found 2 MarkDuplicates reports
[2026-06-02 15:10:39,016] multiqc.utils.util_functions [DEBUG ] Wrote data file picard_histogram.txt
[2026-06-02 15:10:39,016] multiqc.utils.util_functions [DEBUG ] Wrote data file picard_histogram_1.txt
[2026-06-02 15:10:39,016] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_picard_RnaSeqMetrics.txt
[2026-06-02 15:10:39,021] multiqc.modules.picard.picard [INFO ] Found 2 RnaSeqMetrics reports
[2026-06-02 15:10:39,021] multiqc.utils.util_functions [DEBUG ] Wrote data file picard_histogram_2.txt
[2026-06-02 15:10:39,030] multiqc.modules.preseq.preseq [INFO ] Found 2 reports
[2026-06-02 15:10:39,400] multiqc.utils.util_functions [DEBUG ] Wrote data file preseq.txt
[2026-06-02 15:10:39,411] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_rseqc_read_distribution.txt
[2026-06-02 15:10:39,415] multiqc.modules.rseqc.rseqc [INFO ] Found 2 read_distribution reports
[2026-06-02 15:10:39,415] multiqc.utils.util_functions [DEBUG ] Wrote data file rseqc_inner_distance.txt
[2026-06-02 15:10:39,417] multiqc.modules.rseqc.rseqc [INFO ] Found 2 inner_distance reports
[2026-06-02 15:10:39,419] multiqc.utils.util_functions [DEBUG ] Wrote data file rseqc_read_dups.txt
[2026-06-02 15:10:39,421] multiqc.modules.rseqc.rseqc [INFO ] Found 2 read_duplication reports
[2026-06-02 15:10:39,422] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_rseqc_junction_annotation.txt
[2026-06-02 15:10:39,425] multiqc.modules.rseqc.rseqc [INFO ] Found 2 junction_annotation reports
[2026-06-02 15:10:39,426] multiqc.utils.util_functions [DEBUG ] Wrote data file rseqc_junction_saturation_all.txt
[2026-06-02 15:10:39,426] multiqc.utils.util_functions [DEBUG ] Wrote data file junction_saturation_known.txt
[2026-06-02 15:10:39,426] multiqc.utils.util_functions [DEBUG ] Wrote data file junction_saturation_novel.txt
[2026-06-02 15:10:39,428] multiqc.modules.rseqc.rseqc [INFO ] Found 2 junction_saturation reports
[2026-06-02 15:10:39,429] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_rseqc_infer_experiment.txt
[2026-06-02 15:10:39,432] multiqc.modules.rseqc.rseqc [INFO ] Found 2 infer_experiment reports
[2026-06-02 15:10:39,433] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_rseqc_bam_stat.txt
[2026-06-02 15:10:39,440] multiqc.modules.rseqc.rseqc [INFO ] Found 2 bam_stat reports
[2026-06-02 15:10:39,466] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: rna_s1200_S21
[2026-06-02 15:10:39,489] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: rna_s1221_S42
[2026-06-02 15:10:39,489] multiqc.modules.star.star [INFO ] Found 2 reports and 2 gene count files
[2026-06-02 15:10:39,489] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_star.txt
[2026-06-02 15:10:39,498] multiqc.modules.fastp.fastp [INFO ] Found 2 reports
[2026-06-02 15:10:39,498] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: rna_s1200_S21
[2026-06-02 15:10:39,499] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: rna_s1221_S42
[2026-06-02 15:10:39,501] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_fastp.txt
[2026-06-02 15:10:39,513] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '12/rna_s1221_S42_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,514] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '4/rna_s1221_S42_2_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,515] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '5/rna_s1200_S21_1_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,516] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '13/rna_s1200_S21_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,517] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '3/rna_s1221_S42_1_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,518] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '11/rna_s1221_S42_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,519] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '6/rna_s1200_S21_2_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,519] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '14/rna_s1200_S21_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC (raw)'
[2026-06-02 15:10:39,520] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports
[2026-06-02 15:10:39,521] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_fastqc.txt
[2026-06-02 15:10:39,552] multiqc.plots.plotly.heatmap [DEBUG ] Heatmap size: 495x480, px per element: 45.00x60.00
[2026-06-02 15:10:39,556] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '12/rna_s1221_S42_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,557] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping '4/rna_s1221_S42_2_fastqc.zip' as it didn't match the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,557] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping '5/rna_s1200_S21_1_fastqc.zip' as it didn't match the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,557] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '13/rna_s1200_S21_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,558] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping '3/rna_s1221_S42_1_fastqc.zip' as it didn't match the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,558] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '11/rna_s1221_S42_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,559] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping '6/rna_s1200_S21_2_fastqc.zip' as it didn't match the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,559] multiqc.modules.base_module [DEBUG ] fastqc/zip - Selecting '14/rna_s1200_S21_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC (trimmed)'
[2026-06-02 15:10:39,560] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports
[2026-06-02 15:10:39,560] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_fastqc_1.txt
[2026-06-02 15:10:39,586] multiqc.plots.plotly.heatmap [DEBUG ] Heatmap size: 495x320, px per element: 45.00x80.00
[2026-06-02 15:10:39,588] multiqc.utils.software_versions [DEBUG ] Reading software versions from config.software_versions
[2026-06-02 15:10:39,588] multiqc.utils.software_versions [DEBUG ] Reading software versions settings from: 57/nf_core_pipeline_software_mqc_versions.yml
[2026-06-02 15:10:39,592] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_software_versions.txt
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'Kallisto'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Kallisto'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'Kallisto'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'Picard'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Picard'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'Picard'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'Preseq'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Preseq'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'Preseq'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'RSeQC'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'RSeQC'.
[2026-06-02 15:10:39,592] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'RSeQC'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'STAR'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'STAR'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'STAR'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'fastp'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'fastp'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'fastp'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'FastQC (raw)'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'FastQC (raw)'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'FastQC (raw)'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'FastQC (trimmed)'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'FastQC (trimmed)'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'FastQC (trimmed)'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'Software Versions'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Software Versions'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'Software Versions'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'nf-core/rnafusion Methods Description'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'nf-core/rnafusion Methods Description'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'nf-core/rnafusion Methods Description'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-methods-description' not found for module 'nf-core/rnafusion Workflow Summary'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'nf-core/rnafusion Workflow Summary'.
[2026-06-02 15:10:39,593] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnafusion-summary' not found for module 'nf-core/rnafusion Workflow Summary'.
[2026-06-02 15:10:39,611] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_general_stats.txt
[2026-06-02 15:10:39,612] multiqc [DEBUG ] Compressing plot data
[2026-06-02 15:10:39,925] multiqc.utils.util_functions [DEBUG ] Wrote data file multiqc_data.json
[2026-06-02 15:10:39,926] multiqc [INFO ] Report : multiqc_report.html
[2026-06-02 15:10:39,926] multiqc [INFO ] Data : multiqc_data
[2026-06-02 15:10:39,926] multiqc [DEBUG ] Moving data file from '/tmp/tmp2qc50he1/multiqc_data' to '/tmp/nxf.zmjcXr5f3s/multiqc_data'
[2026-06-02 15:10:39,928] multiqc [DEBUG ] Full report path: /tmp/nxf.zmjcXr5f3s/multiqc_report.html
[2026-06-02 15:10:39,928] multiqc [INFO ] Plots : multiqc_plots
[2026-06-02 15:10:39,928] multiqc [DEBUG ] Moving plots directory from '/tmp/tmp2qc50he1/multiqc_plots' to '/tmp/nxf.zmjcXr5f3s/multiqc_plots'
[2026-06-02 15:10:39,985] multiqc [INFO ] MultiQC complete