[2025-12-11 09:27:32,948] multiqc [DEBUG ] This is MultiQC v1.18 [2025-12-11 09:27:32,978] multiqc [DEBUG ] Loading config settings from: multiqc_config.yml [2025-12-11 09:27:32,978] multiqc [DEBUG ] New config: {'report_comment': 'This report has been generated by the nf-core/rnasplice analysis pipeline. For information about how to interpret these results, please see the documentation.\n', 'report_section_order': {'nf-core-rnasplice-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-rnasplice-summary': {'order': -1002}}, 'export_plots': True, 'top_modules': ['fail_trimmed_samples'], 'custom_data': {'fail_trimmed_samples': {'section_name': 'WARNING: Fail Trimming Check', 'description': "List of samples that failed the minimum trimmed reads threshold specified via the '--min_trimmed_reads' parameter. These samples have still be used downstream but should be examined further.", 'plot_type': 'table', 'pconfig': {'id': 'fail_trimmed_samples_table', 'table_title': 'Samples failed trimming threshold', 'namespace': 'Samples failed trimming threshold', 'format': '{:.0f}'}}}} [2025-12-11 09:27:32,980] multiqc [DEBUG ] Loading config settings from: multiqc_config.yml [2025-12-11 09:27:32,980] multiqc [DEBUG ] New config: {'report_comment': 'This report has been generated by the nf-core/rnasplice analysis pipeline. For information about how to interpret these results, please see the documentation.\n', 'report_section_order': {'nf-core-rnasplice-methods-description': {'order': -1000}, 'software_versions': {'order': -1001}, 'nf-core-rnasplice-summary': {'order': -1002}}, 'export_plots': True, 'top_modules': ['fail_trimmed_samples'], 'custom_data': {'fail_trimmed_samples': {'section_name': 'WARNING: Fail Trimming Check', 'description': "List of samples that failed the minimum trimmed reads threshold specified via the '--min_trimmed_reads' parameter. These samples have still be used downstream but should be examined further.", 'plot_type': 'table', 'pconfig': {'id': 'fail_trimmed_samples_table', 'table_title': 'Samples failed trimming threshold', 'namespace': 'Samples failed trimming threshold', 'format': '{:.0f}'}}}} [2025-12-11 09:27:32,980] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc --force --config multiqc_config.yml . [2025-12-11 09:27:34,011] multiqc [WARNING] MultiQC Version v1.33 now available! [2025-12-11 09:27:34,011] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/srlab/nxf.xxRlPtQ3Zq [2025-12-11 09:27:34,011] multiqc [DEBUG ] Template : default [2025-12-11 09:27:34,011] multiqc [DEBUG ] Running Python 3.11.6 | packaged by conda-forge | (main, Oct 3 2023, 10:40:35) [GCC 12.3.0] [2025-12-11 09:27:34,012] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, sambamba, 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, qc3C, nanostat, samblaster, samtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umitools, truvari, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, cellranger, snpsplit, odgi, pangolin, nextclade, freyja, humid, kat, leehom, librarian, adapterRemoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, bracken, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, xenome, xengsort [2025-12-11 09:27:34,016] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpvrngr329 [2025-12-11 09:27:34,017] multiqc [INFO ] Search path : /gscratch/scrubbed/srlab/nxf.xxRlPtQ3Zq [2025-12-11 09:27:36,582] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_module_specific_max_filesize: 275] // [skipped_no_match: 4] [2025-12-11 09:27:37,393] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.8.1 [2025-12-11 09:27:37,395] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.8.1 [2025-12-11 09:27:37,460] multiqc.modules.custom_content.custom_content [INFO ] nf-core-rnasplice-methods-description: Found 1 sample (html) [2025-12-11 09:27:37,460] multiqc.modules.custom_content.custom_content [INFO ] nf-core-rnasplice-summary: Found 1 sample (html) [2025-12-11 09:27:37,460] multiqc.modules.custom_content.custom_content [INFO ] software_versions: Found 1 sample (html) [2025-12-11 09:27:37,467] multiqc.modules.featureCounts.feature_counts [INFO ] Found 39 reports [2025-12-11 09:27:41,087] multiqc.modules.samtools.samtools [INFO ] Found 39 stats reports [2025-12-11 09:27:41,097] multiqc.modules.samtools.samtools [INFO ] Found 39 flagstat reports [2025-12-11 09:27:46,426] multiqc.modules.samtools.samtools [INFO ] Found 39 idxstats reports [2025-12-11 09:27:46,426] multiqc.utils.software_versions [DEBUG ] Reading software versions from config.software_versions [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-methods-description' not found for module 'featureCounts'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'featureCounts'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-summary' not found for module 'featureCounts'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-methods-description' not found for module 'Samtools'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Samtools'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-summary' not found for module 'Samtools'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-methods-description' not found for module 'Software Versions'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'Software Versions'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-summary' not found for module 'Software Versions'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-methods-description' not found for module 'nf-core/rnasplice Methods Description'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'nf-core/rnasplice Methods Description'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-summary' not found for module 'nf-core/rnasplice Methods Description'. [2025-12-11 09:27:46,427] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-methods-description' not found for module 'nf-core/rnasplice Software Versions'. [2025-12-11 09:27:46,428] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'nf-core/rnasplice Software Versions'. [2025-12-11 09:27:46,428] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-summary' not found for module 'nf-core/rnasplice Software Versions'. [2025-12-11 09:27:46,428] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-methods-description' not found for module 'nf-core/rnasplice Workflow Summary'. [2025-12-11 09:27:46,428] multiqc [DEBUG ] Reordering sections: anchor 'software_versions' not found for module 'nf-core/rnasplice Workflow Summary'. [2025-12-11 09:27:46,428] multiqc [DEBUG ] Reordering sections: anchor 'nf-core-rnasplice-summary' not found for module 'nf-core/rnasplice Workflow Summary'. [2025-12-11 09:27:46,460] multiqc [DEBUG ] Compressing plot data [2025-12-11 09:27:46,572] multiqc [INFO ] Report : multiqc_report.html [2025-12-11 09:27:46,572] multiqc [INFO ] Data : multiqc_data [2025-12-11 09:27:46,572] multiqc [DEBUG ] Moving data file from '/tmp/tmpvrngr329/multiqc_data' to '/gscratch/scrubbed/srlab/nxf.xxRlPtQ3Zq/multiqc_data' [2025-12-11 09:27:46,582] multiqc [DEBUG ] Full report path: /gscratch/scrubbed/srlab/nxf.xxRlPtQ3Zq/multiqc_report.html [2025-12-11 09:27:46,582] multiqc [INFO ] Plots : multiqc_plots [2025-12-11 09:27:46,582] multiqc [DEBUG ] Moving plots directory from '/tmp/tmpvrngr329/multiqc_plots' to '/gscratch/scrubbed/srlab/nxf.xxRlPtQ3Zq/multiqc_plots' [2025-12-11 09:27:46,660] multiqc [INFO ] MultiQC complete