[2024-01-11 11:26:35,717] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-11 11:26:35,717] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-11 11:26:35,717] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-11 11:26:35,720] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-01-11 11:26:35,721] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2024-01-11 11:26:35,721] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-11 11:26:35,863] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-11 11:26:35,863] multiqc [INFO ] This is MultiQC v1.9 [2024-01-11 11:26:35,864] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-11 11:26:35,864] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/6d/0743710221fd2141252142b1c6f3d6/merged [2024-01-11 11:26:35,864] multiqc [INFO ] Template : default [2024-01-11 11:26:35,864] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-11 11:26:35,864] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/6d/0743710221fd2141252142b1c6f3d6/merged [2024-01-11 11:26:35,864] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean [2024-01-11 11:26:35,864] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-41739682/tmpti8s7pz6 [2024-01-11 11:26:36,004] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCYHDRX3_1_fastqc.html [2024-01-11 11:26:36,012] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCYHDRX3_1_fastqc.html [2024-01-11 11:26:36,099] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCYHDRX3_2_fastqc.html [2024-01-11 11:26:36,107] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCYHDRX3_2_fastqc.html [2024-01-11 11:26:36,177] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCYHDRX3_3_fastqc.html [2024-01-11 11:26:36,184] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCYHDRX3_3_fastqc.html [2024-01-11 11:26:36,258] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCYHDRX3_4_fastqc.html [2024-01-11 11:26:36,264] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCYHDRX3_4_fastqc.html [2024-01-11 11:26:36,923] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-11 11:26:36,926] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-11 11:26:36,931] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-11 11:26:36,938] multiqc [DEBUG ] No samples found: conpair [2024-01-11 11:26:36,944] multiqc [DEBUG ] No samples found: peddy [2024-01-11 11:26:36,951] multiqc [DEBUG ] No samples found: somalier [2024-01-11 11:26:36,958] multiqc [DEBUG ] No samples found: methylQA [2024-01-11 11:26:36,969] multiqc [DEBUG ] No samples found: mosdepth [2024-01-11 11:26:36,975] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-11 11:26:36,979] multiqc [DEBUG ] No samples found: qualimap [2024-01-11 11:26:36,986] multiqc [DEBUG ] No samples found: preseq [2024-01-11 11:26:36,992] multiqc [DEBUG ] No samples found: quast [2024-01-11 11:26:36,998] multiqc [DEBUG ] No samples found: qorts [2024-01-11 11:26:37,005] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-11 11:26:37,010] multiqc [DEBUG ] No samples found: rockhopper [2024-01-11 11:26:37,017] multiqc [DEBUG ] No samples found: rsem [2024-01-11 11:26:37,031] multiqc [DEBUG ] No samples found: rseqc [2024-01-11 11:26:37,037] multiqc [DEBUG ] No samples found: busco [2024-01-11 11:26:37,043] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-11 11:26:37,049] multiqc [DEBUG ] No samples found: disambiguate [2024-01-11 11:26:37,055] multiqc [DEBUG ] No samples found: supernova [2024-01-11 11:26:37,073] multiqc [DEBUG ] No samples found: deeptools [2024-01-11 11:26:37,079] multiqc [DEBUG ] No samples found: sargasso [2024-01-11 11:26:37,085] multiqc [DEBUG ] No samples found: verifybamid [2024-01-11 11:26:37,091] multiqc [DEBUG ] No samples found: mirtrace [2024-01-11 11:26:37,098] multiqc [DEBUG ] No samples found: happy [2024-01-11 11:26:37,104] multiqc [DEBUG ] No samples found: mirtop [2024-01-11 11:26:37,113] multiqc [DEBUG ] No samples found: homer [2024-01-11 11:26:37,119] multiqc [DEBUG ] No samples found: macs2 [2024-01-11 11:26:37,124] multiqc [DEBUG ] No samples found: theta2 [2024-01-11 11:26:37,131] multiqc [DEBUG ] No samples found: snpeff [2024-01-11 11:26:37,140] multiqc [DEBUG ] No samples found: gatk [2024-01-11 11:26:37,146] multiqc [DEBUG ] No samples found: htseq [2024-01-11 11:26:37,153] multiqc [DEBUG ] No samples found: bcftools [2024-01-11 11:26:37,160] multiqc [DEBUG ] No samples found: featureCounts [2024-01-11 11:26:37,168] multiqc [DEBUG ] No samples found: fgbio [2024-01-11 11:26:37,184] multiqc [DEBUG ] No samples found: dragen [2024-01-11 11:26:37,190] multiqc [DEBUG ] No samples found: dedup [2024-01-11 11:26:37,197] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-11 11:26:37,227] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-11 11:26:37,234] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-11 11:26:37,236] multiqc [DEBUG ] No samples found: picard [2024-01-11 11:26:37,242] multiqc [DEBUG ] No samples found: prokka [2024-01-11 11:26:37,248] multiqc [DEBUG ] No samples found: samblaster [2024-01-11 11:26:37,259] multiqc [DEBUG ] No samples found: samtools [2024-01-11 11:26:37,265] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-11 11:26:37,272] multiqc [DEBUG ] No samples found: bamtools [2024-01-11 11:26:37,279] multiqc [DEBUG ] No samples found: jellyfish [2024-01-11 11:26:37,289] multiqc [DEBUG ] No samples found: vcftools [2024-01-11 11:26:37,295] multiqc [DEBUG ] No samples found: longranger [2024-01-11 11:26:37,301] multiqc [DEBUG ] No samples found: stacks [2024-01-11 11:26:37,307] multiqc [DEBUG ] No samples found: varscan2 [2024-01-11 11:26:37,325] multiqc [DEBUG ] No samples found: bbmap [2024-01-11 11:26:37,332] multiqc [DEBUG ] No samples found: bismark [2024-01-11 11:26:37,339] multiqc [DEBUG ] No samples found: biscuit [2024-01-11 11:26:37,345] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-11 11:26:37,352] multiqc [DEBUG ] No samples found: hicup [2024-01-11 11:26:37,358] multiqc [DEBUG ] No samples found: hicpro [2024-01-11 11:26:37,363] multiqc [DEBUG ] No samples found: salmon [2024-01-11 11:26:37,369] multiqc [DEBUG ] No samples found: kallisto [2024-01-11 11:26:37,375] multiqc [DEBUG ] No samples found: slamdunk [2024-01-11 11:26:37,381] multiqc [DEBUG ] No samples found: star [2024-01-11 11:26:37,387] multiqc [DEBUG ] No samples found: hisat2 [2024-01-11 11:26:37,393] multiqc [DEBUG ] No samples found: tophat [2024-01-11 11:26:37,400] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-11 11:26:37,406] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-11 11:26:37,412] multiqc [DEBUG ] No samples found: snpsplit [2024-01-11 11:26:37,419] multiqc [DEBUG ] No samples found: kat [2024-01-11 11:26:37,424] multiqc [DEBUG ] No samples found: leehom [2024-01-11 11:26:37,431] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-11 11:26:37,437] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-11 11:26:37,445] multiqc [DEBUG ] No samples found: cutadapt [2024-01-11 11:26:37,452] multiqc [DEBUG ] No samples found: flexbar [2024-01-11 11:26:37,459] multiqc [DEBUG ] No samples found: kaiju [2024-01-11 11:26:37,465] multiqc [DEBUG ] No samples found: kraken [2024-01-11 11:26:37,476] multiqc [DEBUG ] No samples found: malt [2024-01-11 11:26:37,484] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-11 11:26:37,493] multiqc [DEBUG ] No samples found: sickle [2024-01-11 11:26:37,499] multiqc [DEBUG ] No samples found: skewer [2024-01-11 11:26:37,507] multiqc [DEBUG ] No samples found: sortmerna [2024-01-11 11:26:37,513] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-11 11:26:37,524] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-11 11:26:37,530] multiqc [DEBUG ] No samples found: afterqc [2024-01-11 11:26:37,540] multiqc [DEBUG ] No samples found: fastp [2024-01-11 11:26:37,665] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-01-11 11:26:37,724] multiqc [DEBUG ] No samples found: pycoqc [2024-01-11 11:26:37,729] multiqc [DEBUG ] No samples found: minionqc [2024-01-11 11:26:37,735] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-11 11:26:37,741] multiqc [DEBUG ] No samples found: clusterflow [2024-01-11 11:26:37,747] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-11 11:26:37,754] multiqc [DEBUG ] No samples found: interop [2024-01-11 11:26:37,760] multiqc [DEBUG ] No samples found: ivar [2024-01-11 11:26:37,766] multiqc [DEBUG ] No samples found: flash [2024-01-11 11:26:37,771] multiqc [DEBUG ] No samples found: seqyclean [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-11 11:26:37,771] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-11 11:26:37,772] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-11 11:26:37,772] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-11 11:26:37,777] multiqc [INFO ] Compressing plot data [2024-01-11 11:26:37,854] multiqc [INFO ] Report : multiqc_report.html [2024-01-11 11:26:37,854] multiqc [INFO ] Data : multiqc_data [2024-01-11 11:26:37,854] multiqc [DEBUG ] Moving data file from '/state/partition1/job-41739682/tmpti8s7pz6/multiqc_data' to '/vast/gencore/GENEFLOW/work/6d/0743710221fd2141252142b1c6f3d6/merged/multiqc_data' [2024-01-11 11:26:38,021] multiqc [INFO ] MultiQC complete