[2023-12-12 13:45:06,163] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-12 13:45:06,163] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-12 13:45:06,164] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-12 13:45:06,167] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-12-12 13:45:06,167] 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}} [2023-12-12 13:45:06,167] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-12 13:45:06,373] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-12 13:45:06,373] multiqc [INFO ] This is MultiQC v1.9 [2023-12-12 13:45:06,373] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-12 13:45:06,373] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/66/1f7eb20f8a8277da63c675030911f8/merged [2023-12-12 13:45:06,373] multiqc [INFO ] Template : default [2023-12-12 13:45:06,373] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-12 13:45:06,374] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/66/1f7eb20f8a8277da63c675030911f8/merged [2023-12-12 13:45:06,374] 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 [2023-12-12 13:45:06,374] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40796073/tmp0oa3pc04 [2023-12-12 13:45:06,534] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3NDRX3_1_fastqc.html [2023-12-12 13:45:06,542] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3NDRX3_1_fastqc.html [2023-12-12 13:45:06,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3NDRX3_2_fastqc.html [2023-12-12 13:45:06,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3NDRX3_2_fastqc.html [2023-12-12 13:45:06,683] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3NDRX3_3_fastqc.html [2023-12-12 13:45:06,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3NDRX3_3_fastqc.html [2023-12-12 13:45:06,758] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3NDRX3_4_fastqc.html [2023-12-12 13:45:06,765] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3NDRX3_4_fastqc.html [2023-12-12 13:45:07,741] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-12 13:45:07,744] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-12 13:45:07,758] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-12 13:45:07,789] multiqc [DEBUG ] No samples found: conpair [2023-12-12 13:45:07,806] multiqc [DEBUG ] No samples found: peddy [2023-12-12 13:45:07,824] multiqc [DEBUG ] No samples found: somalier [2023-12-12 13:45:07,845] multiqc [DEBUG ] No samples found: methylQA [2023-12-12 13:45:07,876] multiqc [DEBUG ] No samples found: mosdepth [2023-12-12 13:45:07,896] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-12 13:45:07,900] multiqc [DEBUG ] No samples found: qualimap [2023-12-12 13:45:07,926] multiqc [DEBUG ] No samples found: preseq [2023-12-12 13:45:07,953] multiqc [DEBUG ] No samples found: quast [2023-12-12 13:45:07,969] multiqc [DEBUG ] No samples found: qorts [2023-12-12 13:45:07,990] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-12 13:45:07,996] multiqc [DEBUG ] No samples found: rockhopper [2023-12-12 13:45:08,031] multiqc [DEBUG ] No samples found: rsem [2023-12-12 13:45:08,076] multiqc [DEBUG ] No samples found: rseqc [2023-12-12 13:45:08,107] multiqc [DEBUG ] No samples found: busco [2023-12-12 13:45:08,130] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-12 13:45:08,146] multiqc [DEBUG ] No samples found: disambiguate [2023-12-12 13:45:08,170] multiqc [DEBUG ] No samples found: supernova [2023-12-12 13:45:08,228] multiqc [DEBUG ] No samples found: deeptools [2023-12-12 13:45:08,253] multiqc [DEBUG ] No samples found: sargasso [2023-12-12 13:45:08,270] multiqc [DEBUG ] No samples found: verifybamid [2023-12-12 13:45:08,297] multiqc [DEBUG ] No samples found: mirtrace [2023-12-12 13:45:08,312] multiqc [DEBUG ] No samples found: happy [2023-12-12 13:45:08,346] multiqc [DEBUG ] No samples found: mirtop [2023-12-12 13:45:08,374] multiqc [DEBUG ] No samples found: homer [2023-12-12 13:45:08,397] multiqc [DEBUG ] No samples found: macs2 [2023-12-12 13:45:08,432] multiqc [DEBUG ] No samples found: theta2 [2023-12-12 13:45:08,452] multiqc [DEBUG ] No samples found: snpeff [2023-12-12 13:45:08,480] multiqc [DEBUG ] No samples found: gatk [2023-12-12 13:45:08,491] multiqc [DEBUG ] No samples found: htseq [2023-12-12 13:45:08,515] multiqc [DEBUG ] No samples found: bcftools [2023-12-12 13:45:08,532] multiqc [DEBUG ] No samples found: featureCounts [2023-12-12 13:45:08,551] multiqc [DEBUG ] No samples found: fgbio [2023-12-12 13:45:08,584] multiqc [DEBUG ] No samples found: dragen [2023-12-12 13:45:08,608] multiqc [DEBUG ] No samples found: dedup [2023-12-12 13:45:08,630] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-12 13:45:08,701] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-12 13:45:08,728] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-12 13:45:08,731] multiqc [DEBUG ] No samples found: picard [2023-12-12 13:45:08,745] multiqc [DEBUG ] No samples found: prokka [2023-12-12 13:45:08,766] multiqc [DEBUG ] No samples found: samblaster [2023-12-12 13:45:08,817] multiqc [DEBUG ] No samples found: samtools [2023-12-12 13:45:08,839] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-12 13:45:08,869] multiqc [DEBUG ] No samples found: bamtools [2023-12-12 13:45:08,887] multiqc [DEBUG ] No samples found: jellyfish [2023-12-12 13:45:08,931] multiqc [DEBUG ] No samples found: vcftools [2023-12-12 13:45:08,960] multiqc [DEBUG ] No samples found: longranger [2023-12-12 13:45:08,981] multiqc [DEBUG ] No samples found: stacks [2023-12-12 13:45:09,015] multiqc [DEBUG ] No samples found: varscan2 [2023-12-12 13:45:09,091] multiqc [DEBUG ] No samples found: bbmap [2023-12-12 13:45:09,131] multiqc [DEBUG ] No samples found: bismark [2023-12-12 13:45:09,163] multiqc [DEBUG ] No samples found: biscuit [2023-12-12 13:45:09,181] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-12 13:45:09,203] multiqc [DEBUG ] No samples found: hicup [2023-12-12 13:45:09,225] multiqc [DEBUG ] No samples found: hicpro [2023-12-12 13:45:09,247] multiqc [DEBUG ] No samples found: salmon [2023-12-12 13:45:09,258] multiqc [DEBUG ] No samples found: kallisto [2023-12-12 13:45:09,292] multiqc [DEBUG ] No samples found: slamdunk [2023-12-12 13:45:09,311] multiqc [DEBUG ] No samples found: star [2023-12-12 13:45:09,321] multiqc [DEBUG ] No samples found: hisat2 [2023-12-12 13:45:09,328] multiqc [DEBUG ] No samples found: tophat [2023-12-12 13:45:09,351] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-12 13:45:09,375] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-12 13:45:09,396] multiqc [DEBUG ] No samples found: snpsplit [2023-12-12 13:45:09,418] multiqc [DEBUG ] No samples found: kat [2023-12-12 13:45:09,442] multiqc [DEBUG ] No samples found: leehom [2023-12-12 13:45:09,474] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-12 13:45:09,504] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-12 13:45:09,521] multiqc [DEBUG ] No samples found: cutadapt [2023-12-12 13:45:09,542] multiqc [DEBUG ] No samples found: flexbar [2023-12-12 13:45:09,548] multiqc [DEBUG ] No samples found: kaiju [2023-12-12 13:45:09,574] multiqc [DEBUG ] No samples found: kraken [2023-12-12 13:45:09,597] multiqc [DEBUG ] No samples found: malt [2023-12-12 13:45:09,620] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-12 13:45:09,654] multiqc [DEBUG ] No samples found: sickle [2023-12-12 13:45:09,679] multiqc [DEBUG ] No samples found: skewer [2023-12-12 13:45:09,694] multiqc [DEBUG ] No samples found: sortmerna [2023-12-12 13:45:09,700] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-12 13:45:09,725] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-12 13:45:09,742] multiqc [DEBUG ] No samples found: afterqc [2023-12-12 13:45:09,749] multiqc [DEBUG ] No samples found: fastp [2023-12-12 13:45:09,846] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-12-12 13:45:09,908] multiqc [DEBUG ] No samples found: pycoqc [2023-12-12 13:45:09,925] multiqc [DEBUG ] No samples found: minionqc [2023-12-12 13:45:09,931] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-12 13:45:09,942] multiqc [DEBUG ] No samples found: clusterflow [2023-12-12 13:45:09,954] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-12 13:45:09,971] multiqc [DEBUG ] No samples found: interop [2023-12-12 13:45:09,977] multiqc [DEBUG ] No samples found: ivar [2023-12-12 13:45:09,990] multiqc [DEBUG ] No samples found: flash [2023-12-12 13:45:10,011] multiqc [DEBUG ] No samples found: seqyclean [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-12 13:45:10,012] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-12 13:45:10,018] multiqc [INFO ] Compressing plot data [2023-12-12 13:45:10,087] multiqc [INFO ] Report : multiqc_report.html [2023-12-12 13:45:10,087] multiqc [INFO ] Data : multiqc_data [2023-12-12 13:45:10,087] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40796073/tmp0oa3pc04/multiqc_data' to '/vast/gencore/GENEFLOW/work/66/1f7eb20f8a8277da63c675030911f8/merged/multiqc_data' [2023-12-12 13:45:10,279] multiqc [INFO ] MultiQC complete