[2023-12-15 17:11:00,021] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-15 17:11:00,021] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-15 17:11:00,022] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-15 17:11:00,024] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-12-15 17:11:00,024] 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}} [2023-12-15 17:11:00,024] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKVTJDRX3/merged [2023-12-15 17:11:00,204] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-15 17:11:00,205] multiqc [INFO ] This is MultiQC v1.9 [2023-12-15 17:11:00,205] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKVTJDRX3/merged [2023-12-15 17:11:00,205] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKVTJDRX3/merged [2023-12-15 17:11:00,205] multiqc [INFO ] Template : default [2023-12-15 17:11:00,205] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-15 17:11:00,205] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKVTJDRX3/merged [2023-12-15 17:11:00,205] 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 [2023-12-15 17:11:00,205] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40856920/tmp4lvh85ld [2023-12-15 17:11:00,322] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKVTJDRX3_2_fastqc.html [2023-12-15 17:11:00,324] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKVTJDRX3_2_fastqc.html [2023-12-15 17:11:00,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKVTJDRX3_1_fastqc.html [2023-12-15 17:11:00,373] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKVTJDRX3_1_fastqc.html [2023-12-15 17:11:00,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKVTJDRX3_3_fastqc.html [2023-12-15 17:11:00,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKVTJDRX3_3_fastqc.html [2023-12-15 17:11:00,957] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-15 17:11:00,958] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-15 17:11:00,963] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-12-15 17:11:00,964] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-15 17:11:00,973] multiqc [DEBUG ] No samples found: conpair [2023-12-15 17:11:00,978] multiqc [DEBUG ] No samples found: peddy [2023-12-15 17:11:00,983] multiqc [DEBUG ] No samples found: somalier [2023-12-15 17:11:00,987] multiqc [DEBUG ] No samples found: methylQA [2023-12-15 17:11:00,995] multiqc [DEBUG ] No samples found: mosdepth [2023-12-15 17:11:01,000] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-15 17:11:01,003] multiqc [DEBUG ] No samples found: qualimap [2023-12-15 17:11:01,007] multiqc [DEBUG ] No samples found: preseq [2023-12-15 17:11:01,012] multiqc [DEBUG ] No samples found: quast [2023-12-15 17:11:01,016] multiqc [DEBUG ] No samples found: qorts [2023-12-15 17:11:01,021] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-15 17:11:01,025] multiqc [DEBUG ] No samples found: rockhopper [2023-12-15 17:11:01,029] multiqc [DEBUG ] No samples found: rsem [2023-12-15 17:11:01,038] multiqc [DEBUG ] No samples found: rseqc [2023-12-15 17:11:01,042] multiqc [DEBUG ] No samples found: busco [2023-12-15 17:11:01,046] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-15 17:11:01,050] multiqc [DEBUG ] No samples found: disambiguate [2023-12-15 17:11:01,055] multiqc [DEBUG ] No samples found: supernova [2023-12-15 17:11:01,066] multiqc [DEBUG ] No samples found: deeptools [2023-12-15 17:11:01,070] multiqc [DEBUG ] No samples found: sargasso [2023-12-15 17:11:01,074] multiqc [DEBUG ] No samples found: verifybamid [2023-12-15 17:11:01,078] multiqc [DEBUG ] No samples found: mirtrace [2023-12-15 17:11:01,083] multiqc [DEBUG ] No samples found: happy [2023-12-15 17:11:01,087] multiqc [DEBUG ] No samples found: mirtop [2023-12-15 17:11:01,092] multiqc [DEBUG ] No samples found: homer [2023-12-15 17:11:01,096] multiqc [DEBUG ] No samples found: macs2 [2023-12-15 17:11:01,100] multiqc [DEBUG ] No samples found: theta2 [2023-12-15 17:11:01,104] multiqc [DEBUG ] No samples found: snpeff [2023-12-15 17:11:01,110] multiqc [DEBUG ] No samples found: gatk [2023-12-15 17:11:01,114] multiqc [DEBUG ] No samples found: htseq [2023-12-15 17:11:01,119] multiqc [DEBUG ] No samples found: bcftools [2023-12-15 17:11:01,123] multiqc [DEBUG ] No samples found: featureCounts [2023-12-15 17:11:01,128] multiqc [DEBUG ] No samples found: fgbio [2023-12-15 17:11:01,139] multiqc [DEBUG ] No samples found: dragen [2023-12-15 17:11:01,143] multiqc [DEBUG ] No samples found: dedup [2023-12-15 17:11:01,148] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-15 17:11:01,172] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-15 17:11:01,177] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-15 17:11:01,180] multiqc [DEBUG ] No samples found: picard [2023-12-15 17:11:01,184] multiqc [DEBUG ] No samples found: prokka [2023-12-15 17:11:01,188] multiqc [DEBUG ] No samples found: samblaster [2023-12-15 17:11:01,196] multiqc [DEBUG ] No samples found: samtools [2023-12-15 17:11:01,200] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-15 17:11:01,205] multiqc [DEBUG ] No samples found: bamtools [2023-12-15 17:11:01,209] multiqc [DEBUG ] No samples found: jellyfish [2023-12-15 17:11:01,216] multiqc [DEBUG ] No samples found: vcftools [2023-12-15 17:11:01,220] multiqc [DEBUG ] No samples found: longranger [2023-12-15 17:11:01,224] multiqc [DEBUG ] No samples found: stacks [2023-12-15 17:11:01,229] multiqc [DEBUG ] No samples found: varscan2 [2023-12-15 17:11:01,240] multiqc [DEBUG ] No samples found: bbmap [2023-12-15 17:11:01,244] multiqc [DEBUG ] No samples found: bismark [2023-12-15 17:11:01,249] multiqc [DEBUG ] No samples found: biscuit [2023-12-15 17:11:01,253] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-15 17:11:01,260] multiqc [DEBUG ] No samples found: hicup [2023-12-15 17:11:01,265] multiqc [DEBUG ] No samples found: hicpro [2023-12-15 17:11:01,269] multiqc [DEBUG ] No samples found: salmon [2023-12-15 17:11:01,273] multiqc [DEBUG ] No samples found: kallisto [2023-12-15 17:11:01,278] multiqc [DEBUG ] No samples found: slamdunk [2023-12-15 17:11:01,282] multiqc [DEBUG ] No samples found: star [2023-12-15 17:11:01,287] multiqc [DEBUG ] No samples found: hisat2 [2023-12-15 17:11:01,291] multiqc [DEBUG ] No samples found: tophat [2023-12-15 17:11:01,296] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-15 17:11:01,300] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-15 17:11:01,304] multiqc [DEBUG ] No samples found: snpsplit [2023-12-15 17:11:01,308] multiqc [DEBUG ] No samples found: kat [2023-12-15 17:11:01,312] multiqc [DEBUG ] No samples found: leehom [2023-12-15 17:11:01,316] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-15 17:11:01,320] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-15 17:11:01,324] multiqc [DEBUG ] No samples found: cutadapt [2023-12-15 17:11:01,328] multiqc [DEBUG ] No samples found: flexbar [2023-12-15 17:11:01,332] multiqc [DEBUG ] No samples found: kaiju [2023-12-15 17:11:01,336] multiqc [DEBUG ] No samples found: kraken [2023-12-15 17:11:01,340] multiqc [DEBUG ] No samples found: malt [2023-12-15 17:11:01,345] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-15 17:11:01,349] multiqc [DEBUG ] No samples found: sickle [2023-12-15 17:11:01,353] multiqc [DEBUG ] No samples found: skewer [2023-12-15 17:11:01,357] multiqc [DEBUG ] No samples found: sortmerna [2023-12-15 17:11:01,361] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-15 17:11:01,366] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-15 17:11:01,370] multiqc [DEBUG ] No samples found: afterqc [2023-12-15 17:11:01,374] multiqc [DEBUG ] No samples found: fastp [2023-12-15 17:11:01,434] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2023-12-15 17:11:01,488] multiqc [DEBUG ] No samples found: pycoqc [2023-12-15 17:11:01,492] multiqc [DEBUG ] No samples found: minionqc [2023-12-15 17:11:01,496] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-15 17:11:01,500] multiqc [DEBUG ] No samples found: clusterflow [2023-12-15 17:11:01,504] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-15 17:11:01,508] multiqc [DEBUG ] No samples found: interop [2023-12-15 17:11:01,513] multiqc [DEBUG ] No samples found: ivar [2023-12-15 17:11:01,517] multiqc [DEBUG ] No samples found: flash [2023-12-15 17:11:01,521] multiqc [DEBUG ] No samples found: seqyclean [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-15 17:11:01,521] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-15 17:11:01,526] multiqc [INFO ] Compressing plot data [2023-12-15 17:11:01,586] multiqc [INFO ] Report : multiqc_report.html [2023-12-15 17:11:01,586] multiqc [INFO ] Data : multiqc_data [2023-12-15 17:11:01,586] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40856920/tmp4lvh85ld/multiqc_data' to '/scratch/gencore/logs/html/HKVTJDRX3/merged/multiqc_data' [2023-12-15 17:11:01,706] multiqc [INFO ] MultiQC complete