[2022-03-16 01:10:57,759] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-16 01:10:57,759] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-16 01:10:57,759] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-16 01:10:57,760] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-16 01:10:57,760] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-16 01:10:57,760] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJMLNAFX3/merged [2022-03-16 01:10:58,408] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-16 01:10:58,408] multiqc [INFO ] This is MultiQC v1.9 [2022-03-16 01:10:58,408] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJMLNAFX3/merged [2022-03-16 01:10:58,408] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJMLNAFX3/merged [2022-03-16 01:10:58,408] multiqc [INFO ] Template : default [2022-03-16 01:10:58,408] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-16 01:10:58,408] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJMLNAFX3/merged [2022-03-16 01:10:58,408] 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 [2022-03-16 01:10:58,409] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16073289/tmpe8ir2lro [2022-03-16 01:10:58,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMLNAFX3_n01_10xPDFgs_rep2_fastqc.html [2022-03-16 01:10:58,535] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMLNAFX3_n01_10xPDFgs_rep2_fastqc.html [2022-03-16 01:10:58,575] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMLNAFX3_n02_undetermined_fastqc.html [2022-03-16 01:10:58,577] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMLNAFX3_n02_undetermined_fastqc.html [2022-03-16 01:10:58,597] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMLNAFX3_n02_10xPDFgs_rep2_fastqc.html [2022-03-16 01:10:58,599] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMLNAFX3_n02_10xPDFgs_rep2_fastqc.html [2022-03-16 01:10:58,640] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMLNAFX3_n01_undetermined_fastqc.html [2022-03-16 01:10:58,642] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMLNAFX3_n01_undetermined_fastqc.html [2022-03-16 01:10:58,990] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-16 01:10:58,992] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-16 01:10:58,997] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-03-16 01:10:58,999] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2022-03-16 01:10:59,001] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-16 01:10:59,006] multiqc [DEBUG ] No samples found: conpair [2022-03-16 01:10:59,011] multiqc [DEBUG ] No samples found: peddy [2022-03-16 01:10:59,017] multiqc [DEBUG ] No samples found: somalier [2022-03-16 01:10:59,022] multiqc [DEBUG ] No samples found: methylQA [2022-03-16 01:10:59,031] multiqc [DEBUG ] No samples found: mosdepth [2022-03-16 01:10:59,037] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-16 01:10:59,040] multiqc [DEBUG ] No samples found: qualimap [2022-03-16 01:10:59,046] multiqc [DEBUG ] No samples found: preseq [2022-03-16 01:10:59,051] multiqc [DEBUG ] No samples found: quast [2022-03-16 01:10:59,056] multiqc [DEBUG ] No samples found: qorts [2022-03-16 01:10:59,062] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-16 01:10:59,067] multiqc [DEBUG ] No samples found: rockhopper [2022-03-16 01:10:59,072] multiqc [DEBUG ] No samples found: rsem [2022-03-16 01:10:59,085] multiqc [DEBUG ] No samples found: rseqc [2022-03-16 01:10:59,090] multiqc [DEBUG ] No samples found: busco [2022-03-16 01:10:59,095] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-16 01:10:59,101] multiqc [DEBUG ] No samples found: disambiguate [2022-03-16 01:10:59,106] multiqc [DEBUG ] No samples found: supernova [2022-03-16 01:10:59,119] multiqc [DEBUG ] No samples found: deeptools [2022-03-16 01:10:59,124] multiqc [DEBUG ] No samples found: sargasso [2022-03-16 01:10:59,129] multiqc [DEBUG ] No samples found: verifybamid [2022-03-16 01:10:59,134] multiqc [DEBUG ] No samples found: mirtrace [2022-03-16 01:10:59,140] multiqc [DEBUG ] No samples found: happy [2022-03-16 01:10:59,145] multiqc [DEBUG ] No samples found: mirtop [2022-03-16 01:10:59,152] multiqc [DEBUG ] No samples found: homer [2022-03-16 01:10:59,157] multiqc [DEBUG ] No samples found: macs2 [2022-03-16 01:10:59,161] multiqc [DEBUG ] No samples found: theta2 [2022-03-16 01:10:59,166] multiqc [DEBUG ] No samples found: snpeff [2022-03-16 01:10:59,174] multiqc [DEBUG ] No samples found: gatk [2022-03-16 01:10:59,178] multiqc [DEBUG ] No samples found: htseq [2022-03-16 01:10:59,184] multiqc [DEBUG ] No samples found: bcftools [2022-03-16 01:10:59,190] multiqc [DEBUG ] No samples found: featureCounts [2022-03-16 01:10:59,196] multiqc [DEBUG ] No samples found: fgbio [2022-03-16 01:10:59,210] multiqc [DEBUG ] No samples found: dragen [2022-03-16 01:10:59,216] multiqc [DEBUG ] No samples found: dedup [2022-03-16 01:10:59,222] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-16 01:10:59,244] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-16 01:10:59,250] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-16 01:10:59,252] multiqc [DEBUG ] No samples found: picard [2022-03-16 01:10:59,257] multiqc [DEBUG ] No samples found: prokka [2022-03-16 01:10:59,263] multiqc [DEBUG ] No samples found: samblaster [2022-03-16 01:10:59,272] multiqc [DEBUG ] No samples found: samtools [2022-03-16 01:10:59,277] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-16 01:10:59,283] multiqc [DEBUG ] No samples found: bamtools [2022-03-16 01:10:59,288] multiqc [DEBUG ] No samples found: jellyfish [2022-03-16 01:10:59,298] multiqc [DEBUG ] No samples found: vcftools [2022-03-16 01:10:59,303] multiqc [DEBUG ] No samples found: longranger [2022-03-16 01:10:59,309] multiqc [DEBUG ] No samples found: stacks [2022-03-16 01:10:59,314] multiqc [DEBUG ] No samples found: varscan2 [2022-03-16 01:10:59,329] multiqc [DEBUG ] No samples found: bbmap [2022-03-16 01:10:59,335] multiqc [DEBUG ] No samples found: bismark [2022-03-16 01:10:59,340] multiqc [DEBUG ] No samples found: biscuit [2022-03-16 01:10:59,346] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-16 01:10:59,351] multiqc [DEBUG ] No samples found: hicup [2022-03-16 01:10:59,357] multiqc [DEBUG ] No samples found: hicpro [2022-03-16 01:10:59,362] multiqc [DEBUG ] No samples found: salmon [2022-03-16 01:10:59,368] multiqc [DEBUG ] No samples found: kallisto [2022-03-16 01:10:59,373] multiqc [DEBUG ] No samples found: slamdunk [2022-03-16 01:10:59,378] multiqc [DEBUG ] No samples found: star [2022-03-16 01:10:59,384] multiqc [DEBUG ] No samples found: hisat2 [2022-03-16 01:10:59,389] multiqc [DEBUG ] No samples found: tophat [2022-03-16 01:10:59,395] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-16 01:10:59,400] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-16 01:10:59,406] multiqc [DEBUG ] No samples found: snpsplit [2022-03-16 01:10:59,411] multiqc [DEBUG ] No samples found: kat [2022-03-16 01:10:59,417] multiqc [DEBUG ] No samples found: leehom [2022-03-16 01:10:59,421] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-16 01:10:59,428] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-16 01:10:59,433] multiqc [DEBUG ] No samples found: cutadapt [2022-03-16 01:10:59,438] multiqc [DEBUG ] No samples found: flexbar [2022-03-16 01:10:59,444] multiqc [DEBUG ] No samples found: kaiju [2022-03-16 01:10:59,449] multiqc [DEBUG ] No samples found: kraken [2022-03-16 01:10:59,454] multiqc [DEBUG ] No samples found: malt [2022-03-16 01:10:59,460] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-16 01:10:59,465] multiqc [DEBUG ] No samples found: sickle [2022-03-16 01:10:59,470] multiqc [DEBUG ] No samples found: skewer [2022-03-16 01:10:59,475] multiqc [DEBUG ] No samples found: sortmerna [2022-03-16 01:10:59,480] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-16 01:10:59,486] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-16 01:10:59,492] multiqc [DEBUG ] No samples found: afterqc [2022-03-16 01:10:59,497] multiqc [DEBUG ] No samples found: fastp [2022-03-16 01:10:59,547] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-03-16 01:10:59,547] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJMLNAFX3_n01_undetermined' [2022-03-16 01:10:59,551] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJMLNAFX3_n02_undetermined' [2022-03-16 01:10:59,597] multiqc [DEBUG ] No samples found: pycoqc [2022-03-16 01:10:59,602] multiqc [DEBUG ] No samples found: minionqc [2022-03-16 01:10:59,607] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-16 01:10:59,613] multiqc [DEBUG ] No samples found: clusterflow [2022-03-16 01:10:59,618] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-16 01:10:59,624] multiqc [DEBUG ] No samples found: interop [2022-03-16 01:10:59,630] multiqc [DEBUG ] No samples found: ivar [2022-03-16 01:10:59,635] multiqc [DEBUG ] No samples found: flash [2022-03-16 01:10:59,641] multiqc [DEBUG ] No samples found: seqyclean [2022-03-16 01:10:59,641] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-16 01:10:59,641] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-16 01:10:59,641] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-16 01:10:59,647] multiqc [INFO ] Compressing plot data [2022-03-16 01:10:59,702] multiqc [INFO ] Report : multiqc_report.html [2022-03-16 01:10:59,703] multiqc [INFO ] Data : multiqc_data [2022-03-16 01:10:59,703] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16073289/tmpe8ir2lro/multiqc_data' to '/scratch/gencore/logs/html/HJMLNAFX3/merged/multiqc_data' [2022-03-16 01:10:59,823] multiqc [INFO ] MultiQC complete