[2021-03-05 16:46:34,881] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-05 16:46:34,881] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-05 16:46:34,882] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-05 16:46:34,882] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-05 16:46:34,883] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-05 16:46:34,883] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H273YDRXY/1 [2021-03-05 16:46:36,268] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-03-05 16:46:36,268] multiqc [INFO ] This is MultiQC v1.9 [2021-03-05 16:46:36,268] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H273YDRXY/1 [2021-03-05 16:46:36,268] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H273YDRXY/1 [2021-03-05 16:46:36,268] multiqc [INFO ] Template : default [2021-03-05 16:46:36,268] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-05 16:46:36,269] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H273YDRXY/1 [2021-03-05 16:46:36,269] 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 [2021-03-05 16:46:36,269] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-3382663/tmpaat58emi [2021-03-05 16:46:36,396] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_H03_T0_fastqc.html [2021-03-05 16:46:36,399] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_H03_T0_fastqc.html [2021-03-05 16:46:36,488] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_D03_T0_fastqc.html [2021-03-05 16:46:36,490] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_D03_T0_fastqc.html [2021-03-05 16:46:36,580] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_D03_T0_fastqc.html [2021-03-05 16:46:36,582] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_D03_T0_fastqc.html [2021-03-05 16:46:36,676] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_G04_T0_fastqc.html [2021-03-05 16:46:36,678] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_G04_T0_fastqc.html [2021-03-05 16:46:36,762] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_B03_T0_fastqc.html [2021-03-05 16:46:36,764] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_B03_T0_fastqc.html [2021-03-05 16:46:36,854] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_C04_T0_fastqc.html [2021-03-05 16:46:36,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_C04_T0_fastqc.html [2021-03-05 16:46:36,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_E04_T0_fastqc.html [2021-03-05 16:46:36,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_E04_T0_fastqc.html [2021-03-05 16:46:37,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_F03_T0_fastqc.html [2021-03-05 16:46:37,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_F03_T0_fastqc.html [2021-03-05 16:46:37,117] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_G04_T0_fastqc.html [2021-03-05 16:46:37,119] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_G04_T0_fastqc.html [2021-03-05 16:46:37,186] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_A04_T0_fastqc.html [2021-03-05 16:46:37,187] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_A04_T0_fastqc.html [2021-03-05 16:46:37,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_E04_T0_fastqc.html [2021-03-05 16:46:37,273] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_E04_T0_fastqc.html [2021-03-05 16:46:37,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_G06_T0_fastqc.html [2021-03-05 16:46:37,359] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_G06_T0_fastqc.html [2021-03-05 16:46:37,471] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_G06_T0_fastqc.html [2021-03-05 16:46:37,473] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_G06_T0_fastqc.html [2021-03-05 16:46:37,563] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_C06_T0_fastqc.html [2021-03-05 16:46:37,565] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_C06_T0_fastqc.html [2021-03-05 16:46:37,646] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_F03_T0_fastqc.html [2021-03-05 16:46:37,648] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_F03_T0_fastqc.html [2021-03-05 16:46:37,731] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_A06_T0_fastqc.html [2021-03-05 16:46:37,733] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_A06_T0_fastqc.html [2021-03-05 16:46:37,818] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_E06_T0_fastqc.html [2021-03-05 16:46:37,819] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_E06_T0_fastqc.html [2021-03-05 16:46:37,896] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_undetermined_fastqc.html [2021-03-05 16:46:37,898] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_undetermined_fastqc.html [2021-03-05 16:46:37,955] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_H03_T0_fastqc.html [2021-03-05 16:46:37,957] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_H03_T0_fastqc.html [2021-03-05 16:46:38,043] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_E06_T0_fastqc.html [2021-03-05 16:46:38,045] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_E06_T0_fastqc.html [2021-03-05 16:46:38,126] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_C06_T0_fastqc.html [2021-03-05 16:46:38,128] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n02_Fluc_bc_C06_T0_fastqc.html [2021-03-05 16:46:38,202] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_A04_T0_fastqc.html [2021-03-05 16:46:38,203] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_A04_T0_fastqc.html [2021-03-05 16:46:38,280] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_undetermined_fastqc.html [2021-03-05 16:46:38,282] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_undetermined_fastqc.html [2021-03-05 16:46:38,384] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_B03_T0_fastqc.html [2021-03-05 16:46:38,385] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_B03_T0_fastqc.html [2021-03-05 16:46:38,452] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_C04_T0_fastqc.html [2021-03-05 16:46:38,454] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_C04_T0_fastqc.html [2021-03-05 16:46:38,520] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_A06_T0_fastqc.html [2021-03-05 16:46:38,522] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H273YDRXY_l01_n01_Fluc_bc_A06_T0_fastqc.html [2021-03-05 16:46:38,972] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-05 16:46:38,974] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-05 16:46:38,981] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-05 16:46:38,991] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-05 16:46:38,998] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 13 samples (table) [2021-03-05 16:46:39,003] multiqc [DEBUG ] No samples found: conpair [2021-03-05 16:46:39,007] multiqc [DEBUG ] No samples found: peddy [2021-03-05 16:46:39,012] multiqc [DEBUG ] No samples found: somalier [2021-03-05 16:46:39,016] multiqc [DEBUG ] No samples found: methylQA [2021-03-05 16:46:39,024] multiqc [DEBUG ] No samples found: mosdepth [2021-03-05 16:46:39,029] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-05 16:46:39,032] multiqc [DEBUG ] No samples found: qualimap [2021-03-05 16:46:39,037] multiqc [DEBUG ] No samples found: preseq [2021-03-05 16:46:39,041] multiqc [DEBUG ] No samples found: quast [2021-03-05 16:46:39,045] multiqc [DEBUG ] No samples found: qorts [2021-03-05 16:46:39,050] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-05 16:46:39,054] multiqc [DEBUG ] No samples found: rockhopper [2021-03-05 16:46:39,059] multiqc [DEBUG ] No samples found: rsem [2021-03-05 16:46:39,069] multiqc [DEBUG ] No samples found: rseqc [2021-03-05 16:46:39,073] multiqc [DEBUG ] No samples found: busco [2021-03-05 16:46:39,078] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-05 16:46:39,082] multiqc [DEBUG ] No samples found: disambiguate [2021-03-05 16:46:39,087] multiqc [DEBUG ] No samples found: supernova [2021-03-05 16:46:39,097] multiqc [DEBUG ] No samples found: deeptools [2021-03-05 16:46:39,102] multiqc [DEBUG ] No samples found: sargasso [2021-03-05 16:46:39,106] multiqc [DEBUG ] No samples found: verifybamid [2021-03-05 16:46:39,110] multiqc [DEBUG ] No samples found: mirtrace [2021-03-05 16:46:39,115] multiqc [DEBUG ] No samples found: happy [2021-03-05 16:46:39,119] multiqc [DEBUG ] No samples found: mirtop [2021-03-05 16:46:39,125] multiqc [DEBUG ] No samples found: homer [2021-03-05 16:46:39,129] multiqc [DEBUG ] No samples found: macs2 [2021-03-05 16:46:39,133] multiqc [DEBUG ] No samples found: theta2 [2021-03-05 16:46:39,137] multiqc [DEBUG ] No samples found: snpeff [2021-03-05 16:46:39,143] multiqc [DEBUG ] No samples found: gatk [2021-03-05 16:46:39,147] multiqc [DEBUG ] No samples found: htseq [2021-03-05 16:46:39,152] multiqc [DEBUG ] No samples found: bcftools [2021-03-05 16:46:39,156] multiqc [DEBUG ] No samples found: featureCounts [2021-03-05 16:46:39,162] multiqc [DEBUG ] No samples found: fgbio [2021-03-05 16:46:39,173] multiqc [DEBUG ] No samples found: dragen [2021-03-05 16:46:39,177] multiqc [DEBUG ] No samples found: dedup [2021-03-05 16:46:39,182] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-05 16:46:39,202] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-05 16:46:39,206] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-05 16:46:39,209] multiqc [DEBUG ] No samples found: picard [2021-03-05 16:46:39,213] multiqc [DEBUG ] No samples found: prokka [2021-03-05 16:46:39,217] multiqc [DEBUG ] No samples found: samblaster [2021-03-05 16:46:39,224] multiqc [DEBUG ] No samples found: samtools [2021-03-05 16:46:39,228] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-05 16:46:39,233] multiqc [DEBUG ] No samples found: bamtools [2021-03-05 16:46:39,237] multiqc [DEBUG ] No samples found: jellyfish [2021-03-05 16:46:39,244] multiqc [DEBUG ] No samples found: vcftools [2021-03-05 16:46:39,248] multiqc [DEBUG ] No samples found: longranger [2021-03-05 16:46:39,252] multiqc [DEBUG ] No samples found: stacks [2021-03-05 16:46:39,256] multiqc [DEBUG ] No samples found: varscan2 [2021-03-05 16:46:39,268] multiqc [DEBUG ] No samples found: bbmap [2021-03-05 16:46:39,272] multiqc [DEBUG ] No samples found: bismark [2021-03-05 16:46:39,277] multiqc [DEBUG ] No samples found: biscuit [2021-03-05 16:46:39,281] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-05 16:46:39,286] multiqc [DEBUG ] No samples found: hicup [2021-03-05 16:46:39,290] multiqc [DEBUG ] No samples found: hicpro [2021-03-05 16:46:39,293] multiqc [DEBUG ] No samples found: salmon [2021-03-05 16:46:39,298] multiqc [DEBUG ] No samples found: kallisto [2021-03-05 16:46:39,302] multiqc [DEBUG ] No samples found: slamdunk [2021-03-05 16:46:39,306] multiqc [DEBUG ] No samples found: star [2021-03-05 16:46:39,310] multiqc [DEBUG ] No samples found: hisat2 [2021-03-05 16:46:39,315] multiqc [DEBUG ] No samples found: tophat [2021-03-05 16:46:39,319] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-05 16:46:39,323] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-05 16:46:39,327] multiqc [DEBUG ] No samples found: snpsplit [2021-03-05 16:46:39,331] multiqc [DEBUG ] No samples found: kat [2021-03-05 16:46:39,334] multiqc [DEBUG ] No samples found: leehom [2021-03-05 16:46:39,339] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-05 16:46:39,343] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-05 16:46:39,347] multiqc [DEBUG ] No samples found: cutadapt [2021-03-05 16:46:39,351] multiqc [DEBUG ] No samples found: flexbar [2021-03-05 16:46:39,355] multiqc [DEBUG ] No samples found: kaiju [2021-03-05 16:46:39,359] multiqc [DEBUG ] No samples found: kraken [2021-03-05 16:46:39,364] multiqc [DEBUG ] No samples found: malt [2021-03-05 16:46:39,369] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-05 16:46:39,373] multiqc [DEBUG ] No samples found: sickle [2021-03-05 16:46:39,377] multiqc [DEBUG ] No samples found: skewer [2021-03-05 16:46:39,381] multiqc [DEBUG ] No samples found: sortmerna [2021-03-05 16:46:39,385] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-05 16:46:39,389] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-05 16:46:39,393] multiqc [DEBUG ] No samples found: afterqc [2021-03-05 16:46:39,397] multiqc [DEBUG ] No samples found: fastp [2021-03-05 16:46:40,863] multiqc.modules.fastqc.fastqc [INFO ] Found 26 reports [2021-03-05 16:46:41,248] multiqc [DEBUG ] No samples found: pycoqc [2021-03-05 16:46:41,252] multiqc [DEBUG ] No samples found: minionqc [2021-03-05 16:46:41,257] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-05 16:46:41,262] multiqc [DEBUG ] No samples found: clusterflow [2021-03-05 16:46:41,266] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-05 16:46:41,271] multiqc [DEBUG ] No samples found: interop [2021-03-05 16:46:41,276] multiqc [DEBUG ] No samples found: ivar [2021-03-05 16:46:41,280] multiqc [DEBUG ] No samples found: flash [2021-03-05 16:46:41,284] multiqc [DEBUG ] No samples found: seqyclean [2021-03-05 16:46:41,284] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-03-05 16:46:41,284] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-03-05 16:46:41,285] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-05 16:46:41,285] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-03-05 16:46:41,285] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-05 16:46:41,316] multiqc [INFO ] Compressing plot data [2021-03-05 16:46:41,731] multiqc [INFO ] Report : multiqc_report.html [2021-03-05 16:46:41,731] multiqc [INFO ] Data : multiqc_data [2021-03-05 16:46:41,731] multiqc [DEBUG ] Moving data file from '/state/partition1/job-3382663/tmpaat58emi/multiqc_data' to '/scratch/gencore/logs/html/H273YDRXY/1/multiqc_data' [2021-03-05 16:46:41,847] multiqc [INFO ] MultiQC complete