[2022-08-22 18:45:05,432] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-08-22 18:45:05,432] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-08-22 18:45:05,432] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-08-22 18:45:05,433] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-08-22 18:45:05,433] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-08-22 18:45:05,433] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFKFTDMXY/merged [2022-08-22 18:45:05,941] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-08-22 18:45:05,941] multiqc [INFO ] This is MultiQC v1.9 [2022-08-22 18:45:05,941] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFKFTDMXY/merged [2022-08-22 18:45:05,941] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFKFTDMXY/merged [2022-08-22 18:45:05,941] multiqc [INFO ] Template : default [2022-08-22 18:45:05,942] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-08-22 18:45:05,942] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFKFTDMXY/merged [2022-08-22 18:45:05,942] 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 [2022-08-22 18:45:05,942] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-23925434/tmp99k81gxq [2022-08-22 18:45:06,069] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n01_U1-23_fastqc.html [2022-08-22 18:45:06,072] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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18:45:10,857] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-27_fastqc.html [2022-08-22 18:45:10,859] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-27_fastqc.html [2022-08-22 18:45:10,901] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-28_fastqc.html [2022-08-22 18:45:10,903] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-28_fastqc.html [2022-08-22 18:45:10,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-22_fastqc.html [2022-08-22 18:45:10,960] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-22_fastqc.html [2022-08-22 18:45:11,039] multiqc [DEBUG ] File ignored by 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HFKFTDMXY_n01_U2-19_fastqc.html [2022-08-22 18:45:16,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n01_U2-19_fastqc.html [2022-08-22 18:45:16,899] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n01_U1-21_fastqc.html [2022-08-22 18:45:16,901] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n01_U1-21_fastqc.html [2022-08-22 18:45:16,956] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-35_fastqc.html [2022-08-22 18:45:16,958] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U1-35_fastqc.html [2022-08-22 18:45:17,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U2-39_fastqc.html [2022-08-22 18:45:17,020] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U2-39_fastqc.html [2022-08-22 18:45:17,059] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U2-10_fastqc.html [2022-08-22 18:45:17,061] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_U2-10_fastqc.html [2022-08-22 18:45:17,113] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n01_U1-13_fastqc.html [2022-08-22 18:45:17,115] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n01_U1-13_fastqc.html [2022-08-22 18:45:17,165] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n01_CA1100L16_fastqc.html [2022-08-22 18:45:17,168] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n01_CA1100L16_fastqc.html [2022-08-22 18:45:17,210] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_CA2100L37_fastqc.html [2022-08-22 18:45:17,212] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_CA2100L37_fastqc.html [2022-08-22 18:45:17,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFKFTDMXY_n02_CA1100L70_fastqc.html [2022-08-22 18:45:17,273] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFKFTDMXY_n02_CA1100L70_fastqc.html [2022-08-22 18:45:17,893] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-22 18:45:17,894] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-22 18:45:17,904] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-08-22 18:45:17,915] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-08-22 18:45:17,962] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 97 samples (table) [2022-08-22 18:45:17,968] multiqc [DEBUG ] No samples found: conpair [2022-08-22 18:45:17,973] multiqc [DEBUG ] No samples found: peddy [2022-08-22 18:45:17,978] multiqc [DEBUG ] No samples found: somalier [2022-08-22 18:45:17,983] multiqc [DEBUG ] No samples found: methylQA [2022-08-22 18:45:17,992] multiqc [DEBUG ] No samples found: mosdepth [2022-08-22 18:45:17,997] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-08-22 18:45:18,000] multiqc [DEBUG ] No samples found: qualimap [2022-08-22 18:45:18,006] multiqc [DEBUG ] No samples found: preseq [2022-08-22 18:45:18,011] multiqc [DEBUG ] No samples found: quast [2022-08-22 18:45:18,016] multiqc [DEBUG ] No samples found: qorts [2022-08-22 18:45:18,021] multiqc [DEBUG ] No samples found: rna_seqc [2022-08-22 18:45:18,026] multiqc [DEBUG ] No samples found: rockhopper [2022-08-22 18:45:18,031] multiqc [DEBUG ] No samples found: rsem [2022-08-22 18:45:18,042] multiqc [DEBUG ] No samples found: rseqc [2022-08-22 18:45:18,047] multiqc [DEBUG ] No samples found: busco [2022-08-22 18:45:18,052] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-08-22 18:45:18,057] multiqc [DEBUG ] No samples found: disambiguate [2022-08-22 18:45:18,062] multiqc [DEBUG ] No samples found: supernova [2022-08-22 18:45:18,075] multiqc [DEBUG ] No samples found: deeptools [2022-08-22 18:45:18,080] multiqc [DEBUG ] No samples found: sargasso [2022-08-22 18:45:18,085] multiqc [DEBUG ] No samples found: verifybamid [2022-08-22 18:45:18,090] multiqc [DEBUG ] No samples found: mirtrace [2022-08-22 18:45:18,094] multiqc [DEBUG ] No samples found: happy [2022-08-22 18:45:18,099] multiqc [DEBUG ] No samples found: mirtop [2022-08-22 18:45:18,105] multiqc [DEBUG ] No samples found: homer [2022-08-22 18:45:18,110] multiqc [DEBUG ] No samples found: macs2 [2022-08-22 18:45:18,114] multiqc [DEBUG ] No samples found: theta2 [2022-08-22 18:45:18,120] multiqc [DEBUG ] No samples found: snpeff [2022-08-22 18:45:18,127] multiqc [DEBUG ] No samples found: gatk [2022-08-22 18:45:18,132] multiqc [DEBUG ] No samples found: htseq [2022-08-22 18:45:18,138] multiqc [DEBUG ] No samples found: bcftools [2022-08-22 18:45:18,142] multiqc [DEBUG ] No samples found: featureCounts [2022-08-22 18:45:18,149] multiqc [DEBUG ] No samples found: fgbio [2022-08-22 18:45:18,162] multiqc [DEBUG ] No samples found: dragen [2022-08-22 18:45:18,167] multiqc [DEBUG ] No samples found: dedup [2022-08-22 18:45:18,172] multiqc [DEBUG ] No samples found: damageprofiler [2022-08-22 18:45:18,195] multiqc [DEBUG ] No samples found: biobambam2 [2022-08-22 18:45:18,200] multiqc [DEBUG ] No samples found: mtnucratio [2022-08-22 18:45:18,202] multiqc [DEBUG ] No samples found: picard [2022-08-22 18:45:18,207] multiqc [DEBUG ] No samples found: prokka [2022-08-22 18:45:18,212] multiqc [DEBUG ] No samples found: samblaster [2022-08-22 18:45:18,220] multiqc [DEBUG ] No samples found: samtools [2022-08-22 18:45:18,225] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-08-22 18:45:18,230] multiqc [DEBUG ] No samples found: bamtools [2022-08-22 18:45:18,235] multiqc [DEBUG ] No samples found: jellyfish [2022-08-22 18:45:18,242] multiqc [DEBUG ] No samples found: vcftools [2022-08-22 18:45:18,248] multiqc [DEBUG ] No samples found: longranger [2022-08-22 18:45:18,253] multiqc [DEBUG ] No samples found: stacks [2022-08-22 18:45:18,258] multiqc [DEBUG ] No samples found: varscan2 [2022-08-22 18:45:18,273] multiqc [DEBUG ] No samples found: bbmap [2022-08-22 18:45:18,279] multiqc [DEBUG ] No samples found: bismark [2022-08-22 18:45:18,284] multiqc [DEBUG ] No samples found: biscuit [2022-08-22 18:45:18,289] multiqc [DEBUG ] No samples found: hicexplorer [2022-08-22 18:45:18,294] multiqc [DEBUG ] No samples found: hicup [2022-08-22 18:45:18,299] multiqc [DEBUG ] No samples found: hicpro [2022-08-22 18:45:18,303] multiqc [DEBUG ] No samples found: salmon [2022-08-22 18:45:18,308] multiqc [DEBUG ] No samples found: kallisto [2022-08-22 18:45:18,313] multiqc [DEBUG ] No samples found: slamdunk [2022-08-22 18:45:18,318] multiqc [DEBUG ] No samples found: star [2022-08-22 18:45:18,323] multiqc [DEBUG ] No samples found: hisat2 [2022-08-22 18:45:18,327] multiqc [DEBUG ] No samples found: tophat [2022-08-22 18:45:18,332] multiqc [DEBUG ] No samples found: bowtie2 [2022-08-22 18:45:18,337] multiqc [DEBUG ] No samples found: bowtie1 [2022-08-22 18:45:18,342] multiqc [DEBUG ] No samples found: snpsplit [2022-08-22 18:45:18,346] multiqc [DEBUG ] No samples found: kat [2022-08-22 18:45:18,351] multiqc [DEBUG ] No samples found: leehom [2022-08-22 18:45:18,355] multiqc [DEBUG ] No samples found: adapterRemoval [2022-08-22 18:45:18,360] multiqc [DEBUG ] No samples found: clipandmerge [2022-08-22 18:45:18,364] multiqc [DEBUG ] No samples found: cutadapt [2022-08-22 18:45:18,369] multiqc [DEBUG ] No samples found: flexbar [2022-08-22 18:45:18,373] multiqc [DEBUG ] No samples found: kaiju [2022-08-22 18:45:18,378] multiqc [DEBUG ] No samples found: kraken [2022-08-22 18:45:18,382] multiqc [DEBUG ] No samples found: malt [2022-08-22 18:45:18,387] multiqc [DEBUG ] No samples found: trimmomatic [2022-08-22 18:45:18,392] multiqc [DEBUG ] No samples found: sickle [2022-08-22 18:45:18,397] multiqc [DEBUG ] No samples found: skewer [2022-08-22 18:45:18,401] multiqc [DEBUG ] No samples found: sortmerna [2022-08-22 18:45:18,406] multiqc [DEBUG ] No samples found: biobloomtools [2022-08-22 18:45:18,411] multiqc [DEBUG ] No samples found: fastq_screen [2022-08-22 18:45:18,415] multiqc [DEBUG ] No samples found: afterqc [2022-08-22 18:45:18,420] multiqc [DEBUG ] No samples found: fastp [2022-08-22 18:45:54,531] multiqc.modules.fastqc.fastqc [INFO ] Found 194 reports [2022-08-22 18:46:19,780] multiqc [DEBUG ] No samples found: pycoqc [2022-08-22 18:46:19,785] multiqc [DEBUG ] No samples found: minionqc [2022-08-22 18:46:19,790] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-08-22 18:46:19,795] multiqc [DEBUG ] No samples found: clusterflow [2022-08-22 18:46:19,800] multiqc [DEBUG ] No samples found: bcl2fastq [2022-08-22 18:46:19,805] multiqc [DEBUG ] No samples found: interop [2022-08-22 18:46:19,810] multiqc [DEBUG ] No samples found: ivar [2022-08-22 18:46:19,815] multiqc [DEBUG ] No samples found: flash [2022-08-22 18:46:19,819] multiqc [DEBUG ] No samples found: seqyclean [2022-08-22 18:46:19,820] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-08-22 18:46:19,820] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-08-22 18:46:19,820] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-08-22 18:46:19,820] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-08-22 18:46:20,049] multiqc [INFO ] Compressing plot data [2022-08-22 18:46:20,117] multiqc [INFO ] Report : multiqc_report.html [2022-08-22 18:46:20,117] multiqc [INFO ] Data : multiqc_data [2022-08-22 18:46:20,117] multiqc [DEBUG ] Moving data file from '/state/partition1/job-23925434/tmp99k81gxq/multiqc_data' to '/scratch/gencore/logs/html/HFKFTDMXY/merged/multiqc_data' [2022-08-22 18:46:20,263] multiqc [INFO ] MultiQC complete