[2022-01-12 01:37:13,274] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-12 01:37:13,274] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-12 01:37:13,274] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-12 01:37:13,276] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-12 01:37:13,276] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-12 01:37:13,276] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF5W3AFX3/merged [2022-01-12 01:37:15,027] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-12 01:37:15,027] multiqc [INFO ] This is MultiQC v1.9 [2022-01-12 01:37:15,027] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF5W3AFX3/merged [2022-01-12 01:37:15,027] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HF5W3AFX3/merged [2022-01-12 01:37:15,027] multiqc [INFO ] Template : default [2022-01-12 01:37:15,028] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-12 01:37:15,028] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HF5W3AFX3/merged [2022-01-12 01:37:15,028] 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 [2022-01-12 01:37:15,028] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13722710/tmpbf_dky48 [2022-01-12 01:37:15,139] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-12 01:37:15,143] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-12 01:37:15,440] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_undetermined_fastqc.html [2022-01-12 01:37:15,443] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_undetermined_fastqc.html [2022-01-12 01:37:15,489] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-7_fastqc.html [2022-01-12 01:37:15,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-7_fastqc.html [2022-01-12 01:37:15,542] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-3_fastqc.html [2022-01-12 01:37:15,544] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-3_fastqc.html [2022-01-12 01:37:15,594] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-6_fastqc.html [2022-01-12 01:37:15,597] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-6_fastqc.html [2022-01-12 01:37:15,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-2_fastqc.html [2022-01-12 01:37:15,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-2_fastqc.html [2022-01-12 01:37:15,696] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-2_fastqc.html [2022-01-12 01:37:15,699] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-2_fastqc.html [2022-01-12 01:37:15,747] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_undetermined_fastqc.html [2022-01-12 01:37:15,749] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_undetermined_fastqc.html [2022-01-12 01:37:15,796] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-8_fastqc.html [2022-01-12 01:37:15,798] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-8_fastqc.html [2022-01-12 01:37:15,846] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-4_fastqc.html [2022-01-12 01:37:15,849] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-4_fastqc.html [2022-01-12 01:37:15,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-5_fastqc.html [2022-01-12 01:37:15,900] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-5_fastqc.html [2022-01-12 01:37:15,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-1_fastqc.html [2022-01-12 01:37:15,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-1_fastqc.html [2022-01-12 01:37:15,996] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-1_fastqc.html [2022-01-12 01:37:15,998] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-1_fastqc.html [2022-01-12 01:37:16,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-7_fastqc.html [2022-01-12 01:37:16,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-7_fastqc.html [2022-01-12 01:37:16,095] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-3_fastqc.html [2022-01-12 01:37:16,098] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-3_fastqc.html [2022-01-12 01:37:16,145] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-4_fastqc.html [2022-01-12 01:37:16,148] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-4_fastqc.html [2022-01-12 01:37:16,195] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-6_fastqc.html [2022-01-12 01:37:16,198] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-6_fastqc.html [2022-01-12 01:37:16,245] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-5_fastqc.html [2022-01-12 01:37:16,247] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n02_as2-5_fastqc.html [2022-01-12 01:37:16,293] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-8_fastqc.html [2022-01-12 01:37:16,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5W3AFX3_n01_as2-8_fastqc.html [2022-01-12 01:37:16,936] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-12 01:37:16,938] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-12 01:37:16,945] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-12 01:37:16,950] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2022-01-12 01:37:16,960] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-12 01:37:16,965] multiqc [DEBUG ] No samples found: conpair [2022-01-12 01:37:16,970] multiqc [DEBUG ] No samples found: peddy [2022-01-12 01:37:16,975] multiqc [DEBUG ] No samples found: somalier [2022-01-12 01:37:16,980] multiqc [DEBUG ] No samples found: methylQA [2022-01-12 01:37:16,988] multiqc [DEBUG ] No samples found: mosdepth [2022-01-12 01:37:16,993] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-12 01:37:16,996] multiqc [DEBUG ] No samples found: qualimap [2022-01-12 01:37:17,001] multiqc [DEBUG ] No samples found: preseq [2022-01-12 01:37:17,007] multiqc [DEBUG ] No samples found: quast [2022-01-12 01:37:17,025] multiqc [DEBUG ] No samples found: qorts [2022-01-12 01:37:17,032] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-12 01:37:17,037] multiqc [DEBUG ] No samples found: rockhopper [2022-01-12 01:37:17,043] multiqc [DEBUG ] No samples found: rsem [2022-01-12 01:37:17,058] multiqc [DEBUG ] No samples found: rseqc [2022-01-12 01:37:17,063] multiqc [DEBUG ] No samples found: busco [2022-01-12 01:37:17,069] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-12 01:37:17,073] multiqc [DEBUG ] No samples found: disambiguate [2022-01-12 01:37:17,079] multiqc [DEBUG ] No samples found: supernova [2022-01-12 01:37:17,093] multiqc [DEBUG ] No samples found: deeptools [2022-01-12 01:37:17,098] multiqc [DEBUG ] No samples found: sargasso [2022-01-12 01:37:17,103] multiqc [DEBUG ] No samples found: verifybamid [2022-01-12 01:37:17,108] multiqc [DEBUG ] No samples found: mirtrace [2022-01-12 01:37:17,114] multiqc [DEBUG ] No samples found: happy [2022-01-12 01:37:17,119] multiqc [DEBUG ] No samples found: mirtop [2022-01-12 01:37:17,125] multiqc [DEBUG ] No samples found: homer [2022-01-12 01:37:17,131] multiqc [DEBUG ] No samples found: macs2 [2022-01-12 01:37:17,135] multiqc [DEBUG ] No samples found: theta2 [2022-01-12 01:37:17,140] multiqc [DEBUG ] No samples found: snpeff [2022-01-12 01:37:17,147] multiqc [DEBUG ] No samples found: gatk [2022-01-12 01:37:17,152] multiqc [DEBUG ] No samples found: htseq [2022-01-12 01:37:17,158] multiqc [DEBUG ] No samples found: bcftools [2022-01-12 01:37:17,163] multiqc [DEBUG ] No samples found: featureCounts [2022-01-12 01:37:17,170] multiqc [DEBUG ] No samples found: fgbio [2022-01-12 01:37:17,186] multiqc [DEBUG ] No samples found: dragen [2022-01-12 01:37:17,192] multiqc [DEBUG ] No samples found: dedup [2022-01-12 01:37:17,197] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-12 01:37:17,222] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-12 01:37:17,228] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-12 01:37:17,230] multiqc [DEBUG ] No samples found: picard [2022-01-12 01:37:17,235] multiqc [DEBUG ] No samples found: prokka [2022-01-12 01:37:17,240] multiqc [DEBUG ] No samples found: samblaster [2022-01-12 01:37:17,251] multiqc [DEBUG ] No samples found: samtools [2022-01-12 01:37:17,256] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-12 01:37:17,261] multiqc [DEBUG ] No samples found: bamtools [2022-01-12 01:37:17,266] multiqc [DEBUG ] No samples found: jellyfish [2022-01-12 01:37:17,275] multiqc [DEBUG ] No samples found: vcftools [2022-01-12 01:37:17,280] multiqc [DEBUG ] No samples found: longranger [2022-01-12 01:37:17,286] multiqc [DEBUG ] No samples found: stacks [2022-01-12 01:37:17,291] multiqc [DEBUG ] No samples found: varscan2 [2022-01-12 01:37:17,306] multiqc [DEBUG ] No samples found: bbmap [2022-01-12 01:37:17,312] multiqc [DEBUG ] No samples found: bismark [2022-01-12 01:37:17,317] multiqc [DEBUG ] No samples found: biscuit [2022-01-12 01:37:17,323] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-12 01:37:17,328] multiqc [DEBUG ] No samples found: hicup [2022-01-12 01:37:17,333] multiqc [DEBUG ] No samples found: hicpro [2022-01-12 01:37:17,338] multiqc [DEBUG ] No samples found: salmon [2022-01-12 01:37:17,343] multiqc [DEBUG ] No samples found: kallisto [2022-01-12 01:37:17,349] multiqc [DEBUG ] No samples found: slamdunk [2022-01-12 01:37:17,354] multiqc [DEBUG ] No samples found: star [2022-01-12 01:37:17,359] multiqc [DEBUG ] No samples found: hisat2 [2022-01-12 01:37:17,364] multiqc [DEBUG ] No samples found: tophat [2022-01-12 01:37:17,369] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-12 01:37:17,374] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-12 01:37:17,380] multiqc [DEBUG ] No samples found: snpsplit [2022-01-12 01:37:17,384] multiqc [DEBUG ] No samples found: kat [2022-01-12 01:37:17,389] multiqc [DEBUG ] No samples found: leehom [2022-01-12 01:37:17,394] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-12 01:37:17,398] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-12 01:37:17,403] multiqc [DEBUG ] No samples found: cutadapt [2022-01-12 01:37:17,408] multiqc [DEBUG ] No samples found: flexbar [2022-01-12 01:37:17,413] multiqc [DEBUG ] No samples found: kaiju [2022-01-12 01:37:17,418] multiqc [DEBUG ] No samples found: kraken [2022-01-12 01:37:17,423] multiqc [DEBUG ] No samples found: malt [2022-01-12 01:37:17,428] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-12 01:37:17,433] multiqc [DEBUG ] No samples found: sickle [2022-01-12 01:37:17,438] multiqc [DEBUG ] No samples found: skewer [2022-01-12 01:37:17,443] multiqc [DEBUG ] No samples found: sortmerna [2022-01-12 01:37:17,447] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-12 01:37:17,453] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-12 01:37:17,458] multiqc [DEBUG ] No samples found: afterqc [2022-01-12 01:37:17,463] multiqc [DEBUG ] No samples found: fastp [2022-01-12 01:37:17,903] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2022-01-12 01:37:18,272] multiqc [DEBUG ] No samples found: pycoqc [2022-01-12 01:37:18,277] multiqc [DEBUG ] No samples found: minionqc [2022-01-12 01:37:18,282] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-12 01:37:18,287] multiqc [DEBUG ] No samples found: clusterflow [2022-01-12 01:37:18,293] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-12 01:37:18,298] multiqc [DEBUG ] No samples found: interop [2022-01-12 01:37:18,303] multiqc [DEBUG ] No samples found: ivar [2022-01-12 01:37:18,308] multiqc [DEBUG ] No samples found: flash [2022-01-12 01:37:18,313] multiqc [DEBUG ] No samples found: seqyclean [2022-01-12 01:37:18,313] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-12 01:37:18,313] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-12 01:37:18,313] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-12 01:37:18,313] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-12 01:37:18,336] multiqc [INFO ] Compressing plot data [2022-01-12 01:37:18,678] multiqc [INFO ] Report : multiqc_report.html [2022-01-12 01:37:18,679] multiqc [INFO ] Data : multiqc_data [2022-01-12 01:37:18,679] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13722710/tmpbf_dky48/multiqc_data' to '/scratch/gencore/logs/html/HF5W3AFX3/merged/multiqc_data' [2022-01-12 01:37:18,869] multiqc [INFO ] MultiQC complete