[2021-10-22 13:36:51,301] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-22 13:36:51,301] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-22 13:36:51,301] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-22 13:36:51,302] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-22 13:36:51,302] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-22 13:36:51,302] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJML5DRXY/merged [2021-10-22 13:36:52,691] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-22 13:36:52,691] multiqc [INFO ] This is MultiQC v1.9 [2021-10-22 13:36:52,691] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJML5DRXY/merged [2021-10-22 13:36:52,691] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJML5DRXY/merged [2021-10-22 13:36:52,691] multiqc [INFO ] Template : default [2021-10-22 13:36:52,691] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-22 13:36:52,691] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJML5DRXY/merged [2021-10-22 13:36:52,692] 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 [2021-10-22 13:36:52,692] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11106514/tmpb4ozhdl_ [2021-10-22 13:36:52,833] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJML5DRXY_1_fastqc.html [2021-10-22 13:36:52,835] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJML5DRXY_1_fastqc.html [2021-10-22 13:36:52,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJML5DRXY_3_fastqc.html [2021-10-22 13:36:52,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJML5DRXY_3_fastqc.html [2021-10-22 13:36:52,931] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJML5DRXY_2_fastqc.html [2021-10-22 13:36:52,932] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJML5DRXY_2_fastqc.html [2021-10-22 13:36:53,436] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-22 13:36:53,439] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-22 13:36:53,445] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2021-10-22 13:36:53,448] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-22 13:36:53,457] multiqc [DEBUG ] No samples found: conpair [2021-10-22 13:36:53,463] multiqc [DEBUG ] No samples found: peddy [2021-10-22 13:36:53,470] multiqc [DEBUG ] No samples found: somalier [2021-10-22 13:36:53,476] multiqc [DEBUG ] No samples found: methylQA [2021-10-22 13:36:53,490] multiqc [DEBUG ] No samples found: mosdepth [2021-10-22 13:36:53,497] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-22 13:36:53,502] multiqc [DEBUG ] No samples found: qualimap [2021-10-22 13:36:53,508] multiqc [DEBUG ] No samples found: preseq [2021-10-22 13:36:53,517] multiqc [DEBUG ] No samples found: quast [2021-10-22 13:36:53,525] multiqc [DEBUG ] No samples found: qorts [2021-10-22 13:36:53,536] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-22 13:36:53,544] multiqc [DEBUG ] No samples found: rockhopper [2021-10-22 13:36:53,552] multiqc [DEBUG ] No samples found: rsem [2021-10-22 13:36:53,575] multiqc [DEBUG ] No samples found: rseqc [2021-10-22 13:36:53,580] multiqc [DEBUG ] No samples found: busco [2021-10-22 13:36:53,589] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-22 13:36:53,595] multiqc [DEBUG ] No samples found: disambiguate [2021-10-22 13:36:53,602] multiqc [DEBUG ] No samples found: supernova [2021-10-22 13:36:53,631] multiqc [DEBUG ] No samples found: deeptools [2021-10-22 13:36:53,639] multiqc [DEBUG ] No samples found: sargasso [2021-10-22 13:36:53,645] multiqc [DEBUG ] No samples found: verifybamid [2021-10-22 13:36:53,653] multiqc [DEBUG ] No samples found: mirtrace [2021-10-22 13:36:53,658] multiqc [DEBUG ] No samples found: happy [2021-10-22 13:36:53,666] multiqc [DEBUG ] No samples found: mirtop [2021-10-22 13:36:53,680] multiqc [DEBUG ] No samples found: homer [2021-10-22 13:36:53,687] multiqc [DEBUG ] No samples found: macs2 [2021-10-22 13:36:53,693] multiqc [DEBUG ] No samples found: theta2 [2021-10-22 13:36:53,704] multiqc [DEBUG ] No samples found: snpeff [2021-10-22 13:36:53,715] multiqc [DEBUG ] No samples found: gatk [2021-10-22 13:36:53,724] multiqc [DEBUG ] No samples found: htseq [2021-10-22 13:36:53,732] multiqc [DEBUG ] No samples found: bcftools [2021-10-22 13:36:53,740] multiqc [DEBUG ] No samples found: featureCounts [2021-10-22 13:36:53,751] multiqc [DEBUG ] No samples found: fgbio [2021-10-22 13:36:53,778] multiqc [DEBUG ] No samples found: dragen [2021-10-22 13:36:53,784] multiqc [DEBUG ] No samples found: dedup [2021-10-22 13:36:53,788] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-22 13:36:53,838] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-22 13:36:53,845] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-22 13:36:53,848] multiqc [DEBUG ] No samples found: picard [2021-10-22 13:36:53,855] multiqc [DEBUG ] No samples found: prokka [2021-10-22 13:36:53,860] multiqc [DEBUG ] No samples found: samblaster [2021-10-22 13:36:53,878] multiqc [DEBUG ] No samples found: samtools [2021-10-22 13:36:53,885] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-22 13:36:53,892] multiqc [DEBUG ] No samples found: bamtools [2021-10-22 13:36:53,900] multiqc [DEBUG ] No samples found: jellyfish [2021-10-22 13:36:53,915] multiqc [DEBUG ] No samples found: vcftools [2021-10-22 13:36:53,922] multiqc [DEBUG ] No samples found: longranger [2021-10-22 13:36:53,928] multiqc [DEBUG ] No samples found: stacks [2021-10-22 13:36:53,936] multiqc [DEBUG ] No samples found: varscan2 [2021-10-22 13:36:53,969] multiqc [DEBUG ] No samples found: bbmap [2021-10-22 13:36:53,977] multiqc [DEBUG ] No samples found: bismark [2021-10-22 13:36:53,985] multiqc [DEBUG ] No samples found: biscuit [2021-10-22 13:36:53,993] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-22 13:36:54,003] multiqc [DEBUG ] No samples found: hicup [2021-10-22 13:36:54,009] multiqc [DEBUG ] No samples found: hicpro [2021-10-22 13:36:54,015] multiqc [DEBUG ] No samples found: salmon [2021-10-22 13:36:54,026] multiqc [DEBUG ] No samples found: kallisto [2021-10-22 13:36:54,033] multiqc [DEBUG ] No samples found: slamdunk [2021-10-22 13:36:54,040] multiqc [DEBUG ] No samples found: star [2021-10-22 13:36:54,046] multiqc [DEBUG ] No samples found: hisat2 [2021-10-22 13:36:54,053] multiqc [DEBUG ] No samples found: tophat [2021-10-22 13:36:54,059] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-22 13:36:54,066] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-22 13:36:54,073] multiqc [DEBUG ] No samples found: snpsplit [2021-10-22 13:36:54,080] multiqc [DEBUG ] No samples found: kat [2021-10-22 13:36:54,086] multiqc [DEBUG ] No samples found: leehom [2021-10-22 13:36:54,094] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-22 13:36:54,100] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-22 13:36:54,109] multiqc [DEBUG ] No samples found: cutadapt [2021-10-22 13:36:54,115] multiqc [DEBUG ] No samples found: flexbar [2021-10-22 13:36:54,122] multiqc [DEBUG ] No samples found: kaiju [2021-10-22 13:36:54,128] multiqc [DEBUG ] No samples found: kraken [2021-10-22 13:36:54,135] multiqc [DEBUG ] No samples found: malt [2021-10-22 13:36:54,139] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-22 13:36:54,146] multiqc [DEBUG ] No samples found: sickle [2021-10-22 13:36:54,153] multiqc [DEBUG ] No samples found: skewer [2021-10-22 13:36:54,159] multiqc [DEBUG ] No samples found: sortmerna [2021-10-22 13:36:54,167] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-22 13:36:54,178] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-22 13:36:54,188] multiqc [DEBUG ] No samples found: afterqc [2021-10-22 13:36:54,194] multiqc [DEBUG ] No samples found: fastp [2021-10-22 13:36:54,369] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2021-10-22 13:36:54,419] multiqc [DEBUG ] No samples found: pycoqc [2021-10-22 13:36:54,427] multiqc [DEBUG ] No samples found: minionqc [2021-10-22 13:36:54,434] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-22 13:36:54,441] multiqc [DEBUG ] No samples found: clusterflow [2021-10-22 13:36:54,448] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-22 13:36:54,455] multiqc [DEBUG ] No samples found: interop [2021-10-22 13:36:54,463] multiqc [DEBUG ] No samples found: ivar [2021-10-22 13:36:54,469] multiqc [DEBUG ] No samples found: flash [2021-10-22 13:36:54,476] multiqc [DEBUG ] No samples found: seqyclean [2021-10-22 13:36:54,476] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-10-22 13:36:54,476] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-22 13:36:54,476] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-22 13:36:54,480] multiqc [INFO ] Compressing plot data [2021-10-22 13:36:54,533] multiqc [INFO ] Report : multiqc_report.html [2021-10-22 13:36:54,533] multiqc [INFO ] Data : multiqc_data [2021-10-22 13:36:54,533] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11106514/tmpb4ozhdl_/multiqc_data' to '/scratch/gencore/logs/html/HJML5DRXY/merged/multiqc_data' [2021-10-22 13:36:54,669] multiqc [INFO ] MultiQC complete