[2022-01-09 20:07:09,192] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-09 20:07:09,192] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-09 20:07:09,192] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-09 20:07:09,193] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-09 20:07:09,193] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-09 20:07:09,194] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNMK2DRXY/merged [2022-01-09 20:07:10,793] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-09 20:07:10,793] multiqc [INFO ] This is MultiQC v1.9 [2022-01-09 20:07:10,793] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNMK2DRXY/merged [2022-01-09 20:07:10,793] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNMK2DRXY/merged [2022-01-09 20:07:10,793] multiqc [INFO ] Template : default [2022-01-09 20:07:10,793] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-09 20:07:10,793] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNMK2DRXY/merged [2022-01-09 20:07:10,794] 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 [2022-01-09 20:07:10,794] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13661903/tmp06tph4dq [2022-01-09 20:07:10,894] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK86_fastqc.html [2022-01-09 20:07:10,896] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK86_fastqc.html [2022-01-09 20:07:10,936] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:10,938] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-09 20:07:14,820] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK85_fastqc.html [2022-01-09 20:07:14,822] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK85_fastqc.html [2022-01-09 20:07:14,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n01_undetermined_fastqc.html [2022-01-09 20:07:14,876] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n01_undetermined_fastqc.html [2022-01-09 20:07:14,939] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK14_hic_2_fastqc.html [2022-01-09 20:07:14,940] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK14_hic_2_fastqc.html [2022-01-09 20:07:14,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK85_fastqc.html [2022-01-09 20:07:14,982] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK85_fastqc.html [2022-01-09 20:07:15,043] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n02_undetermined_fastqc.html [2022-01-09 20:07:15,045] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n02_undetermined_fastqc.html [2022-01-09 20:07:15,085] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK14_hic_2_fastqc.html [2022-01-09 20:07:15,087] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK14_hic_2_fastqc.html [2022-01-09 20:07:15,126] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK86_fastqc.html [2022-01-09 20:07:15,128] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK86_fastqc.html [2022-01-09 20:07:15,166] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK87_fastqc.html [2022-01-09 20:07:15,167] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n01_JK87_fastqc.html [2022-01-09 20:07:15,220] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK87_fastqc.html [2022-01-09 20:07:15,222] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNMK2DRXY_n02_JK87_fastqc.html [2022-01-09 20:07:15,530] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-09 20:07:15,532] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-09 20:07:15,538] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-09 20:07:15,548] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-09 20:07:15,551] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2022-01-09 20:07:15,557] multiqc [DEBUG ] No samples found: conpair [2022-01-09 20:07:15,561] multiqc [DEBUG ] No samples found: peddy [2022-01-09 20:07:15,567] multiqc [DEBUG ] No samples found: somalier [2022-01-09 20:07:15,571] multiqc [DEBUG ] No samples found: methylQA [2022-01-09 20:07:15,578] multiqc [DEBUG ] No samples found: mosdepth [2022-01-09 20:07:15,581] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-09 20:07:15,586] multiqc [DEBUG ] No samples found: qualimap [2022-01-09 20:07:15,590] multiqc [DEBUG ] No samples found: preseq [2022-01-09 20:07:15,594] multiqc [DEBUG ] No samples found: quast [2022-01-09 20:07:15,598] multiqc [DEBUG ] No samples found: qorts [2022-01-09 20:07:15,602] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-09 20:07:15,608] multiqc [DEBUG ] No samples found: rockhopper [2022-01-09 20:07:15,612] multiqc [DEBUG ] No samples found: rsem [2022-01-09 20:07:15,624] multiqc [DEBUG ] No samples found: rseqc [2022-01-09 20:07:15,628] multiqc [DEBUG ] No samples found: busco [2022-01-09 20:07:15,633] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-09 20:07:15,636] multiqc [DEBUG ] No samples found: disambiguate [2022-01-09 20:07:15,640] multiqc [DEBUG ] No samples found: supernova [2022-01-09 20:07:15,653] multiqc [DEBUG ] No samples found: deeptools [2022-01-09 20:07:15,657] multiqc [DEBUG ] No samples found: sargasso [2022-01-09 20:07:15,662] multiqc [DEBUG ] No samples found: verifybamid [2022-01-09 20:07:15,665] multiqc [DEBUG ] No samples found: mirtrace [2022-01-09 20:07:15,670] multiqc [DEBUG ] No samples found: happy [2022-01-09 20:07:15,674] multiqc [DEBUG ] No samples found: mirtop [2022-01-09 20:07:15,680] multiqc [DEBUG ] No samples found: homer [2022-01-09 20:07:15,684] multiqc [DEBUG ] No samples found: macs2 [2022-01-09 20:07:15,688] multiqc [DEBUG ] No samples found: theta2 [2022-01-09 20:07:15,692] multiqc [DEBUG ] No samples found: snpeff [2022-01-09 20:07:15,699] multiqc [DEBUG ] No samples found: gatk [2022-01-09 20:07:15,702] multiqc [DEBUG ] No samples found: htseq [2022-01-09 20:07:15,708] multiqc [DEBUG ] No samples found: bcftools [2022-01-09 20:07:15,712] multiqc [DEBUG ] No samples found: featureCounts [2022-01-09 20:07:15,717] multiqc [DEBUG ] No samples found: fgbio [2022-01-09 20:07:15,732] multiqc [DEBUG ] No samples found: dragen [2022-01-09 20:07:15,737] multiqc [DEBUG ] No samples found: dedup [2022-01-09 20:07:15,742] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-09 20:07:15,762] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-09 20:07:15,767] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-09 20:07:15,769] multiqc [DEBUG ] No samples found: picard [2022-01-09 20:07:15,773] multiqc [DEBUG ] No samples found: prokka [2022-01-09 20:07:15,777] multiqc [DEBUG ] No samples found: samblaster [2022-01-09 20:07:15,784] multiqc [DEBUG ] No samples found: samtools [2022-01-09 20:07:15,788] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-09 20:07:15,793] multiqc [DEBUG ] No samples found: bamtools [2022-01-09 20:07:15,797] multiqc [DEBUG ] No samples found: jellyfish [2022-01-09 20:07:15,803] multiqc [DEBUG ] No samples found: vcftools [2022-01-09 20:07:15,807] multiqc [DEBUG ] No samples found: longranger [2022-01-09 20:07:15,811] multiqc [DEBUG ] No samples found: stacks [2022-01-09 20:07:15,815] multiqc [DEBUG ] No samples found: varscan2 [2022-01-09 20:07:15,830] multiqc [DEBUG ] No samples found: bbmap [2022-01-09 20:07:15,834] multiqc [DEBUG ] No samples found: bismark [2022-01-09 20:07:15,839] multiqc [DEBUG ] No samples found: biscuit [2022-01-09 20:07:15,843] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-09 20:07:15,847] multiqc [DEBUG ] No samples found: hicup [2022-01-09 20:07:15,852] multiqc [DEBUG ] No samples found: hicpro [2022-01-09 20:07:15,856] multiqc [DEBUG ] No samples found: salmon [2022-01-09 20:07:15,860] multiqc [DEBUG ] No samples found: kallisto [2022-01-09 20:07:15,864] multiqc [DEBUG ] No samples found: slamdunk [2022-01-09 20:07:15,867] multiqc [DEBUG ] No samples found: star [2022-01-09 20:07:15,872] multiqc [DEBUG ] No samples found: hisat2 [2022-01-09 20:07:15,876] multiqc [DEBUG ] No samples found: tophat [2022-01-09 20:07:15,882] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-09 20:07:15,886] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-09 20:07:15,891] multiqc [DEBUG ] No samples found: snpsplit [2022-01-09 20:07:15,895] multiqc [DEBUG ] No samples found: kat [2022-01-09 20:07:15,899] multiqc [DEBUG ] No samples found: leehom [2022-01-09 20:07:15,903] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-09 20:07:15,907] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-09 20:07:15,912] multiqc [DEBUG ] No samples found: cutadapt [2022-01-09 20:07:15,917] multiqc [DEBUG ] No samples found: flexbar [2022-01-09 20:07:15,920] multiqc [DEBUG ] No samples found: kaiju [2022-01-09 20:07:15,924] multiqc [DEBUG ] No samples found: kraken [2022-01-09 20:07:15,929] multiqc [DEBUG ] No samples found: malt [2022-01-09 20:07:15,933] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-09 20:07:15,937] multiqc [DEBUG ] No samples found: sickle [2022-01-09 20:07:15,940] multiqc [DEBUG ] No samples found: skewer [2022-01-09 20:07:15,946] multiqc [DEBUG ] No samples found: sortmerna [2022-01-09 20:07:15,950] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-09 20:07:15,955] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-09 20:07:15,959] multiqc [DEBUG ] No samples found: afterqc [2022-01-09 20:07:15,963] multiqc [DEBUG ] No samples found: fastp [2022-01-09 20:07:16,362] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2022-01-09 20:07:16,510] multiqc [DEBUG ] No samples found: pycoqc [2022-01-09 20:07:16,514] multiqc [DEBUG ] No samples found: minionqc [2022-01-09 20:07:16,545] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-09 20:07:16,550] multiqc [DEBUG ] No samples found: clusterflow [2022-01-09 20:07:16,554] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-09 20:07:16,558] multiqc [DEBUG ] No samples found: interop [2022-01-09 20:07:16,564] multiqc [DEBUG ] No samples found: ivar [2022-01-09 20:07:16,568] multiqc [DEBUG ] No samples found: flash [2022-01-09 20:07:16,574] multiqc [DEBUG ] No samples found: seqyclean [2022-01-09 20:07:16,574] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-09 20:07:16,574] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-09 20:07:16,574] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-09 20:07:16,574] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-09 20:07:16,587] multiqc [INFO ] Compressing plot data [2022-01-09 20:07:16,763] multiqc [INFO ] Report : multiqc_report.html [2022-01-09 20:07:16,764] multiqc [INFO ] Data : multiqc_data [2022-01-09 20:07:16,764] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13661903/tmp06tph4dq/multiqc_data' to '/scratch/gencore/logs/html/HNMK2DRXY/merged/multiqc_data' [2022-01-09 20:07:16,877] multiqc [INFO ] MultiQC complete