[2021-10-21 04:50:02,645] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-21 04:50:02,645] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-21 04:50:02,645] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-21 04:50:02,646] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-21 04:50:02,646] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-21 04:50:02,646] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJWL3DRXY/merged [2021-10-21 04:50:04,246] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-21 04:50:04,246] multiqc [INFO ] This is MultiQC v1.9 [2021-10-21 04:50:04,246] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJWL3DRXY/merged [2021-10-21 04:50:04,246] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJWL3DRXY/merged [2021-10-21 04:50:04,246] multiqc [INFO ] Template : default [2021-10-21 04:50:04,246] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-21 04:50:04,246] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJWL3DRXY/merged [2021-10-21 04:50:04,246] 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 [2021-10-21 04:50:04,247] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11075813/tmpybdfu16i [2021-10-21 04:50:04,348] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-21 04:50:04,350] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-21 04:50:04,891] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M2Tak_fastqc.html [2021-10-21 04:50:04,892] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M2Tak_fastqc.html [2021-10-21 04:50:04,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G13Tak_fastqc.html [2021-10-21 04:50:04,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G13Tak_fastqc.html [2021-10-21 04:50:05,009] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S3Nug_fastqc.html [2021-10-21 04:50:05,010] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S3Nug_fastqc.html [2021-10-21 04:50:05,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S3Tak_fastqc.html [2021-10-21 04:50:05,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S3Tak_fastqc.html [2021-10-21 04:50:05,091] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G11Tak_fastqc.html [2021-10-21 04:50:05,093] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G11Tak_fastqc.html [2021-10-21 04:50:05,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G11Nug_fastqc.html [2021-10-21 04:50:05,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G11Nug_fastqc.html [2021-10-21 04:50:05,215] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M1Tak_fastqc.html [2021-10-21 04:50:05,217] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M1Tak_fastqc.html [2021-10-21 04:50:05,277] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G13Nug_fastqc.html [2021-10-21 04:50:05,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G13Nug_fastqc.html [2021-10-21 04:50:05,319] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S1Tak_fastqc.html [2021-10-21 04:50:05,320] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S1Tak_fastqc.html [2021-10-21 04:50:05,382] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M2Nug_fastqc.html [2021-10-21 04:50:05,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M2Nug_fastqc.html [2021-10-21 04:50:05,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G12Nug_fastqc.html [2021-10-21 04:50:05,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G12Nug_fastqc.html [2021-10-21 04:50:05,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S1Nug_fastqc.html [2021-10-21 04:50:05,499] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S1Nug_fastqc.html [2021-10-21 04:50:05,559] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M1Nug_fastqc.html [2021-10-21 04:50:05,561] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G2M1Nug_fastqc.html [2021-10-21 04:50:05,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S2Tak_fastqc.html [2021-10-21 04:50:05,630] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S2Tak_fastqc.html [2021-10-21 04:50:05,688] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S2Nug_fastqc.html [2021-10-21 04:50:05,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_S2Nug_fastqc.html [2021-10-21 04:50:05,731] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_undetermined_fastqc.html [2021-10-21 04:50:05,732] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_undetermined_fastqc.html [2021-10-21 04:50:05,781] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G12Tak_fastqc.html [2021-10-21 04:50:05,783] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWL3DRXY_n01_G12Tak_fastqc.html [2021-10-21 04:50:06,112] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-21 04:50:06,114] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-21 04:50:06,123] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-21 04:50:06,133] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-21 04:50:06,141] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2021-10-21 04:50:06,148] multiqc [DEBUG ] No samples found: conpair [2021-10-21 04:50:06,154] multiqc [DEBUG ] No samples found: peddy [2021-10-21 04:50:06,162] multiqc [DEBUG ] No samples found: somalier [2021-10-21 04:50:06,166] multiqc [DEBUG ] No samples found: methylQA [2021-10-21 04:50:06,179] multiqc [DEBUG ] No samples found: mosdepth [2021-10-21 04:50:06,183] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-21 04:50:06,188] multiqc [DEBUG ] No samples found: qualimap [2021-10-21 04:50:06,194] multiqc [DEBUG ] No samples found: preseq [2021-10-21 04:50:06,200] multiqc [DEBUG ] No samples found: quast [2021-10-21 04:50:06,207] multiqc [DEBUG ] No samples found: qorts [2021-10-21 04:50:06,212] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-21 04:50:06,217] multiqc [DEBUG ] No samples found: rockhopper [2021-10-21 04:50:06,223] multiqc [DEBUG ] No samples found: rsem [2021-10-21 04:50:06,238] multiqc [DEBUG ] No samples found: rseqc [2021-10-21 04:50:06,244] multiqc [DEBUG ] No samples found: busco [2021-10-21 04:50:06,249] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-21 04:50:06,254] multiqc [DEBUG ] No samples found: disambiguate [2021-10-21 04:50:06,259] multiqc [DEBUG ] No samples found: supernova [2021-10-21 04:50:06,275] multiqc [DEBUG ] No samples found: deeptools [2021-10-21 04:50:06,281] multiqc [DEBUG ] No samples found: sargasso [2021-10-21 04:50:06,287] multiqc [DEBUG ] No samples found: verifybamid [2021-10-21 04:50:06,292] multiqc [DEBUG ] No samples found: mirtrace [2021-10-21 04:50:06,296] multiqc [DEBUG ] No samples found: happy [2021-10-21 04:50:06,302] multiqc [DEBUG ] No samples found: mirtop [2021-10-21 04:50:06,310] multiqc [DEBUG ] No samples found: homer [2021-10-21 04:50:06,315] multiqc [DEBUG ] No samples found: macs2 [2021-10-21 04:50:06,320] multiqc [DEBUG ] No samples found: theta2 [2021-10-21 04:50:06,326] multiqc [DEBUG ] No samples found: snpeff [2021-10-21 04:50:06,336] multiqc [DEBUG ] No samples found: gatk [2021-10-21 04:50:06,342] multiqc [DEBUG ] No samples found: htseq [2021-10-21 04:50:06,349] multiqc [DEBUG ] No samples found: bcftools [2021-10-21 04:50:06,353] multiqc [DEBUG ] No samples found: featureCounts [2021-10-21 04:50:06,360] multiqc [DEBUG ] No samples found: fgbio [2021-10-21 04:50:06,376] multiqc [DEBUG ] No samples found: dragen [2021-10-21 04:50:06,382] multiqc [DEBUG ] No samples found: dedup [2021-10-21 04:50:06,386] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-21 04:50:06,413] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-21 04:50:06,425] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-21 04:50:06,427] multiqc [DEBUG ] No samples found: picard [2021-10-21 04:50:06,433] multiqc [DEBUG ] No samples found: prokka [2021-10-21 04:50:06,438] multiqc [DEBUG ] No samples found: samblaster [2021-10-21 04:50:06,455] multiqc [DEBUG ] No samples found: samtools [2021-10-21 04:50:06,461] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-21 04:50:06,467] multiqc [DEBUG ] No samples found: bamtools [2021-10-21 04:50:06,471] multiqc [DEBUG ] No samples found: jellyfish [2021-10-21 04:50:06,486] multiqc [DEBUG ] No samples found: vcftools [2021-10-21 04:50:06,491] multiqc [DEBUG ] No samples found: longranger [2021-10-21 04:50:06,497] multiqc [DEBUG ] No samples found: stacks [2021-10-21 04:50:06,504] multiqc [DEBUG ] No samples found: varscan2 [2021-10-21 04:50:06,527] multiqc [DEBUG ] No samples found: bbmap [2021-10-21 04:50:06,534] multiqc [DEBUG ] No samples found: bismark [2021-10-21 04:50:06,542] multiqc [DEBUG ] No samples found: biscuit [2021-10-21 04:50:06,550] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-21 04:50:06,557] multiqc [DEBUG ] No samples found: hicup [2021-10-21 04:50:06,564] multiqc [DEBUG ] No samples found: hicpro [2021-10-21 04:50:06,568] multiqc [DEBUG ] No samples found: salmon [2021-10-21 04:50:06,574] multiqc [DEBUG ] No samples found: kallisto [2021-10-21 04:50:06,581] multiqc [DEBUG ] No samples found: slamdunk [2021-10-21 04:50:06,588] multiqc [DEBUG ] No samples found: star [2021-10-21 04:50:06,594] multiqc [DEBUG ] No samples found: hisat2 [2021-10-21 04:50:06,601] multiqc [DEBUG ] No samples found: tophat [2021-10-21 04:50:06,606] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-21 04:50:06,614] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-21 04:50:06,621] multiqc [DEBUG ] No samples found: snpsplit [2021-10-21 04:50:06,627] multiqc [DEBUG ] No samples found: kat [2021-10-21 04:50:06,633] multiqc [DEBUG ] No samples found: leehom [2021-10-21 04:50:06,639] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-21 04:50:06,644] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-21 04:50:06,650] multiqc [DEBUG ] No samples found: cutadapt [2021-10-21 04:50:06,655] multiqc [DEBUG ] No samples found: flexbar [2021-10-21 04:50:06,662] multiqc [DEBUG ] No samples found: kaiju [2021-10-21 04:50:06,668] multiqc [DEBUG ] No samples found: kraken [2021-10-21 04:50:06,674] multiqc [DEBUG ] No samples found: malt [2021-10-21 04:50:06,679] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-21 04:50:06,684] multiqc [DEBUG ] No samples found: sickle [2021-10-21 04:50:06,689] multiqc [DEBUG ] No samples found: skewer [2021-10-21 04:50:06,694] multiqc [DEBUG ] No samples found: sortmerna [2021-10-21 04:50:06,700] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-21 04:50:06,706] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-21 04:50:06,711] multiqc [DEBUG ] No samples found: afterqc [2021-10-21 04:50:06,718] multiqc [DEBUG ] No samples found: fastp [2021-10-21 04:50:07,703] multiqc.modules.fastqc.fastqc [INFO ] Found 17 reports [2021-10-21 04:50:07,934] multiqc [DEBUG ] No samples found: pycoqc [2021-10-21 04:50:07,940] multiqc [DEBUG ] No samples found: minionqc [2021-10-21 04:50:07,945] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-21 04:50:07,950] multiqc [DEBUG ] No samples found: clusterflow [2021-10-21 04:50:07,956] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-21 04:50:07,962] multiqc [DEBUG ] No samples found: interop [2021-10-21 04:50:07,968] multiqc [DEBUG ] No samples found: ivar [2021-10-21 04:50:07,974] multiqc [DEBUG ] No samples found: flash [2021-10-21 04:50:07,980] multiqc [DEBUG ] No samples found: seqyclean [2021-10-21 04:50:07,980] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-10-21 04:50:07,980] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-21 04:50:07,980] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-21 04:50:07,980] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-21 04:50:08,000] multiqc [INFO ] Compressing plot data [2021-10-21 04:50:08,321] multiqc [INFO ] Report : multiqc_report.html [2021-10-21 04:50:08,321] multiqc [INFO ] Data : multiqc_data [2021-10-21 04:50:08,321] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11075813/tmpybdfu16i/multiqc_data' to '/scratch/gencore/logs/html/HJWL3DRXY/merged/multiqc_data' [2021-10-21 04:50:08,477] multiqc [INFO ] MultiQC complete