[2022-09-28 23:43:01,658] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-09-28 23:43:01,659] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-09-28 23:43:01,659] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-28 23:43:01,660] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-09-28 23:43:01,660] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-09-28 23:43:01,660] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVH3HBGXM/merged [2022-09-28 23:43:02,095] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-09-28 23:43:02,095] multiqc [INFO ] This is MultiQC v1.9 [2022-09-28 23:43:02,095] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVH3HBGXM/merged [2022-09-28 23:43:02,095] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVH3HBGXM/merged [2022-09-28 23:43:02,095] multiqc [INFO ] Template : default [2022-09-28 23:43:02,095] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-09-28 23:43:02,095] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVH3HBGXM/merged [2022-09-28 23:43:02,096] 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 [2022-09-28 23:43:02,096] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-25527093/tmp9xh6ulbs [2022-09-28 23:43:02,211] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ05_fastqc.html [2022-09-28 23:43:02,214] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ05_fastqc.html [2022-09-28 23:43:02,255] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ08_fastqc.html [2022-09-28 23:43:02,257] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ08_fastqc.html [2022-09-28 23:43:02,296] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA60_fastqc.html [2022-09-28 23:43:02,298] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA60_fastqc.html [2022-09-28 23:43:02,335] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-28 23:43:02,336] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-28 23:43:02,460] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ12_fastqc.html [2022-09-28 23:43:02,462] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ12_fastqc.html [2022-09-28 23:43:02,500] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ10_fastqc.html [2022-09-28 23:43:02,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ10_fastqc.html [2022-09-28 23:43:02,541] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA62_fastqc.html [2022-09-28 23:43:02,543] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA62_fastqc.html [2022-09-28 23:43:02,583] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AKM426_fastqc.html [2022-09-28 23:43:02,585] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AKM426_fastqc.html [2022-09-28 23:43:02,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA65_fastqc.html [2022-09-28 23:43:02,625] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA65_fastqc.html [2022-09-28 23:43:02,663] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ09_fastqc.html [2022-09-28 23:43:02,665] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ09_fastqc.html [2022-09-28 23:43:02,705] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA66_fastqc.html [2022-09-28 23:43:02,707] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA66_fastqc.html [2022-09-28 23:43:02,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA61_fastqc.html [2022-09-28 23:43:02,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA61_fastqc.html [2022-09-28 23:43:02,789] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ06_fastqc.html [2022-09-28 23:43:02,791] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ06_fastqc.html [2022-09-28 23:43:02,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA63_fastqc.html [2022-09-28 23:43:02,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA63_fastqc.html [2022-09-28 23:43:02,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ11_fastqc.html [2022-09-28 23:43:02,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ11_fastqc.html [2022-09-28 23:43:02,915] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA64_fastqc.html [2022-09-28 23:43:02,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA64_fastqc.html [2022-09-28 23:43:02,955] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA67_fastqc.html [2022-09-28 23:43:02,957] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA67_fastqc.html [2022-09-28 23:43:02,995] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AKM427_fastqc.html [2022-09-28 23:43:02,997] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AKM427_fastqc.html [2022-09-28 23:43:03,037] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_undetermined_fastqc.html [2022-09-28 23:43:03,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_undetermined_fastqc.html [2022-09-28 23:43:03,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA59_fastqc.html [2022-09-28 23:43:03,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AA59_fastqc.html [2022-09-28 23:43:03,118] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ07_fastqc.html [2022-09-28 23:43:03,120] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_YZ07_fastqc.html [2022-09-28 23:43:03,160] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AKM428_fastqc.html [2022-09-28 23:43:03,162] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3HBGXM_n01_AKM428_fastqc.html [2022-09-28 23:43:03,508] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-28 23:43:03,510] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-28 23:43:03,529] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-09-28 23:43:03,531] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-09-28 23:43:03,541] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2022-09-28 23:43:03,550] multiqc [DEBUG ] No samples found: conpair [2022-09-28 23:43:03,559] multiqc [DEBUG ] No samples found: peddy [2022-09-28 23:43:03,569] multiqc [DEBUG ] No samples found: somalier [2022-09-28 23:43:03,580] multiqc [DEBUG ] No samples found: methylQA [2022-09-28 23:43:03,602] multiqc [DEBUG ] No samples found: mosdepth [2022-09-28 23:43:03,611] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-28 23:43:03,618] multiqc [DEBUG ] No samples found: qualimap [2022-09-28 23:43:03,629] multiqc [DEBUG ] No samples found: preseq [2022-09-28 23:43:03,640] multiqc [DEBUG ] No samples found: quast [2022-09-28 23:43:03,651] multiqc [DEBUG ] No samples found: qorts [2022-09-28 23:43:03,664] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-28 23:43:03,675] multiqc [DEBUG ] No samples found: rockhopper [2022-09-28 23:43:03,686] multiqc [DEBUG ] No samples found: rsem [2022-09-28 23:43:03,720] multiqc [DEBUG ] No samples found: rseqc [2022-09-28 23:43:03,729] multiqc [DEBUG ] No samples found: busco [2022-09-28 23:43:03,742] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-28 23:43:03,751] multiqc [DEBUG ] No samples found: disambiguate [2022-09-28 23:43:03,763] multiqc [DEBUG ] No samples found: supernova [2022-09-28 23:43:03,806] multiqc [DEBUG ] No samples found: deeptools [2022-09-28 23:43:03,817] multiqc [DEBUG ] No samples found: sargasso [2022-09-28 23:43:03,828] multiqc [DEBUG ] No samples found: verifybamid [2022-09-28 23:43:03,839] multiqc [DEBUG ] No samples found: mirtrace [2022-09-28 23:43:03,849] multiqc [DEBUG ] No samples found: happy [2022-09-28 23:43:03,861] multiqc [DEBUG ] No samples found: mirtop [2022-09-28 23:43:03,876] multiqc [DEBUG ] No samples found: homer [2022-09-28 23:43:03,887] multiqc [DEBUG ] No samples found: macs2 [2022-09-28 23:43:03,896] multiqc [DEBUG ] No samples found: theta2 [2022-09-28 23:43:03,906] multiqc [DEBUG ] No samples found: snpeff [2022-09-28 23:43:03,925] multiqc [DEBUG ] No samples found: gatk [2022-09-28 23:43:03,934] multiqc [DEBUG ] No samples found: htseq [2022-09-28 23:43:03,949] multiqc [DEBUG ] No samples found: bcftools [2022-09-28 23:43:03,957] multiqc [DEBUG ] No samples found: featureCounts [2022-09-28 23:43:03,973] multiqc [DEBUG ] No samples found: fgbio [2022-09-28 23:43:04,019] multiqc [DEBUG ] No samples found: dragen [2022-09-28 23:43:04,030] multiqc [DEBUG ] No samples found: dedup [2022-09-28 23:43:04,041] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-28 23:43:04,072] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-28 23:43:04,080] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-28 23:43:04,082] multiqc [DEBUG ] No samples found: picard [2022-09-28 23:43:04,093] multiqc [DEBUG ] No samples found: prokka [2022-09-28 23:43:04,103] multiqc [DEBUG ] No samples found: samblaster [2022-09-28 23:43:04,116] multiqc [DEBUG ] No samples found: samtools [2022-09-28 23:43:04,128] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-28 23:43:04,141] multiqc [DEBUG ] No samples found: bamtools [2022-09-28 23:43:04,150] multiqc [DEBUG ] No samples found: jellyfish [2022-09-28 23:43:04,167] multiqc [DEBUG ] No samples found: vcftools [2022-09-28 23:43:04,181] multiqc [DEBUG ] No samples found: longranger [2022-09-28 23:43:04,194] multiqc [DEBUG ] No samples found: stacks [2022-09-28 23:43:04,208] multiqc [DEBUG ] No samples found: varscan2 [2022-09-28 23:43:04,254] multiqc [DEBUG ] No samples found: bbmap [2022-09-28 23:43:04,270] multiqc [DEBUG ] No samples found: bismark [2022-09-28 23:43:04,281] multiqc [DEBUG ] No samples found: biscuit [2022-09-28 23:43:04,293] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-28 23:43:04,303] multiqc [DEBUG ] No samples found: hicup [2022-09-28 23:43:04,313] multiqc [DEBUG ] No samples found: hicpro [2022-09-28 23:43:04,323] multiqc [DEBUG ] No samples found: salmon [2022-09-28 23:43:04,333] multiqc [DEBUG ] No samples found: kallisto [2022-09-28 23:43:04,344] multiqc [DEBUG ] No samples found: slamdunk [2022-09-28 23:43:04,349] multiqc [DEBUG ] No samples found: star [2022-09-28 23:43:04,361] multiqc [DEBUG ] No samples found: hisat2 [2022-09-28 23:43:04,372] multiqc [DEBUG ] No samples found: tophat [2022-09-28 23:43:04,383] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-28 23:43:04,396] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-28 23:43:04,406] multiqc [DEBUG ] No samples found: snpsplit [2022-09-28 23:43:04,416] multiqc [DEBUG ] No samples found: kat [2022-09-28 23:43:04,424] multiqc [DEBUG ] No samples found: leehom [2022-09-28 23:43:04,436] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-28 23:43:04,445] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-28 23:43:04,455] multiqc [DEBUG ] No samples found: cutadapt [2022-09-28 23:43:04,464] multiqc [DEBUG ] No samples found: flexbar [2022-09-28 23:43:04,474] multiqc [DEBUG ] No samples found: kaiju [2022-09-28 23:43:04,484] multiqc [DEBUG ] No samples found: kraken [2022-09-28 23:43:04,494] multiqc [DEBUG ] No samples found: malt [2022-09-28 23:43:04,504] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-28 23:43:04,515] multiqc [DEBUG ] No samples found: sickle [2022-09-28 23:43:04,526] multiqc [DEBUG ] No samples found: skewer [2022-09-28 23:43:04,535] multiqc [DEBUG ] No samples found: sortmerna [2022-09-28 23:43:04,544] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-28 23:43:04,553] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-28 23:43:04,564] multiqc [DEBUG ] No samples found: afterqc [2022-09-28 23:43:04,568] multiqc [DEBUG ] No samples found: fastp [2022-09-28 23:43:06,082] multiqc.modules.fastqc.fastqc [INFO ] Found 21 reports [2022-09-28 23:43:06,581] multiqc [DEBUG ] No samples found: pycoqc [2022-09-28 23:43:06,592] multiqc [DEBUG ] No samples found: minionqc [2022-09-28 23:43:06,602] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-09-28 23:43:06,614] multiqc [DEBUG ] No samples found: clusterflow [2022-09-28 23:43:06,628] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-28 23:43:06,640] multiqc [DEBUG ] No samples found: interop [2022-09-28 23:43:06,653] multiqc [DEBUG ] No samples found: ivar [2022-09-28 23:43:06,664] multiqc [DEBUG ] No samples found: flash [2022-09-28 23:43:06,675] multiqc [DEBUG ] No samples found: seqyclean [2022-09-28 23:43:06,675] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-09-28 23:43:06,675] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-09-28 23:43:06,675] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-09-28 23:43:06,675] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-09-28 23:43:06,700] multiqc [INFO ] Compressing plot data [2022-09-28 23:43:07,079] multiqc [INFO ] Report : multiqc_report.html [2022-09-28 23:43:07,079] multiqc [INFO ] Data : multiqc_data [2022-09-28 23:43:07,079] multiqc [DEBUG ] Moving data file from '/state/partition1/job-25527093/tmp9xh6ulbs/multiqc_data' to '/scratch/gencore/logs/html/HVH3HBGXM/merged/multiqc_data' [2022-09-28 23:43:07,198] multiqc [INFO ] MultiQC complete