[2021-05-21 23:14:41,805] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-05-21 23:14:41,805] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-05-21 23:14:41,805] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-05-21 23:14:41,806] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-05-21 23:14:41,806] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-05-21 23:14:41,806] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWMLHAFX2/merged [2021-05-21 23:14:43,183] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-05-21 23:14:43,183] multiqc [INFO ] This is MultiQC v1.9 [2021-05-21 23:14:43,183] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWMLHAFX2/merged [2021-05-21 23:14:43,183] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWMLHAFX2/merged [2021-05-21 23:14:43,183] multiqc [INFO ] Template : default [2021-05-21 23:14:43,183] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-05-21 23:14:43,183] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWMLHAFX2/merged [2021-05-21 23:14:43,183] 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 [2021-05-21 23:14:43,183] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7047050/tmpsu_u2sab [2021-05-21 23:14:43,293] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_BTPI3_824_fastqc.html [2021-05-21 23:14:43,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_BTPI3_824_fastqc.html [2021-05-21 23:14:43,341] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_BTPI3_824_fastqc.html [2021-05-21 23:14:43,343] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_BTPI3_824_fastqc.html [2021-05-21 23:14:43,385] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_BTPI3_823_fastqc.html [2021-05-21 23:14:43,387] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_BTPI3_823_fastqc.html [2021-05-21 23:14:43,430] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n02_undetermined_fastqc.html [2021-05-21 23:14:43,432] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n02_undetermined_fastqc.html [2021-05-21 23:14:43,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_BTPI3_820_fastqc.html [2021-05-21 23:14:43,470] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_BTPI3_820_fastqc.html [2021-05-21 23:14:43,514] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_CA015840_837_fastqc.html [2021-05-21 23:14:43,515] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_CA015840_837_fastqc.html [2021-05-21 23:14:43,559] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_CA015840_835_fastqc.html [2021-05-21 23:14:43,560] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_CA015840_835_fastqc.html [2021-05-21 23:14:43,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_CA015840_837_fastqc.html [2021-05-21 23:14:43,604] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_CA015840_837_fastqc.html [2021-05-21 23:14:43,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_BTPI3_823_fastqc.html [2021-05-21 23:14:43,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_BTPI3_823_fastqc.html [2021-05-21 23:14:43,692] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_CA015840_836_fastqc.html [2021-05-21 23:14:43,693] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_CA015840_836_fastqc.html [2021-05-21 23:14:43,735] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_CA015840_836_fastqc.html [2021-05-21 23:14:43,736] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n02_Ts_CA015840_836_fastqc.html [2021-05-21 23:14:43,778] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n01_undetermined_fastqc.html [2021-05-21 23:14:43,780] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n01_undetermined_fastqc.html [2021-05-21 23:14:43,818] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_BTPI3_820_fastqc.html [2021-05-21 23:14:43,820] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_BTPI3_820_fastqc.html [2021-05-21 23:14:43,862] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_CA015840_835_fastqc.html [2021-05-21 23:14:43,864] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMLHAFX2_n01_Ts_CA015840_835_fastqc.html [2021-05-21 23:14:44,365] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-21 23:14:44,367] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-21 23:14:44,374] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-05-21 23:14:44,384] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-05-21 23:14:44,388] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2021-05-21 23:14:44,393] multiqc [DEBUG ] No samples found: conpair [2021-05-21 23:14:44,399] multiqc [DEBUG ] No samples found: peddy [2021-05-21 23:14:44,407] multiqc [DEBUG ] No samples found: somalier [2021-05-21 23:14:44,411] multiqc [DEBUG ] No samples found: methylQA [2021-05-21 23:14:44,419] multiqc [DEBUG ] No samples found: mosdepth [2021-05-21 23:14:44,423] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-05-21 23:14:44,426] multiqc [DEBUG ] No samples found: qualimap [2021-05-21 23:14:44,432] multiqc [DEBUG ] No samples found: preseq [2021-05-21 23:14:44,439] multiqc [DEBUG ] No samples found: quast [2021-05-21 23:14:44,444] multiqc [DEBUG ] No samples found: qorts [2021-05-21 23:14:44,448] multiqc [DEBUG ] No samples found: rna_seqc [2021-05-21 23:14:44,453] multiqc [DEBUG ] No samples found: rockhopper [2021-05-21 23:14:44,458] multiqc [DEBUG ] No samples found: rsem [2021-05-21 23:14:44,470] multiqc [DEBUG ] No samples found: rseqc [2021-05-21 23:14:44,474] multiqc [DEBUG ] No samples found: busco [2021-05-21 23:14:44,481] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-05-21 23:14:44,485] multiqc [DEBUG ] No samples found: disambiguate [2021-05-21 23:14:44,490] multiqc [DEBUG ] No samples found: supernova [2021-05-21 23:14:44,505] multiqc [DEBUG ] No samples found: deeptools [2021-05-21 23:14:44,509] multiqc [DEBUG ] No samples found: sargasso [2021-05-21 23:14:44,514] multiqc [DEBUG ] No samples found: verifybamid [2021-05-21 23:14:44,519] multiqc [DEBUG ] No samples found: mirtrace [2021-05-21 23:14:44,523] multiqc [DEBUG ] No samples found: happy [2021-05-21 23:14:44,528] multiqc [DEBUG ] No samples found: mirtop [2021-05-21 23:14:44,534] multiqc [DEBUG ] No samples found: homer [2021-05-21 23:14:44,539] multiqc [DEBUG ] No samples found: macs2 [2021-05-21 23:14:44,544] multiqc [DEBUG ] No samples found: theta2 [2021-05-21 23:14:44,549] multiqc [DEBUG ] No samples found: snpeff [2021-05-21 23:14:44,557] multiqc [DEBUG ] No samples found: gatk [2021-05-21 23:14:44,561] multiqc [DEBUG ] No samples found: htseq [2021-05-21 23:14:44,568] multiqc [DEBUG ] No samples found: bcftools [2021-05-21 23:14:44,572] multiqc [DEBUG ] No samples found: featureCounts [2021-05-21 23:14:44,580] multiqc [DEBUG ] No samples found: fgbio [2021-05-21 23:14:44,595] multiqc [DEBUG ] No samples found: dragen [2021-05-21 23:14:44,601] multiqc [DEBUG ] No samples found: dedup [2021-05-21 23:14:44,607] multiqc [DEBUG ] No samples found: damageprofiler [2021-05-21 23:14:44,632] multiqc [DEBUG ] No samples found: biobambam2 [2021-05-21 23:14:44,636] multiqc [DEBUG ] No samples found: mtnucratio [2021-05-21 23:14:44,638] multiqc [DEBUG ] No samples found: picard [2021-05-21 23:14:44,643] multiqc [DEBUG ] No samples found: prokka [2021-05-21 23:14:44,647] multiqc [DEBUG ] No samples found: samblaster [2021-05-21 23:14:44,660] multiqc [DEBUG ] No samples found: samtools [2021-05-21 23:14:44,667] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-05-21 23:14:44,672] multiqc [DEBUG ] No samples found: bamtools [2021-05-21 23:14:44,676] multiqc [DEBUG ] No samples found: jellyfish [2021-05-21 23:14:44,686] multiqc [DEBUG ] No samples found: vcftools [2021-05-21 23:14:44,691] multiqc [DEBUG ] No samples found: longranger [2021-05-21 23:14:44,696] multiqc [DEBUG ] No samples found: stacks [2021-05-21 23:14:44,700] multiqc [DEBUG ] No samples found: varscan2 [2021-05-21 23:14:44,716] multiqc [DEBUG ] No samples found: bbmap [2021-05-21 23:14:44,720] multiqc [DEBUG ] No samples found: bismark [2021-05-21 23:14:44,726] multiqc [DEBUG ] No samples found: biscuit [2021-05-21 23:14:44,731] multiqc [DEBUG ] No samples found: hicexplorer [2021-05-21 23:14:44,735] multiqc [DEBUG ] No samples found: hicup [2021-05-21 23:14:44,740] multiqc [DEBUG ] No samples found: hicpro [2021-05-21 23:14:44,745] multiqc [DEBUG ] No samples found: salmon [2021-05-21 23:14:44,750] multiqc [DEBUG ] No samples found: kallisto [2021-05-21 23:14:44,754] multiqc [DEBUG ] No samples found: slamdunk [2021-05-21 23:14:44,759] multiqc [DEBUG ] No samples found: star [2021-05-21 23:14:44,764] multiqc [DEBUG ] No samples found: hisat2 [2021-05-21 23:14:44,768] multiqc [DEBUG ] No samples found: tophat [2021-05-21 23:14:44,773] multiqc [DEBUG ] No samples found: bowtie2 [2021-05-21 23:14:44,777] multiqc [DEBUG ] No samples found: bowtie1 [2021-05-21 23:14:44,783] multiqc [DEBUG ] No samples found: snpsplit [2021-05-21 23:14:44,788] multiqc [DEBUG ] No samples found: kat [2021-05-21 23:14:44,792] multiqc [DEBUG ] No samples found: leehom [2021-05-21 23:14:44,797] multiqc [DEBUG ] No samples found: adapterRemoval [2021-05-21 23:14:44,802] multiqc [DEBUG ] No samples found: clipandmerge [2021-05-21 23:14:44,806] multiqc [DEBUG ] No samples found: cutadapt [2021-05-21 23:14:44,810] multiqc [DEBUG ] No samples found: flexbar [2021-05-21 23:14:44,815] multiqc [DEBUG ] No samples found: kaiju [2021-05-21 23:14:44,819] multiqc [DEBUG ] No samples found: kraken [2021-05-21 23:14:44,824] multiqc [DEBUG ] No samples found: malt [2021-05-21 23:14:44,829] multiqc [DEBUG ] No samples found: trimmomatic [2021-05-21 23:14:44,834] multiqc [DEBUG ] No samples found: sickle [2021-05-21 23:14:44,838] multiqc [DEBUG ] No samples found: skewer [2021-05-21 23:14:44,843] multiqc [DEBUG ] No samples found: sortmerna [2021-05-21 23:14:44,847] multiqc [DEBUG ] No samples found: biobloomtools [2021-05-21 23:14:44,854] multiqc [DEBUG ] No samples found: fastq_screen [2021-05-21 23:14:44,859] multiqc [DEBUG ] No samples found: afterqc [2021-05-21 23:14:44,864] multiqc [DEBUG ] No samples found: fastp [2021-05-21 23:14:45,191] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2021-05-21 23:14:45,588] multiqc [DEBUG ] No samples found: pycoqc [2021-05-21 23:14:45,593] multiqc [DEBUG ] No samples found: minionqc [2021-05-21 23:14:45,599] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-05-21 23:14:45,604] multiqc [DEBUG ] No samples found: clusterflow [2021-05-21 23:14:45,609] multiqc [DEBUG ] No samples found: bcl2fastq [2021-05-21 23:14:45,615] multiqc [DEBUG ] No samples found: interop [2021-05-21 23:14:45,619] multiqc [DEBUG ] No samples found: ivar [2021-05-21 23:14:45,624] multiqc [DEBUG ] No samples found: flash [2021-05-21 23:14:45,629] multiqc [DEBUG ] No samples found: seqyclean [2021-05-21 23:14:45,629] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-05-21 23:14:45,629] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-05-21 23:14:45,629] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-05-21 23:14:45,629] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-05-21 23:14:45,646] multiqc [INFO ] Compressing plot data [2021-05-21 23:14:45,906] multiqc [INFO ] Report : multiqc_report.html [2021-05-21 23:14:45,906] multiqc [INFO ] Data : multiqc_data [2021-05-21 23:14:45,906] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7047050/tmpsu_u2sab/multiqc_data' to '/scratch/gencore/logs/html/HWMLHAFX2/merged/multiqc_data' [2021-05-21 23:14:46,038] multiqc [INFO ] MultiQC complete