[2021-07-21 15:41:42,672] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-07-21 15:41:42,672] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-07-21 15:41:42,672] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-07-21 15:41:42,673] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-07-21 15:41:42,673] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-07-21 15:41:42,673] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HH5MJDRXY/2 [2021-07-21 15:41:43,950] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-07-21 15:41:43,950] multiqc [INFO ] This is MultiQC v1.9 [2021-07-21 15:41:43,950] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HH5MJDRXY/2 [2021-07-21 15:41:43,950] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HH5MJDRXY/2 [2021-07-21 15:41:43,950] multiqc [INFO ] Template : default [2021-07-21 15:41:43,950] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-07-21 15:41:43,950] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HH5MJDRXY/2 [2021-07-21 15:41:43,951] 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 [2021-07-21 15:41:43,951] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8833785/tmp69hu3r3h [2021-07-21 15:41:44,047] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_F09_T18_fastqc.html [2021-07-21 15:41:44,050] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_F09_T18_fastqc.html [2021-07-21 15:41:44,121] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_G06_T18_fastqc.html [2021-07-21 15:41:44,123] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_G06_T18_fastqc.html [2021-07-21 15:41:44,193] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_C10_T18_fastqc.html [2021-07-21 15:41:44,195] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_C10_T18_fastqc.html [2021-07-21 15:41:44,266] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_D09_T18_fastqc.html [2021-07-21 15:41:44,268] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_D09_T18_fastqc.html [2021-07-21 15:41:44,336] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_B09_T18_fastqc.html [2021-07-21 15:41:44,337] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_B09_T18_fastqc.html [2021-07-21 15:41:44,407] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_H09_T18_fastqc.html [2021-07-21 15:41:44,409] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_H09_T18_fastqc.html [2021-07-21 15:41:44,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_G06_T18_fastqc.html [2021-07-21 15:41:44,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_G06_T18_fastqc.html [2021-07-21 15:41:44,552] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_F09_T18_fastqc.html [2021-07-21 15:41:44,554] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_F09_T18_fastqc.html [2021-07-21 15:41:44,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_D09_T18_fastqc.html [2021-07-21 15:41:44,626] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_D09_T18_fastqc.html [2021-07-21 15:41:44,695] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_B09_T18_fastqc.html [2021-07-21 15:41:44,697] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_B09_T18_fastqc.html [2021-07-21 15:41:44,767] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_E10_T18_fastqc.html [2021-07-21 15:41:44,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_E10_T18_fastqc.html [2021-07-21 15:41:44,837] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_C10_T18_fastqc.html [2021-07-21 15:41:44,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_C10_T18_fastqc.html [2021-07-21 15:41:44,908] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_E06_T18_fastqc.html [2021-07-21 15:41:44,910] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_E06_T18_fastqc.html [2021-07-21 15:41:44,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_undetermined_fastqc.html [2021-07-21 15:41:44,982] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_undetermined_fastqc.html [2021-07-21 15:41:45,036] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_C06_T18_fastqc.html [2021-07-21 15:41:45,038] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_C06_T18_fastqc.html [2021-07-21 15:41:45,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_H09_T18_fastqc.html [2021-07-21 15:41:45,107] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_H09_T18_fastqc.html [2021-07-21 15:41:45,177] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_A10_T18_fastqc.html [2021-07-21 15:41:45,178] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_A10_T18_fastqc.html [2021-07-21 15:41:45,248] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_undetermined_fastqc.html [2021-07-21 15:41:45,250] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_undetermined_fastqc.html [2021-07-21 15:41:45,304] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_A10_T18_fastqc.html [2021-07-21 15:41:45,306] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_A10_T18_fastqc.html [2021-07-21 15:41:45,373] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_E10_T18_fastqc.html [2021-07-21 15:41:45,374] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_E10_T18_fastqc.html [2021-07-21 15:41:45,443] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_C06_T18_fastqc.html [2021-07-21 15:41:45,445] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n02_Fluc_bc_C06_T18_fastqc.html [2021-07-21 15:41:45,512] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_E06_T18_fastqc.html [2021-07-21 15:41:45,514] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH5MJDRXY_l02_n01_Fluc_bc_E06_T18_fastqc.html [2021-07-21 15:41:45,813] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-21 15:41:45,814] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-21 15:41:45,824] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 11 samples (table) [2021-07-21 15:41:45,826] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-07-21 15:41:45,835] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-07-21 15:41:45,838] multiqc [DEBUG ] No samples found: conpair [2021-07-21 15:41:45,841] multiqc [DEBUG ] No samples found: peddy [2021-07-21 15:41:45,844] multiqc [DEBUG ] No samples found: somalier [2021-07-21 15:41:45,847] multiqc [DEBUG ] No samples found: methylQA [2021-07-21 15:41:45,850] multiqc [DEBUG ] No samples found: mosdepth [2021-07-21 15:41:45,853] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-07-21 15:41:45,855] multiqc [DEBUG ] No samples found: qualimap [2021-07-21 15:41:45,858] multiqc [DEBUG ] No samples found: preseq [2021-07-21 15:41:45,861] multiqc [DEBUG ] No samples found: quast [2021-07-21 15:41:45,863] multiqc [DEBUG ] No samples found: qorts [2021-07-21 15:41:45,866] multiqc [DEBUG ] No samples found: rna_seqc [2021-07-21 15:41:45,869] multiqc [DEBUG ] No samples found: rockhopper [2021-07-21 15:41:45,871] multiqc [DEBUG ] No samples found: rsem [2021-07-21 15:41:45,876] multiqc [DEBUG ] No samples found: rseqc [2021-07-21 15:41:45,878] multiqc [DEBUG ] No samples found: busco [2021-07-21 15:41:45,881] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-07-21 15:41:45,884] multiqc [DEBUG ] No samples found: disambiguate [2021-07-21 15:41:45,887] multiqc [DEBUG ] No samples found: supernova [2021-07-21 15:41:45,891] multiqc [DEBUG ] No samples found: deeptools [2021-07-21 15:41:45,894] multiqc [DEBUG ] No samples found: sargasso [2021-07-21 15:41:45,896] multiqc [DEBUG ] No samples found: verifybamid [2021-07-21 15:41:45,899] multiqc [DEBUG ] No samples found: mirtrace [2021-07-21 15:41:45,902] multiqc [DEBUG ] No samples found: happy [2021-07-21 15:41:45,904] multiqc [DEBUG ] No samples found: mirtop [2021-07-21 15:41:45,908] multiqc [DEBUG ] No samples found: homer [2021-07-21 15:41:45,910] multiqc [DEBUG ] No samples found: macs2 [2021-07-21 15:41:45,913] multiqc [DEBUG ] No samples found: theta2 [2021-07-21 15:41:45,916] multiqc [DEBUG ] No samples found: snpeff [2021-07-21 15:41:45,919] multiqc [DEBUG ] No samples found: gatk [2021-07-21 15:41:45,921] multiqc [DEBUG ] No samples found: htseq [2021-07-21 15:41:45,924] multiqc [DEBUG ] No samples found: bcftools [2021-07-21 15:41:45,927] multiqc [DEBUG ] No samples found: featureCounts [2021-07-21 15:41:45,930] multiqc [DEBUG ] No samples found: fgbio [2021-07-21 15:41:45,935] multiqc [DEBUG ] No samples found: dragen [2021-07-21 15:41:45,938] multiqc [DEBUG ] No samples found: dedup [2021-07-21 15:41:45,940] multiqc [DEBUG ] No samples found: damageprofiler [2021-07-21 15:41:45,947] multiqc [DEBUG ] No samples found: biobambam2 [2021-07-21 15:41:45,950] multiqc [DEBUG ] No samples found: mtnucratio [2021-07-21 15:41:45,952] multiqc [DEBUG ] No samples found: picard [2021-07-21 15:41:45,955] multiqc [DEBUG ] No samples found: prokka [2021-07-21 15:41:45,958] multiqc [DEBUG ] No samples found: samblaster [2021-07-21 15:41:45,961] multiqc [DEBUG ] No samples found: samtools [2021-07-21 15:41:45,964] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-07-21 15:41:45,967] multiqc [DEBUG ] No samples found: bamtools [2021-07-21 15:41:45,969] multiqc [DEBUG ] No samples found: jellyfish [2021-07-21 15:41:45,973] multiqc [DEBUG ] No samples found: vcftools [2021-07-21 15:41:45,975] multiqc [DEBUG ] No samples found: longranger [2021-07-21 15:41:45,978] multiqc [DEBUG ] No samples found: stacks [2021-07-21 15:41:45,981] multiqc [DEBUG ] No samples found: varscan2 [2021-07-21 15:41:45,986] multiqc [DEBUG ] No samples found: bbmap [2021-07-21 15:41:45,988] multiqc [DEBUG ] No samples found: bismark [2021-07-21 15:41:45,991] multiqc [DEBUG ] No samples found: biscuit [2021-07-21 15:41:45,994] multiqc [DEBUG ] No samples found: hicexplorer [2021-07-21 15:41:45,997] multiqc [DEBUG ] No samples found: hicup [2021-07-21 15:41:45,999] multiqc [DEBUG ] No samples found: hicpro [2021-07-21 15:41:46,002] multiqc [DEBUG ] No samples found: salmon [2021-07-21 15:41:46,004] multiqc [DEBUG ] No samples found: kallisto [2021-07-21 15:41:46,007] multiqc [DEBUG ] No samples found: slamdunk [2021-07-21 15:41:46,010] multiqc [DEBUG ] No samples found: star [2021-07-21 15:41:46,013] multiqc [DEBUG ] No samples found: hisat2 [2021-07-21 15:41:46,015] multiqc [DEBUG ] No samples found: tophat [2021-07-21 15:41:46,018] multiqc [DEBUG ] No samples found: bowtie2 [2021-07-21 15:41:46,021] multiqc [DEBUG ] No samples found: bowtie1 [2021-07-21 15:41:46,023] multiqc [DEBUG ] No samples found: snpsplit [2021-07-21 15:41:46,026] multiqc [DEBUG ] No samples found: kat [2021-07-21 15:41:46,028] multiqc [DEBUG ] No samples found: leehom [2021-07-21 15:41:46,031] multiqc [DEBUG ] No samples found: adapterRemoval [2021-07-21 15:41:46,034] multiqc [DEBUG ] No samples found: clipandmerge [2021-07-21 15:41:46,036] multiqc [DEBUG ] No samples found: cutadapt [2021-07-21 15:41:46,039] multiqc [DEBUG ] No samples found: flexbar [2021-07-21 15:41:46,042] multiqc [DEBUG ] No samples found: kaiju [2021-07-21 15:41:46,044] multiqc [DEBUG ] No samples found: kraken [2021-07-21 15:41:46,047] multiqc [DEBUG ] No samples found: malt [2021-07-21 15:41:46,050] multiqc [DEBUG ] No samples found: trimmomatic [2021-07-21 15:41:46,052] multiqc [DEBUG ] No samples found: sickle [2021-07-21 15:41:46,055] multiqc [DEBUG ] No samples found: skewer [2021-07-21 15:41:46,058] multiqc [DEBUG ] No samples found: sortmerna [2021-07-21 15:41:46,060] multiqc [DEBUG ] No samples found: biobloomtools [2021-07-21 15:41:46,063] multiqc [DEBUG ] No samples found: fastq_screen [2021-07-21 15:41:46,065] multiqc [DEBUG ] No samples found: afterqc [2021-07-21 15:41:46,068] multiqc [DEBUG ] No samples found: fastp [2021-07-21 15:41:46,787] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2021-07-21 15:41:47,100] multiqc [DEBUG ] No samples found: pycoqc [2021-07-21 15:41:47,103] multiqc [DEBUG ] No samples found: minionqc [2021-07-21 15:41:47,105] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-07-21 15:41:47,108] multiqc [DEBUG ] No samples found: clusterflow [2021-07-21 15:41:47,111] multiqc [DEBUG ] No samples found: bcl2fastq [2021-07-21 15:41:47,114] multiqc [DEBUG ] No samples found: interop [2021-07-21 15:41:47,116] multiqc [DEBUG ] No samples found: ivar [2021-07-21 15:41:47,119] multiqc [DEBUG ] No samples found: flash [2021-07-21 15:41:47,122] multiqc [DEBUG ] No samples found: seqyclean [2021-07-21 15:41:47,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-07-21 15:41:47,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2021-07-21 15:41:47,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-07-21 15:41:47,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-07-21 15:41:47,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-07-21 15:41:47,148] multiqc [INFO ] Compressing plot data [2021-07-21 15:41:47,502] multiqc [INFO ] Report : multiqc_report.html [2021-07-21 15:41:47,503] multiqc [INFO ] Data : multiqc_data [2021-07-21 15:41:47,503] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8833785/tmp69hu3r3h/multiqc_data' to '/scratch/gencore/logs/html/HH5MJDRXY/2/multiqc_data' [2021-07-21 15:41:47,596] multiqc [INFO ] MultiQC complete