[2022-11-04 06:29:05,673] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-04 06:29:05,673] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-04 06:29:05,673] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-04 06:29:05,674] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-04 06:29:05,674] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-04 06:29:05,674] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3THTBGXN/merged [2022-11-04 06:29:06,314] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-04 06:29:06,314] multiqc [INFO ] This is MultiQC v1.9 [2022-11-04 06:29:06,314] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3THTBGXN/merged [2022-11-04 06:29:06,314] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3THTBGXN/merged [2022-11-04 06:29:06,314] multiqc [INFO ] Template : default [2022-11-04 06:29:06,314] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-04 06:29:06,314] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3THTBGXN/merged [2022-11-04 06:29:06,315] 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 [2022-11-04 06:29:06,315] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26645105/tmpbjpu2cu4 [2022-11-04 06:29:06,427] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-5R-1_fastqc.html [2022-11-04 06:29:06,430] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-5R-1_fastqc.html [2022-11-04 06:29:06,470] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-04 06:29:06,471] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-04 06:29:06,570] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN5R-1_fastqc.html [2022-11-04 06:29:06,572] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN5R-1_fastqc.html [2022-11-04 06:29:06,611] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-5R-2_fastqc.html [2022-11-04 06:29:06,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-5R-2_fastqc.html [2022-11-04 06:29:06,650] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN255-1_fastqc.html [2022-11-04 06:29:06,652] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN255-1_fastqc.html [2022-11-04 06:29:06,691] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN162-2_fastqc.html [2022-11-04 06:29:06,693] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN162-2_fastqc.html [2022-11-04 06:29:06,732] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-1_fastqc.html [2022-11-04 06:29:06,734] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-1_fastqc.html [2022-11-04 06:29:06,772] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-1_fastqc.html [2022-11-04 06:29:06,774] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-1_fastqc.html [2022-11-04 06:29:06,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_undetermined_fastqc.html [2022-11-04 06:29:06,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_undetermined_fastqc.html [2022-11-04 06:29:06,852] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN255-1_fastqc.html [2022-11-04 06:29:06,854] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN255-1_fastqc.html [2022-11-04 06:29:06,893] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN162-1_fastqc.html [2022-11-04 06:29:06,894] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN162-1_fastqc.html [2022-11-04 06:29:06,933] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN162-1_fastqc.html [2022-11-04 06:29:06,935] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN162-1_fastqc.html [2022-11-04 06:29:06,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-2_fastqc.html [2022-11-04 06:29:06,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-2_fastqc.html [2022-11-04 06:29:07,013] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN5R-2_fastqc.html [2022-11-04 06:29:07,015] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN5R-2_fastqc.html [2022-11-04 06:29:07,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_undetermined_fastqc.html [2022-11-04 06:29:07,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_undetermined_fastqc.html [2022-11-04 06:29:07,098] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN5R-1_fastqc.html [2022-11-04 06:29:07,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN5R-1_fastqc.html [2022-11-04 06:29:07,141] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN162-2_fastqc.html [2022-11-04 06:29:07,143] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN162-2_fastqc.html [2022-11-04 06:29:07,182] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-5R-2_fastqc.html [2022-11-04 06:29:07,184] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-5R-2_fastqc.html [2022-11-04 06:29:07,221] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN255-2_fastqc.html [2022-11-04 06:29:07,222] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_MN255-2_fastqc.html [2022-11-04 06:29:07,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-2_fastqc.html [2022-11-04 06:29:07,264] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n01_581-2_fastqc.html [2022-11-04 06:29:07,301] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN255-2_fastqc.html [2022-11-04 06:29:07,303] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN255-2_fastqc.html [2022-11-04 06:29:07,342] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN5R-2_fastqc.html [2022-11-04 06:29:07,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_MN5R-2_fastqc.html [2022-11-04 06:29:07,383] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-5R-1_fastqc.html [2022-11-04 06:29:07,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3THTBGXN_n02_581-5R-1_fastqc.html [2022-11-04 06:29:07,715] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-04 06:29:07,717] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-04 06:29:07,728] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2022-11-04 06:29:07,730] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-04 06:29:07,739] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-04 06:29:07,744] multiqc [DEBUG ] No samples found: conpair [2022-11-04 06:29:07,749] multiqc [DEBUG ] No samples found: peddy [2022-11-04 06:29:07,754] multiqc [DEBUG ] No samples found: somalier [2022-11-04 06:29:07,759] multiqc [DEBUG ] No samples found: methylQA [2022-11-04 06:29:07,768] multiqc [DEBUG ] No samples found: mosdepth [2022-11-04 06:29:07,772] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-04 06:29:07,776] multiqc [DEBUG ] No samples found: qualimap [2022-11-04 06:29:07,781] multiqc [DEBUG ] No samples found: preseq [2022-11-04 06:29:07,786] multiqc [DEBUG ] No samples found: quast [2022-11-04 06:29:07,791] multiqc [DEBUG ] No samples found: qorts [2022-11-04 06:29:07,796] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-04 06:29:07,801] multiqc [DEBUG ] No samples found: rockhopper [2022-11-04 06:29:07,806] multiqc [DEBUG ] No samples found: rsem [2022-11-04 06:29:07,818] multiqc [DEBUG ] No samples found: rseqc [2022-11-04 06:29:07,822] multiqc [DEBUG ] No samples found: busco [2022-11-04 06:29:07,827] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-04 06:29:07,831] multiqc [DEBUG ] No samples found: disambiguate [2022-11-04 06:29:07,836] multiqc [DEBUG ] No samples found: supernova [2022-11-04 06:29:07,850] multiqc [DEBUG ] No samples found: deeptools [2022-11-04 06:29:07,855] multiqc [DEBUG ] No samples found: sargasso [2022-11-04 06:29:07,860] multiqc [DEBUG ] No samples found: verifybamid [2022-11-04 06:29:07,866] multiqc [DEBUG ] No samples found: mirtrace [2022-11-04 06:29:07,871] multiqc [DEBUG ] No samples found: happy [2022-11-04 06:29:07,876] multiqc [DEBUG ] No samples found: mirtop [2022-11-04 06:29:07,883] multiqc [DEBUG ] No samples found: homer [2022-11-04 06:29:07,888] multiqc [DEBUG ] No samples found: macs2 [2022-11-04 06:29:07,892] multiqc [DEBUG ] No samples found: theta2 [2022-11-04 06:29:07,897] multiqc [DEBUG ] No samples found: snpeff [2022-11-04 06:29:07,904] multiqc [DEBUG ] No samples found: gatk [2022-11-04 06:29:07,909] multiqc [DEBUG ] No samples found: htseq [2022-11-04 06:29:07,914] multiqc [DEBUG ] No samples found: bcftools [2022-11-04 06:29:07,919] multiqc [DEBUG ] No samples found: featureCounts [2022-11-04 06:29:07,926] multiqc [DEBUG ] No samples found: fgbio [2022-11-04 06:29:07,941] multiqc [DEBUG ] No samples found: dragen [2022-11-04 06:29:07,946] multiqc [DEBUG ] No samples found: dedup [2022-11-04 06:29:07,951] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-04 06:29:07,977] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-04 06:29:07,982] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-04 06:29:07,984] multiqc [DEBUG ] No samples found: picard [2022-11-04 06:29:07,989] multiqc [DEBUG ] No samples found: prokka [2022-11-04 06:29:07,993] multiqc [DEBUG ] No samples found: samblaster [2022-11-04 06:29:08,003] multiqc [DEBUG ] No samples found: samtools [2022-11-04 06:29:08,008] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-04 06:29:08,013] multiqc [DEBUG ] No samples found: bamtools [2022-11-04 06:29:08,017] multiqc [DEBUG ] No samples found: jellyfish [2022-11-04 06:29:08,025] multiqc [DEBUG ] No samples found: vcftools [2022-11-04 06:29:08,030] multiqc [DEBUG ] No samples found: longranger [2022-11-04 06:29:08,035] multiqc [DEBUG ] No samples found: stacks [2022-11-04 06:29:08,040] multiqc [DEBUG ] No samples found: varscan2 [2022-11-04 06:29:08,055] multiqc [DEBUG ] No samples found: bbmap [2022-11-04 06:29:08,060] multiqc [DEBUG ] No samples found: bismark [2022-11-04 06:29:08,066] multiqc [DEBUG ] No samples found: biscuit [2022-11-04 06:29:08,071] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-04 06:29:08,076] multiqc [DEBUG ] No samples found: hicup [2022-11-04 06:29:08,081] multiqc [DEBUG ] No samples found: hicpro [2022-11-04 06:29:08,085] multiqc [DEBUG ] No samples found: salmon [2022-11-04 06:29:08,090] multiqc [DEBUG ] No samples found: kallisto [2022-11-04 06:29:08,095] multiqc [DEBUG ] No samples found: slamdunk [2022-11-04 06:29:08,100] multiqc [DEBUG ] No samples found: star [2022-11-04 06:29:08,105] multiqc [DEBUG ] No samples found: hisat2 [2022-11-04 06:29:08,110] multiqc [DEBUG ] No samples found: tophat [2022-11-04 06:29:08,115] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-04 06:29:08,120] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-04 06:29:08,125] multiqc [DEBUG ] No samples found: snpsplit [2022-11-04 06:29:08,129] multiqc [DEBUG ] No samples found: kat [2022-11-04 06:29:08,134] multiqc [DEBUG ] No samples found: leehom [2022-11-04 06:29:08,139] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-04 06:29:08,143] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-04 06:29:08,148] multiqc [DEBUG ] No samples found: cutadapt [2022-11-04 06:29:08,153] multiqc [DEBUG ] No samples found: flexbar [2022-11-04 06:29:08,158] multiqc [DEBUG ] No samples found: kaiju [2022-11-04 06:29:08,163] multiqc [DEBUG ] No samples found: kraken [2022-11-04 06:29:08,168] multiqc [DEBUG ] No samples found: malt [2022-11-04 06:29:08,172] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-04 06:29:08,177] multiqc [DEBUG ] No samples found: sickle [2022-11-04 06:29:08,182] multiqc [DEBUG ] No samples found: skewer [2022-11-04 06:29:08,187] multiqc [DEBUG ] No samples found: sortmerna [2022-11-04 06:29:08,191] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-04 06:29:08,196] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-04 06:29:08,201] multiqc [DEBUG ] No samples found: afterqc [2022-11-04 06:29:08,206] multiqc [DEBUG ] No samples found: fastp [2022-11-04 06:29:09,708] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2022-11-04 06:29:10,177] multiqc [DEBUG ] No samples found: pycoqc [2022-11-04 06:29:10,182] multiqc [DEBUG ] No samples found: minionqc [2022-11-04 06:29:10,186] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-04 06:29:10,191] multiqc [DEBUG ] No samples found: clusterflow [2022-11-04 06:29:10,196] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-04 06:29:10,201] multiqc [DEBUG ] No samples found: interop [2022-11-04 06:29:10,206] multiqc [DEBUG ] No samples found: ivar [2022-11-04 06:29:10,210] multiqc [DEBUG ] No samples found: flash [2022-11-04 06:29:10,215] multiqc [DEBUG ] No samples found: seqyclean [2022-11-04 06:29:10,215] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-04 06:29:10,215] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-04 06:29:10,215] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-04 06:29:10,215] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-04 06:29:10,241] multiqc [INFO ] Compressing plot data [2022-11-04 06:29:10,634] multiqc [INFO ] Report : multiqc_report.html [2022-11-04 06:29:10,634] multiqc [INFO ] Data : multiqc_data [2022-11-04 06:29:10,635] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26645105/tmpbjpu2cu4/multiqc_data' to '/scratch/gencore/logs/html/H3THTBGXN/merged/multiqc_data' [2022-11-04 06:29:10,763] multiqc [INFO ] MultiQC complete