[2021-02-17 08:27:42,563] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-02-17 08:27:42,563] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-02-17 08:27:42,563] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-17 08:27:42,564] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-02-17 08:27:42,564] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-02-17 08:27:42,564] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVHT2DRXX/1 [2021-02-17 08:27:44,045] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-17 08:27:44,045] multiqc [INFO ] This is MultiQC v1.9 [2021-02-17 08:27:44,045] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVHT2DRXX/1 [2021-02-17 08:27:44,045] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVHT2DRXX/1 [2021-02-17 08:27:44,045] multiqc [INFO ] Template : default [2021-02-17 08:27:44,045] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-02-17 08:27:44,045] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVHT2DRXX/1 [2021-02-17 08:27:44,046] 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 [2021-02-17 08:27:44,046] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-2876432/tmpghkh4tbi [2021-02-17 08:27:44,148] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb379_fastqc.html [2021-02-17 08:27:44,151] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb379_fastqc.html [2021-02-17 08:27:44,194] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb389_fastqc.html [2021-02-17 08:27:44,195] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb389_fastqc.html [2021-02-17 08:27:44,234] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-02-17 08:27:44,235] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-02-17 08:27:44,323] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb400_fastqc.html [2021-02-17 08:27:44,325] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb400_fastqc.html [2021-02-17 08:27:44,363] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb383_fastqc.html [2021-02-17 08:27:44,365] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb383_fastqc.html [2021-02-17 08:27:44,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb384_fastqc.html [2021-02-17 08:27:44,407] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb384_fastqc.html [2021-02-17 08:27:44,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb399_fastqc.html [2021-02-17 08:27:44,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb399_fastqc.html [2021-02-17 08:27:44,488] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb390_fastqc.html [2021-02-17 08:27:44,489] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb390_fastqc.html [2021-02-17 08:27:44,530] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb387_fastqc.html [2021-02-17 08:27:44,531] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb387_fastqc.html [2021-02-17 08:27:44,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb403_fastqc.html [2021-02-17 08:27:44,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb403_fastqc.html [2021-02-17 08:27:44,611] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb386_fastqc.html [2021-02-17 08:27:44,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb386_fastqc.html [2021-02-17 08:27:44,653] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb385_fastqc.html [2021-02-17 08:27:44,655] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb385_fastqc.html [2021-02-17 08:27:44,695] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb401_fastqc.html [2021-02-17 08:27:44,697] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb401_fastqc.html [2021-02-17 08:27:44,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb388_fastqc.html [2021-02-17 08:27:44,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb388_fastqc.html [2021-02-17 08:27:44,778] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb402_fastqc.html [2021-02-17 08:27:44,779] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb402_fastqc.html [2021-02-17 08:27:44,821] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb395_fastqc.html [2021-02-17 08:27:44,823] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb395_fastqc.html [2021-02-17 08:27:44,862] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb380_fastqc.html [2021-02-17 08:27:44,863] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb380_fastqc.html [2021-02-17 08:27:44,903] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb382_fastqc.html [2021-02-17 08:27:44,905] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb382_fastqc.html [2021-02-17 08:27:44,945] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb381_fastqc.html [2021-02-17 08:27:44,946] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb381_fastqc.html [2021-02-17 08:27:44,986] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb398_fastqc.html [2021-02-17 08:27:44,988] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb398_fastqc.html [2021-02-17 08:27:45,026] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb404_fastqc.html [2021-02-17 08:27:45,028] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb404_fastqc.html [2021-02-17 08:27:45,066] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb397_fastqc.html [2021-02-17 08:27:45,068] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb397_fastqc.html [2021-02-17 08:27:45,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb396_fastqc.html [2021-02-17 08:27:45,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_mb396_fastqc.html [2021-02-17 08:27:45,150] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_undetermined_fastqc.html [2021-02-17 08:27:45,152] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l01_n01_undetermined_fastqc.html [2021-02-17 08:27:45,610] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-17 08:27:45,611] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-17 08:27:45,627] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-02-17 08:27:45,638] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 23 samples (table) [2021-02-17 08:27:45,640] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-02-17 08:27:45,645] multiqc [DEBUG ] No samples found: conpair [2021-02-17 08:27:45,650] multiqc [DEBUG ] No samples found: peddy [2021-02-17 08:27:45,654] multiqc [DEBUG ] No samples found: somalier [2021-02-17 08:27:45,659] multiqc [DEBUG ] No samples found: methylQA [2021-02-17 08:27:45,666] multiqc [DEBUG ] No samples found: mosdepth [2021-02-17 08:27:45,671] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-17 08:27:45,674] multiqc [DEBUG ] No samples found: qualimap [2021-02-17 08:27:45,679] multiqc [DEBUG ] No samples found: preseq [2021-02-17 08:27:45,683] multiqc [DEBUG ] No samples found: quast [2021-02-17 08:27:45,688] multiqc [DEBUG ] No samples found: qorts [2021-02-17 08:27:45,692] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-17 08:27:45,697] multiqc [DEBUG ] No samples found: rockhopper [2021-02-17 08:27:45,702] multiqc [DEBUG ] No samples found: rsem [2021-02-17 08:27:45,712] multiqc [DEBUG ] No samples found: rseqc [2021-02-17 08:27:45,716] multiqc [DEBUG ] No samples found: busco [2021-02-17 08:27:45,721] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-17 08:27:45,725] multiqc [DEBUG ] No samples found: disambiguate [2021-02-17 08:27:45,730] multiqc [DEBUG ] No samples found: supernova [2021-02-17 08:27:45,742] multiqc [DEBUG ] No samples found: deeptools [2021-02-17 08:27:45,747] multiqc [DEBUG ] No samples found: sargasso [2021-02-17 08:27:45,752] multiqc [DEBUG ] No samples found: verifybamid [2021-02-17 08:27:45,756] multiqc [DEBUG ] No samples found: mirtrace [2021-02-17 08:27:45,761] multiqc [DEBUG ] No samples found: happy [2021-02-17 08:27:45,765] multiqc [DEBUG ] No samples found: mirtop [2021-02-17 08:27:45,771] multiqc [DEBUG ] No samples found: homer [2021-02-17 08:27:45,776] multiqc [DEBUG ] No samples found: macs2 [2021-02-17 08:27:45,780] multiqc [DEBUG ] No samples found: theta2 [2021-02-17 08:27:45,785] multiqc [DEBUG ] No samples found: snpeff [2021-02-17 08:27:45,791] multiqc [DEBUG ] No samples found: gatk [2021-02-17 08:27:45,796] multiqc [DEBUG ] No samples found: htseq [2021-02-17 08:27:45,801] multiqc [DEBUG ] No samples found: bcftools [2021-02-17 08:27:45,805] multiqc [DEBUG ] No samples found: featureCounts [2021-02-17 08:27:45,812] multiqc [DEBUG ] No samples found: fgbio [2021-02-17 08:27:45,822] multiqc [DEBUG ] No samples found: dragen [2021-02-17 08:27:45,827] multiqc [DEBUG ] No samples found: dedup [2021-02-17 08:27:45,831] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-17 08:27:45,852] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-17 08:27:45,856] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-17 08:27:45,858] multiqc [DEBUG ] No samples found: picard [2021-02-17 08:27:45,862] multiqc [DEBUG ] No samples found: prokka [2021-02-17 08:27:45,866] multiqc [DEBUG ] No samples found: samblaster [2021-02-17 08:27:45,873] multiqc [DEBUG ] No samples found: samtools [2021-02-17 08:27:45,878] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-17 08:27:45,883] multiqc [DEBUG ] No samples found: bamtools [2021-02-17 08:27:45,887] multiqc [DEBUG ] No samples found: jellyfish [2021-02-17 08:27:45,894] multiqc [DEBUG ] No samples found: vcftools [2021-02-17 08:27:45,899] multiqc [DEBUG ] No samples found: longranger [2021-02-17 08:27:45,904] multiqc [DEBUG ] No samples found: stacks [2021-02-17 08:27:45,908] multiqc [DEBUG ] No samples found: varscan2 [2021-02-17 08:27:45,920] multiqc [DEBUG ] No samples found: bbmap [2021-02-17 08:27:45,925] multiqc [DEBUG ] No samples found: bismark [2021-02-17 08:27:45,930] multiqc [DEBUG ] No samples found: biscuit [2021-02-17 08:27:45,934] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-17 08:27:45,939] multiqc [DEBUG ] No samples found: hicup [2021-02-17 08:27:45,944] multiqc [DEBUG ] No samples found: hicpro [2021-02-17 08:27:45,948] multiqc [DEBUG ] No samples found: salmon [2021-02-17 08:27:45,952] multiqc [DEBUG ] No samples found: kallisto [2021-02-17 08:27:45,956] multiqc [DEBUG ] No samples found: slamdunk [2021-02-17 08:27:45,961] multiqc [DEBUG ] No samples found: star [2021-02-17 08:27:45,965] multiqc [DEBUG ] No samples found: hisat2 [2021-02-17 08:27:45,969] multiqc [DEBUG ] No samples found: tophat [2021-02-17 08:27:45,974] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-17 08:27:45,978] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-17 08:27:45,983] multiqc [DEBUG ] No samples found: snpsplit [2021-02-17 08:27:45,987] multiqc [DEBUG ] No samples found: kat [2021-02-17 08:27:45,991] multiqc [DEBUG ] No samples found: leehom [2021-02-17 08:27:45,996] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-17 08:27:46,000] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-17 08:27:46,004] multiqc [DEBUG ] No samples found: cutadapt [2021-02-17 08:27:46,008] multiqc [DEBUG ] No samples found: flexbar [2021-02-17 08:27:46,013] multiqc [DEBUG ] No samples found: kaiju [2021-02-17 08:27:46,018] multiqc [DEBUG ] No samples found: kraken [2021-02-17 08:27:46,022] multiqc [DEBUG ] No samples found: malt [2021-02-17 08:27:46,026] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-17 08:27:46,030] multiqc [DEBUG ] No samples found: sickle [2021-02-17 08:27:46,034] multiqc [DEBUG ] No samples found: skewer [2021-02-17 08:27:46,038] multiqc [DEBUG ] No samples found: sortmerna [2021-02-17 08:27:46,042] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-17 08:27:46,047] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-17 08:27:46,051] multiqc [DEBUG ] No samples found: afterqc [2021-02-17 08:27:46,056] multiqc [DEBUG ] No samples found: fastp [2021-02-17 08:27:47,521] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2021-02-17 08:27:47,856] multiqc [DEBUG ] No samples found: pycoqc [2021-02-17 08:27:47,860] multiqc [DEBUG ] No samples found: minionqc [2021-02-17 08:27:47,864] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-17 08:27:47,869] multiqc [DEBUG ] No samples found: clusterflow [2021-02-17 08:27:47,873] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-17 08:27:47,878] multiqc [DEBUG ] No samples found: interop [2021-02-17 08:27:47,882] multiqc [DEBUG ] No samples found: ivar [2021-02-17 08:27:47,886] multiqc [DEBUG ] No samples found: flash [2021-02-17 08:27:47,890] multiqc [DEBUG ] No samples found: seqyclean [2021-02-17 08:27:47,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-02-17 08:27:47,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-02-17 08:27:47,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-02-17 08:27:47,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-02-17 08:27:47,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-02-17 08:27:47,917] multiqc [INFO ] Compressing plot data [2021-02-17 08:27:48,344] multiqc [INFO ] Report : multiqc_report.html [2021-02-17 08:27:48,344] multiqc [INFO ] Data : multiqc_data [2021-02-17 08:27:48,344] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2876432/tmpghkh4tbi/multiqc_data' to '/scratch/gencore/logs/html/HVHT2DRXX/1/multiqc_data' [2021-02-17 08:27:48,467] multiqc [INFO ] MultiQC complete