[2021-11-18 07:01:42,012] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-18 07:01:42,012] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-18 07:01:42,012] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-18 07:01:42,013] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-18 07:01:42,013] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-18 07:01:42,014] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-K4F74/1 [2021-11-18 07:01:43,299] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-18 07:01:43,299] multiqc [INFO ] This is MultiQC v1.9 [2021-11-18 07:01:43,299] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-K4F74/1 [2021-11-18 07:01:43,299] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-K4F74/1 [2021-11-18 07:01:43,299] multiqc [INFO ] Template : default [2021-11-18 07:01:43,299] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-18 07:01:43,299] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-K4F74/1 [2021-11-18 07:01:43,300] 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 [2021-11-18 07:01:43,300] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12108782/tmp1mdjwyv4 [2021-11-18 07:01:43,485] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K4F74_l01_n01_BRCA_Library_Plasmid_fastqc.html [2021-11-18 07:01:43,487] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K4F74_l01_n01_BRCA_Library_Plasmid_fastqc.html [2021-11-18 07:01:43,543] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K4F74_l01_n01_undetermined_fastqc.html [2021-11-18 07:01:43,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K4F74_l01_n01_undetermined_fastqc.html [2021-11-18 07:01:43,864] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 07:01:43,866] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 07:01:43,873] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2021-11-18 07:01:43,876] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 2 samples (table) [2021-11-18 07:01:43,877] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-18 07:01:43,886] multiqc [DEBUG ] No samples found: conpair [2021-11-18 07:01:43,892] multiqc [DEBUG ] No samples found: peddy [2021-11-18 07:01:43,900] multiqc [DEBUG ] No samples found: somalier [2021-11-18 07:01:43,909] multiqc [DEBUG ] No samples found: methylQA [2021-11-18 07:01:43,925] multiqc [DEBUG ] No samples found: mosdepth [2021-11-18 07:01:43,931] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-18 07:01:43,936] multiqc [DEBUG ] No samples found: qualimap [2021-11-18 07:01:43,943] multiqc [DEBUG ] No samples found: preseq [2021-11-18 07:01:43,952] multiqc [DEBUG ] No samples found: quast [2021-11-18 07:01:43,959] multiqc [DEBUG ] No samples found: qorts [2021-11-18 07:01:43,967] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-18 07:01:43,976] multiqc [DEBUG ] No samples found: rockhopper [2021-11-18 07:01:43,982] multiqc [DEBUG ] No samples found: rsem [2021-11-18 07:01:44,000] multiqc [DEBUG ] No samples found: rseqc [2021-11-18 07:01:44,008] multiqc [DEBUG ] No samples found: busco [2021-11-18 07:01:44,017] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-18 07:01:44,023] multiqc [DEBUG ] No samples found: disambiguate [2021-11-18 07:01:44,032] multiqc [DEBUG ] No samples found: supernova [2021-11-18 07:01:44,056] multiqc [DEBUG ] No samples found: deeptools [2021-11-18 07:01:44,065] multiqc [DEBUG ] No samples found: sargasso [2021-11-18 07:01:44,073] multiqc [DEBUG ] No samples found: verifybamid [2021-11-18 07:01:44,081] multiqc [DEBUG ] No samples found: mirtrace [2021-11-18 07:01:44,090] multiqc [DEBUG ] No samples found: happy [2021-11-18 07:01:44,096] multiqc [DEBUG ] No samples found: mirtop [2021-11-18 07:01:44,107] multiqc [DEBUG ] No samples found: homer [2021-11-18 07:01:44,117] multiqc [DEBUG ] No samples found: macs2 [2021-11-18 07:01:44,124] multiqc [DEBUG ] No samples found: theta2 [2021-11-18 07:01:44,134] multiqc [DEBUG ] No samples found: snpeff [2021-11-18 07:01:44,148] multiqc [DEBUG ] No samples found: gatk [2021-11-18 07:01:44,155] multiqc [DEBUG ] No samples found: htseq [2021-11-18 07:01:44,162] multiqc [DEBUG ] No samples found: bcftools [2021-11-18 07:01:44,167] multiqc [DEBUG ] No samples found: featureCounts [2021-11-18 07:01:44,178] multiqc [DEBUG ] No samples found: fgbio [2021-11-18 07:01:44,208] multiqc [DEBUG ] No samples found: dragen [2021-11-18 07:01:44,217] multiqc [DEBUG ] No samples found: dedup [2021-11-18 07:01:44,223] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-18 07:01:44,249] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-18 07:01:44,259] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-18 07:01:44,261] multiqc [DEBUG ] No samples found: picard [2021-11-18 07:01:44,272] multiqc [DEBUG ] No samples found: prokka [2021-11-18 07:01:44,280] multiqc [DEBUG ] No samples found: samblaster [2021-11-18 07:01:44,291] multiqc [DEBUG ] No samples found: samtools [2021-11-18 07:01:44,299] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-18 07:01:44,306] multiqc [DEBUG ] No samples found: bamtools [2021-11-18 07:01:44,315] multiqc [DEBUG ] No samples found: jellyfish [2021-11-18 07:01:44,328] multiqc [DEBUG ] No samples found: vcftools [2021-11-18 07:01:44,335] multiqc [DEBUG ] No samples found: longranger [2021-11-18 07:01:44,344] multiqc [DEBUG ] No samples found: stacks [2021-11-18 07:01:44,354] multiqc [DEBUG ] No samples found: varscan2 [2021-11-18 07:01:44,379] multiqc [DEBUG ] No samples found: bbmap [2021-11-18 07:01:44,389] multiqc [DEBUG ] No samples found: bismark [2021-11-18 07:01:44,399] multiqc [DEBUG ] No samples found: biscuit [2021-11-18 07:01:44,409] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-18 07:01:44,416] multiqc [DEBUG ] No samples found: hicup [2021-11-18 07:01:44,424] multiqc [DEBUG ] No samples found: hicpro [2021-11-18 07:01:44,432] multiqc [DEBUG ] No samples found: salmon [2021-11-18 07:01:44,441] multiqc [DEBUG ] No samples found: kallisto [2021-11-18 07:01:44,450] multiqc [DEBUG ] No samples found: slamdunk [2021-11-18 07:01:44,456] multiqc [DEBUG ] No samples found: star [2021-11-18 07:01:44,462] multiqc [DEBUG ] No samples found: hisat2 [2021-11-18 07:01:44,472] multiqc [DEBUG ] No samples found: tophat [2021-11-18 07:01:44,482] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-18 07:01:44,489] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-18 07:01:44,498] multiqc [DEBUG ] No samples found: snpsplit [2021-11-18 07:01:44,506] multiqc [DEBUG ] No samples found: kat [2021-11-18 07:01:44,513] multiqc [DEBUG ] No samples found: leehom [2021-11-18 07:01:44,522] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-18 07:01:44,532] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-18 07:01:44,539] multiqc [DEBUG ] No samples found: cutadapt [2021-11-18 07:01:44,548] multiqc [DEBUG ] No samples found: flexbar [2021-11-18 07:01:44,555] multiqc [DEBUG ] No samples found: kaiju [2021-11-18 07:01:44,564] multiqc [DEBUG ] No samples found: kraken [2021-11-18 07:01:44,571] multiqc [DEBUG ] No samples found: malt [2021-11-18 07:01:44,577] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-18 07:01:44,586] multiqc [DEBUG ] No samples found: sickle [2021-11-18 07:01:44,596] multiqc [DEBUG ] No samples found: skewer [2021-11-18 07:01:44,605] multiqc [DEBUG ] No samples found: sortmerna [2021-11-18 07:01:44,614] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-18 07:01:44,622] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-18 07:01:44,628] multiqc [DEBUG ] No samples found: afterqc [2021-11-18 07:01:44,633] multiqc [DEBUG ] No samples found: fastp [2021-11-18 07:01:44,651] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2021-11-18 07:01:44,651] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-K4F74_l01_n01_undetermined' [2021-11-18 07:01:44,700] multiqc [DEBUG ] No samples found: pycoqc [2021-11-18 07:01:44,714] multiqc [DEBUG ] No samples found: minionqc [2021-11-18 07:01:44,723] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-18 07:01:44,730] multiqc [DEBUG ] No samples found: clusterflow [2021-11-18 07:01:44,737] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-18 07:01:44,745] multiqc [DEBUG ] No samples found: interop [2021-11-18 07:01:44,752] multiqc [DEBUG ] No samples found: ivar [2021-11-18 07:01:44,759] multiqc [DEBUG ] No samples found: flash [2021-11-18 07:01:44,767] multiqc [DEBUG ] No samples found: seqyclean [2021-11-18 07:01:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-11-18 07:01:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-11-18 07:01:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-11-18 07:01:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-18 07:01:44,771] multiqc [INFO ] Compressing plot data [2021-11-18 07:01:44,804] multiqc [INFO ] Report : multiqc_report.html [2021-11-18 07:01:44,804] multiqc [INFO ] Data : multiqc_data [2021-11-18 07:01:44,804] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12108782/tmp1mdjwyv4/multiqc_data' to '/scratch/gencore/logs/html/000000000-K4F74/1/multiqc_data' [2021-11-18 07:01:44,922] multiqc [INFO ] MultiQC complete