[2022-05-02 20:24:58,576] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-02 20:24:58,577] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-02 20:24:58,577] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-02 20:24:58,577] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-02 20:24:58,578] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-02 20:24:58,578] 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-K6NVC/1 [2022-05-02 20:24:59,221] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-02 20:24:59,221] multiqc [INFO ] This is MultiQC v1.9 [2022-05-02 20:24:59,221] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-K6NVC/1 [2022-05-02 20:24:59,221] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-K6NVC/1 [2022-05-02 20:24:59,221] multiqc [INFO ] Template : default [2022-05-02 20:24:59,221] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-02 20:24:59,221] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-K6NVC/1 [2022-05-02 20:24:59,222] 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 [2022-05-02 20:24:59,222] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-18944897/tmpqdrpezni [2022-05-02 20:24:59,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_1981_d08_rep1_fastqc.html [2022-05-02 20:24:59,346] multiqc [DEBUG ] File ignored by longranger/invocation 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000000000-K6NVC_l01_n01_FCC_PCR_Neg_rep2_fastqc.html [2022-05-02 20:25:02,450] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_1983_d02_rep2_fastqc.html [2022-05-02 20:25:02,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_1983_d02_rep2_fastqc.html [2022-05-02 20:25:02,495] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_Seq_Neg_rep2_fastqc.html [2022-05-02 20:25:02,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_Seq_Neg_rep2_fastqc.html [2022-05-02 20:25:02,541] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_1981_d08_rep2_fastqc.html [2022-05-02 20:25:02,543] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_1981_d08_rep2_fastqc.html [2022-05-02 20:25:02,584] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_2233_d02_rep1_fastqc.html [2022-05-02 20:25:02,585] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_2233_d02_rep1_fastqc.html [2022-05-02 20:25:02,627] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_PCR_Neg_rep2_fastqc.html [2022-05-02 20:25:02,629] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_PCR_Neg_rep2_fastqc.html [2022-05-02 20:25:02,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_2233_d02_rep1_fastqc.html [2022-05-02 20:25:02,676] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_2233_d02_rep1_fastqc.html [2022-05-02 20:25:02,717] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_Seq_Neg_rep1_fastqc.html [2022-05-02 20:25:02,719] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_Seq_Neg_rep1_fastqc.html [2022-05-02 20:25:02,764] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_2232_d04_rep2_fastqc.html [2022-05-02 20:25:02,766] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_2232_d04_rep2_fastqc.html [2022-05-02 20:25:02,806] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_1797_d06_rep1_fastqc.html [2022-05-02 20:25:02,808] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_1797_d06_rep1_fastqc.html [2022-05-02 20:25:02,849] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_SynRNA_10_rep1_fastqc.html [2022-05-02 20:25:02,850] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_SynRNA_10_rep1_fastqc.html [2022-05-02 20:25:02,892] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_SynRNA_2.5_rep2_fastqc.html [2022-05-02 20:25:02,893] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_SynRNA_2.5_rep2_fastqc.html [2022-05-02 20:25:02,935] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_2232_d04_rep1_fastqc.html [2022-05-02 20:25:02,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_2232_d04_rep1_fastqc.html [2022-05-02 20:25:02,977] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_SynRNA_10_rep1_fastqc.html [2022-05-02 20:25:02,979] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n01_FCC_SynRNA_10_rep1_fastqc.html [2022-05-02 20:25:03,020] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_PCR_Neg_rep1_fastqc.html [2022-05-02 20:25:03,022] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6NVC_l01_n02_FCC_PCR_Neg_rep1_fastqc.html [2022-05-02 20:25:03,566] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-02 20:25:03,567] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-02 20:25:03,590] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 29 samples (table) [2022-05-02 20:25:03,591] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-02 20:25:03,601] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-02 20:25:03,610] multiqc [DEBUG ] No samples found: conpair [2022-05-02 20:25:03,617] multiqc [DEBUG ] No samples found: peddy [2022-05-02 20:25:03,624] multiqc [DEBUG ] No samples found: somalier [2022-05-02 20:25:03,630] multiqc [DEBUG ] No samples found: methylQA [2022-05-02 20:25:03,642] multiqc [DEBUG ] No samples found: mosdepth [2022-05-02 20:25:03,650] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-02 20:25:03,653] multiqc [DEBUG ] No samples found: qualimap [2022-05-02 20:25:03,660] multiqc [DEBUG ] No samples found: preseq [2022-05-02 20:25:03,667] multiqc [DEBUG ] No samples found: quast [2022-05-02 20:25:03,674] multiqc [DEBUG ] No samples found: qorts [2022-05-02 20:25:03,680] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-02 20:25:03,686] multiqc [DEBUG ] No samples found: rockhopper [2022-05-02 20:25:03,693] multiqc [DEBUG ] No samples found: rsem [2022-05-02 20:25:03,715] multiqc [DEBUG ] No samples found: rseqc [2022-05-02 20:25:03,724] multiqc [DEBUG ] No samples found: busco [2022-05-02 20:25:03,729] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-02 20:25:03,737] multiqc [DEBUG ] No samples found: disambiguate [2022-05-02 20:25:03,743] multiqc [DEBUG ] No samples found: supernova [2022-05-02 20:25:03,763] multiqc [DEBUG ] No samples found: deeptools [2022-05-02 20:25:03,769] multiqc [DEBUG ] No samples found: sargasso [2022-05-02 20:25:03,774] multiqc [DEBUG ] No samples found: verifybamid [2022-05-02 20:25:03,779] multiqc [DEBUG ] No samples found: mirtrace [2022-05-02 20:25:03,786] multiqc [DEBUG ] No samples found: happy [2022-05-02 20:25:03,791] multiqc [DEBUG ] No samples found: mirtop [2022-05-02 20:25:03,801] multiqc [DEBUG ] No samples found: homer [2022-05-02 20:25:03,808] multiqc [DEBUG ] No samples found: macs2 [2022-05-02 20:25:03,816] multiqc [DEBUG ] No samples found: theta2 [2022-05-02 20:25:03,823] multiqc [DEBUG ] No samples found: snpeff [2022-05-02 20:25:03,834] multiqc [DEBUG ] No samples found: gatk [2022-05-02 20:25:03,840] multiqc [DEBUG ] No samples found: htseq [2022-05-02 20:25:03,849] multiqc [DEBUG ] No samples found: bcftools [2022-05-02 20:25:03,855] multiqc [DEBUG ] No samples found: featureCounts [2022-05-02 20:25:03,866] multiqc [DEBUG ] No samples found: fgbio [2022-05-02 20:25:03,891] multiqc [DEBUG ] No samples found: dragen [2022-05-02 20:25:03,896] multiqc [DEBUG ] No samples found: dedup [2022-05-02 20:25:03,903] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-02 20:25:03,939] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-02 20:25:03,948] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-02 20:25:03,950] multiqc [DEBUG ] No samples found: picard [2022-05-02 20:25:03,957] multiqc [DEBUG ] No samples found: prokka [2022-05-02 20:25:03,965] multiqc [DEBUG ] No samples found: samblaster [2022-05-02 20:25:03,981] multiqc [DEBUG ] No samples found: samtools [2022-05-02 20:25:03,987] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-02 20:25:03,996] multiqc [DEBUG ] No samples found: bamtools [2022-05-02 20:25:04,003] multiqc [DEBUG ] No samples found: jellyfish [2022-05-02 20:25:04,020] multiqc [DEBUG ] No samples found: vcftools [2022-05-02 20:25:04,026] multiqc [DEBUG ] No samples found: longranger [2022-05-02 20:25:04,033] multiqc [DEBUG ] No samples found: stacks [2022-05-02 20:25:04,039] multiqc [DEBUG ] No samples found: varscan2 [2022-05-02 20:25:04,065] multiqc [DEBUG ] No samples found: bbmap [2022-05-02 20:25:04,072] multiqc [DEBUG ] No samples found: bismark [2022-05-02 20:25:04,078] multiqc [DEBUG ] No samples found: biscuit [2022-05-02 20:25:04,085] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-02 20:25:04,092] multiqc [DEBUG ] No samples found: hicup [2022-05-02 20:25:04,099] multiqc [DEBUG ] No samples found: hicpro [2022-05-02 20:25:04,106] multiqc [DEBUG ] No samples found: salmon [2022-05-02 20:25:04,113] multiqc [DEBUG ] No samples found: kallisto [2022-05-02 20:25:04,119] multiqc [DEBUG ] No samples found: slamdunk [2022-05-02 20:25:04,124] multiqc [DEBUG ] No samples found: star [2022-05-02 20:25:04,129] multiqc [DEBUG ] No samples found: hisat2 [2022-05-02 20:25:04,135] multiqc [DEBUG ] No samples found: tophat [2022-05-02 20:25:04,140] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-02 20:25:04,148] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-02 20:25:04,154] multiqc [DEBUG ] No samples found: snpsplit [2022-05-02 20:25:04,164] multiqc [DEBUG ] No samples found: kat [2022-05-02 20:25:04,170] multiqc [DEBUG ] No samples found: leehom [2022-05-02 20:25:04,175] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-02 20:25:04,184] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-02 20:25:04,190] multiqc [DEBUG ] No samples found: cutadapt [2022-05-02 20:25:04,198] multiqc [DEBUG ] No samples found: flexbar [2022-05-02 20:25:04,204] multiqc [DEBUG ] No samples found: kaiju [2022-05-02 20:25:04,210] multiqc [DEBUG ] No samples found: kraken [2022-05-02 20:25:04,217] multiqc [DEBUG ] No samples found: malt [2022-05-02 20:25:04,224] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-02 20:25:04,229] multiqc [DEBUG ] No samples found: sickle [2022-05-02 20:25:04,235] multiqc [DEBUG ] No samples found: skewer [2022-05-02 20:25:04,242] multiqc [DEBUG ] No samples found: sortmerna [2022-05-02 20:25:04,248] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-02 20:25:04,253] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-02 20:25:04,260] multiqc [DEBUG ] No samples found: afterqc [2022-05-02 20:25:04,267] multiqc [DEBUG ] No samples found: fastp [2022-05-02 20:25:04,601] multiqc.modules.fastqc.fastqc [INFO ] Found 58 reports [2022-05-02 20:25:05,042] multiqc [DEBUG ] No samples found: pycoqc [2022-05-02 20:25:05,049] multiqc [DEBUG ] No samples found: minionqc [2022-05-02 20:25:05,056] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-02 20:25:05,063] multiqc [DEBUG ] No samples found: clusterflow [2022-05-02 20:25:05,070] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-02 20:25:05,077] multiqc [DEBUG ] No samples found: interop [2022-05-02 20:25:05,084] multiqc [DEBUG ] No samples found: ivar [2022-05-02 20:25:05,089] multiqc [DEBUG ] No samples found: flash [2022-05-02 20:25:05,096] multiqc [DEBUG ] No samples found: seqyclean [2022-05-02 20:25:05,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-05-02 20:25:05,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-05-02 20:25:05,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-05-02 20:25:05,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-02 20:25:05,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-02 20:25:05,167] multiqc [INFO ] Compressing plot data [2022-05-02 20:25:05,902] multiqc [INFO ] Report : multiqc_report.html [2022-05-02 20:25:05,902] multiqc [INFO ] Data : multiqc_data [2022-05-02 20:25:05,902] multiqc [DEBUG ] Moving data file from '/state/partition1/job-18944897/tmpqdrpezni/multiqc_data' to '/scratch/gencore/logs/html/000000000-K6NVC/1/multiqc_data' [2022-05-02 20:25:06,037] multiqc [INFO ] MultiQC complete