[2020-12-22 17:53:47,362] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2020-12-22 17:53:47,362] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2020-12-22 17:53:47,362] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-12-22 17:53:47,363] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2020-12-22 17:53:47,363] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-12-22 17:53:47,363] 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-JCJPN/1 [2020-12-22 17:53:48,890] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2020-12-22 17:53:48,891] multiqc [INFO ] This is MultiQC v1.9 [2020-12-22 17:53:48,891] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JCJPN/1 [2020-12-22 17:53:48,891] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-JCJPN/1 [2020-12-22 17:53:48,891] multiqc [INFO ] Template : default [2020-12-22 17:53:48,891] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2020-12-22 17:53:48,891] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-JCJPN/1 [2020-12-22 17:53:48,891] 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 [2020-12-22 17:53:48,891] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-639548/tmpr3efqsae [2020-12-22 17:53:49,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n02_HRB0261L_fastqc.html [2020-12-22 17:53:49,032] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n02_HRB0261L_fastqc.html [2020-12-22 17:53:49,076] multiqc [DEBUG ] File ignored by hicexplorer 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hicexplorer because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n02_HRB0249_fastqc.html [2020-12-22 17:53:54,282] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n02_HRB0249_fastqc.html [2020-12-22 17:53:54,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n02_HRB0263R_fastqc.html [2020-12-22 17:53:54,323] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n02_HRB0263R_fastqc.html [2020-12-22 17:53:54,363] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n01_HRB0259L_fastqc.html [2020-12-22 17:53:54,365] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JCJPN_l01_n01_HRB0259L_fastqc.html [2020-12-22 17:53:54,807] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2020-12-22 17:53:54,808] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2020-12-22 17:53:54,816] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-12-22 17:53:54,838] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 48 samples (table) [2020-12-22 17:53:54,847] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-12-22 17:53:54,851] multiqc [DEBUG ] No samples found: conpair [2020-12-22 17:53:54,855] multiqc [DEBUG ] No samples found: peddy [2020-12-22 17:53:54,859] multiqc [DEBUG ] No samples found: somalier [2020-12-22 17:53:54,863] multiqc [DEBUG ] No samples found: methylQA [2020-12-22 17:53:54,869] multiqc [DEBUG ] No samples found: mosdepth [2020-12-22 17:53:54,872] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-12-22 17:53:54,875] multiqc [DEBUG ] No samples found: qualimap [2020-12-22 17:53:54,879] multiqc [DEBUG ] No samples found: preseq [2020-12-22 17:53:54,882] multiqc [DEBUG ] No samples found: quast [2020-12-22 17:53:54,886] multiqc [DEBUG ] No samples found: qorts [2020-12-22 17:53:54,890] multiqc [DEBUG ] No samples found: rna_seqc [2020-12-22 17:53:54,894] multiqc [DEBUG ] No samples found: rockhopper [2020-12-22 17:53:54,897] multiqc [DEBUG ] No samples found: rsem [2020-12-22 17:53:54,905] multiqc [DEBUG ] No samples found: rseqc [2020-12-22 17:53:54,909] multiqc [DEBUG ] No samples found: busco [2020-12-22 17:53:54,912] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-12-22 17:53:54,916] multiqc [DEBUG ] No samples found: disambiguate [2020-12-22 17:53:54,920] multiqc [DEBUG ] No samples found: supernova [2020-12-22 17:53:54,930] multiqc [DEBUG ] No samples found: deeptools [2020-12-22 17:53:54,933] multiqc [DEBUG ] No samples found: sargasso [2020-12-22 17:53:54,937] multiqc [DEBUG ] No samples found: verifybamid [2020-12-22 17:53:54,941] multiqc [DEBUG ] No samples found: mirtrace [2020-12-22 17:53:54,945] multiqc [DEBUG ] No samples found: happy [2020-12-22 17:53:54,948] multiqc [DEBUG ] No samples found: mirtop [2020-12-22 17:53:54,954] multiqc [DEBUG ] No samples found: homer [2020-12-22 17:53:54,957] multiqc [DEBUG ] No samples found: macs2 [2020-12-22 17:53:54,961] multiqc [DEBUG ] No samples found: theta2 [2020-12-22 17:53:54,964] multiqc [DEBUG ] No samples found: snpeff [2020-12-22 17:53:54,969] multiqc [DEBUG ] No samples found: gatk [2020-12-22 17:53:54,973] multiqc [DEBUG ] No samples found: htseq [2020-12-22 17:53:54,977] multiqc [DEBUG ] No samples found: bcftools [2020-12-22 17:53:54,981] multiqc [DEBUG ] No samples found: featureCounts [2020-12-22 17:53:54,985] multiqc [DEBUG ] No samples found: fgbio [2020-12-22 17:53:54,994] multiqc [DEBUG ] No samples found: dragen [2020-12-22 17:53:54,999] multiqc [DEBUG ] No samples found: dedup [2020-12-22 17:53:55,003] multiqc [DEBUG ] No samples found: damageprofiler [2020-12-22 17:53:55,018] multiqc [DEBUG ] No samples found: biobambam2 [2020-12-22 17:53:55,022] multiqc [DEBUG ] No samples found: mtnucratio [2020-12-22 17:53:55,024] multiqc [DEBUG ] No samples found: picard [2020-12-22 17:53:55,028] multiqc [DEBUG ] No samples found: prokka [2020-12-22 17:53:55,031] multiqc [DEBUG ] No samples found: samblaster [2020-12-22 17:53:55,037] multiqc [DEBUG ] No samples found: samtools [2020-12-22 17:53:55,041] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-12-22 17:53:55,045] multiqc [DEBUG ] No samples found: bamtools [2020-12-22 17:53:55,049] multiqc [DEBUG ] No samples found: jellyfish [2020-12-22 17:53:55,054] multiqc [DEBUG ] No samples found: vcftools [2020-12-22 17:53:55,059] multiqc [DEBUG ] No samples found: longranger [2020-12-22 17:53:55,063] multiqc [DEBUG ] No samples found: stacks [2020-12-22 17:53:55,066] multiqc [DEBUG ] No samples found: varscan2 [2020-12-22 17:53:55,076] multiqc [DEBUG ] No samples found: bbmap [2020-12-22 17:53:55,080] multiqc [DEBUG ] No samples found: bismark [2020-12-22 17:53:55,084] multiqc [DEBUG ] No samples found: biscuit [2020-12-22 17:53:55,088] multiqc [DEBUG ] No samples found: hicexplorer [2020-12-22 17:53:55,091] multiqc [DEBUG ] No samples found: hicup [2020-12-22 17:53:55,095] multiqc [DEBUG ] No samples found: hicpro [2020-12-22 17:53:55,098] multiqc [DEBUG ] No samples found: salmon [2020-12-22 17:53:55,102] multiqc [DEBUG ] No samples found: kallisto [2020-12-22 17:53:55,107] multiqc [DEBUG ] No samples found: slamdunk [2020-12-22 17:53:55,110] multiqc [DEBUG ] No samples found: star [2020-12-22 17:53:55,114] multiqc [DEBUG ] No samples found: hisat2 [2020-12-22 17:53:55,118] multiqc [DEBUG ] No samples found: tophat [2020-12-22 17:53:55,122] multiqc [DEBUG ] No samples found: bowtie2 [2020-12-22 17:53:55,125] multiqc [DEBUG ] No samples found: bowtie1 [2020-12-22 17:53:55,129] multiqc [DEBUG ] No samples found: snpsplit [2020-12-22 17:53:55,132] multiqc [DEBUG ] No samples found: kat [2020-12-22 17:53:55,136] multiqc [DEBUG ] No samples found: leehom [2020-12-22 17:53:55,139] multiqc [DEBUG ] No samples found: adapterRemoval [2020-12-22 17:53:55,143] multiqc [DEBUG ] No samples found: clipandmerge [2020-12-22 17:53:55,147] multiqc [DEBUG ] No samples found: cutadapt [2020-12-22 17:53:55,150] multiqc [DEBUG ] No samples found: flexbar [2020-12-22 17:53:55,154] multiqc [DEBUG ] No samples found: kaiju [2020-12-22 17:53:55,157] multiqc [DEBUG ] No samples found: kraken [2020-12-22 17:53:55,161] multiqc [DEBUG ] No samples found: malt [2020-12-22 17:53:55,165] multiqc [DEBUG ] No samples found: trimmomatic [2020-12-22 17:53:55,168] multiqc [DEBUG ] No samples found: sickle [2020-12-22 17:53:55,172] multiqc [DEBUG ] No samples found: skewer [2020-12-22 17:53:55,175] multiqc [DEBUG ] No samples found: sortmerna [2020-12-22 17:53:55,179] multiqc [DEBUG ] No samples found: biobloomtools [2020-12-22 17:53:55,182] multiqc [DEBUG ] No samples found: fastq_screen [2020-12-22 17:53:55,186] multiqc [DEBUG ] No samples found: afterqc [2020-12-22 17:53:55,190] multiqc [DEBUG ] No samples found: fastp [2020-12-22 17:53:56,246] multiqc.modules.fastqc.fastqc [INFO ] Found 96 reports [2020-12-22 17:53:56,934] multiqc [DEBUG ] No samples found: pycoqc [2020-12-22 17:53:56,938] multiqc [DEBUG ] No samples found: minionqc [2020-12-22 17:53:56,942] multiqc [DEBUG ] No samples found: multivcfanalyzer [2020-12-22 17:53:56,945] multiqc [DEBUG ] No samples found: clusterflow [2020-12-22 17:53:56,949] multiqc [DEBUG ] No samples found: bcl2fastq [2020-12-22 17:53:56,953] multiqc [DEBUG ] No samples found: interop [2020-12-22 17:53:56,957] multiqc [DEBUG ] No samples found: ivar [2020-12-22 17:53:56,960] multiqc [DEBUG ] No samples found: flash [2020-12-22 17:53:56,964] multiqc [DEBUG ] No samples found: seqyclean [2020-12-22 17:53:56,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2020-12-22 17:53:56,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2020-12-22 17:53:56,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2020-12-22 17:53:56,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2020-12-22 17:53:56,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2020-12-22 17:53:57,075] multiqc [INFO ] Compressing plot data [2020-12-22 17:53:58,361] multiqc [INFO ] Report : multiqc_report.html [2020-12-22 17:53:58,361] multiqc [INFO ] Data : multiqc_data [2020-12-22 17:53:58,361] multiqc [DEBUG ] Moving data file from '/state/partition1/job-639548/tmpr3efqsae/multiqc_data' to '/scratch/gencore/logs/html/000000000-JCJPN/1/multiqc_data' [2020-12-22 17:53:58,480] multiqc [INFO ] MultiQC complete