[2021-06-02 09:09:45,607] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-02 09:09:45,607] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-02 09:09:45,608] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-02 09:09:45,608] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-02 09:09:45,608] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-02 09:09:45,609] 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-JR27G/1 [2021-06-02 09:09:46,952] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-02 09:09:46,952] multiqc [INFO ] This is MultiQC v1.9 [2021-06-02 09:09:46,953] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JR27G/1 [2021-06-02 09:09:46,953] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-JR27G/1 [2021-06-02 09:09:46,953] multiqc [INFO ] Template : default [2021-06-02 09:09:46,953] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-02 09:09:46,953] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-JR27G/1 [2021-06-02 09:09:46,953] 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 [2021-06-02 09:09:46,953] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7302697/tmpm75mtmig [2021-06-02 09:09:47,058] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.plusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,061] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.plusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_undetermined_fastqc.html [2021-06-02 09:09:47,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_undetermined_fastqc.html [2021-06-02 09:09:47,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.plusN-1hr.rep1_fastqc.html [2021-06-02 09:09:47,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.plusN-1hr.rep1_fastqc.html [2021-06-02 09:09:47,203] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.minusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,205] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.minusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,249] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.minusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,251] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.minusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,295] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.plusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,297] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.plusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,340] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.plusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,342] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.plusN-1hr.rep2_fastqc.html [2021-06-02 09:09:47,387] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.minusN-1hr.rep1_fastqc.html [2021-06-02 09:09:47,389] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.minusN-1hr.rep1_fastqc.html [2021-06-02 09:09:47,436] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.plusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,438] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.plusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,486] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.minusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,488] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.minusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,536] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.minusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,537] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.minusN-1hr.rep3_fastqc.html [2021-06-02 09:09:47,585] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.minusN-1hr.rep1_fastqc.html [2021-06-02 09:09:47,587] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-shoot.minusN-1hr.rep1_fastqc.html [2021-06-02 09:09:47,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.plusN-1hr.rep1_fastqc.html [2021-06-02 09:09:47,637] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR27G_l01_n01_W22-root.plusN-1hr.rep1_fastqc.html [2021-06-02 09:09:48,073] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-02 09:09:48,075] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-02 09:09:48,087] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 13 samples (table) [2021-06-02 09:09:48,089] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-02 09:09:48,099] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-06-02 09:09:48,103] multiqc [DEBUG ] No samples found: conpair [2021-06-02 09:09:48,108] multiqc [DEBUG ] No samples found: peddy [2021-06-02 09:09:48,113] multiqc [DEBUG ] No samples found: somalier [2021-06-02 09:09:48,117] multiqc [DEBUG ] No samples found: methylQA [2021-06-02 09:09:48,125] multiqc [DEBUG ] No samples found: mosdepth [2021-06-02 09:09:48,129] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-02 09:09:48,139] multiqc [DEBUG ] No samples found: qualimap [2021-06-02 09:09:48,144] multiqc [DEBUG ] No samples found: preseq [2021-06-02 09:09:48,148] multiqc [DEBUG ] No samples found: quast [2021-06-02 09:09:48,153] multiqc [DEBUG ] No samples found: qorts [2021-06-02 09:09:48,157] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-02 09:09:48,162] multiqc [DEBUG ] No samples found: rockhopper [2021-06-02 09:09:48,166] multiqc [DEBUG ] No samples found: rsem [2021-06-02 09:09:48,176] multiqc [DEBUG ] No samples found: rseqc [2021-06-02 09:09:48,180] multiqc [DEBUG ] No samples found: busco [2021-06-02 09:09:48,185] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-02 09:09:48,189] multiqc [DEBUG ] No samples found: disambiguate [2021-06-02 09:09:48,193] multiqc [DEBUG ] No samples found: supernova [2021-06-02 09:09:48,205] multiqc [DEBUG ] No samples found: deeptools [2021-06-02 09:09:48,210] multiqc [DEBUG ] No samples found: sargasso [2021-06-02 09:09:48,214] multiqc [DEBUG ] No samples found: verifybamid [2021-06-02 09:09:48,219] multiqc [DEBUG ] No samples found: mirtrace [2021-06-02 09:09:48,224] multiqc [DEBUG ] No samples found: happy [2021-06-02 09:09:48,228] multiqc [DEBUG ] No samples found: mirtop [2021-06-02 09:09:48,234] multiqc [DEBUG ] No samples found: homer [2021-06-02 09:09:48,239] multiqc [DEBUG ] No samples found: macs2 [2021-06-02 09:09:48,242] multiqc [DEBUG ] No samples found: theta2 [2021-06-02 09:09:48,247] multiqc [DEBUG ] No samples found: snpeff [2021-06-02 09:09:48,253] multiqc [DEBUG ] No samples found: gatk [2021-06-02 09:09:48,258] multiqc [DEBUG ] No samples found: htseq [2021-06-02 09:09:48,263] multiqc [DEBUG ] No samples found: bcftools [2021-06-02 09:09:48,267] multiqc [DEBUG ] No samples found: featureCounts [2021-06-02 09:09:48,273] multiqc [DEBUG ] No samples found: fgbio [2021-06-02 09:09:48,285] multiqc [DEBUG ] No samples found: dragen [2021-06-02 09:09:48,290] multiqc [DEBUG ] No samples found: dedup [2021-06-02 09:09:48,294] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-02 09:09:48,315] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-02 09:09:48,320] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-02 09:09:48,322] multiqc [DEBUG ] No samples found: picard [2021-06-02 09:09:48,327] multiqc [DEBUG ] No samples found: prokka [2021-06-02 09:09:48,331] multiqc [DEBUG ] No samples found: samblaster [2021-06-02 09:09:48,339] multiqc [DEBUG ] No samples found: samtools [2021-06-02 09:09:48,343] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-02 09:09:48,348] multiqc [DEBUG ] No samples found: bamtools [2021-06-02 09:09:48,352] multiqc [DEBUG ] No samples found: jellyfish [2021-06-02 09:09:48,358] multiqc [DEBUG ] No samples found: vcftools [2021-06-02 09:09:48,363] multiqc [DEBUG ] No samples found: longranger [2021-06-02 09:09:48,368] multiqc [DEBUG ] No samples found: stacks [2021-06-02 09:09:48,372] multiqc [DEBUG ] No samples found: varscan2 [2021-06-02 09:09:48,385] multiqc [DEBUG ] No samples found: bbmap [2021-06-02 09:09:48,389] multiqc [DEBUG ] No samples found: bismark [2021-06-02 09:09:48,394] multiqc [DEBUG ] No samples found: biscuit [2021-06-02 09:09:48,399] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-02 09:09:48,403] multiqc [DEBUG ] No samples found: hicup [2021-06-02 09:09:48,408] multiqc [DEBUG ] No samples found: hicpro [2021-06-02 09:09:48,412] multiqc [DEBUG ] No samples found: salmon [2021-06-02 09:09:48,416] multiqc [DEBUG ] No samples found: kallisto [2021-06-02 09:09:48,421] multiqc [DEBUG ] No samples found: slamdunk [2021-06-02 09:09:48,425] multiqc [DEBUG ] No samples found: star [2021-06-02 09:09:48,430] multiqc [DEBUG ] No samples found: hisat2 [2021-06-02 09:09:48,434] multiqc [DEBUG ] No samples found: tophat [2021-06-02 09:09:48,439] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-02 09:09:48,443] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-02 09:09:48,447] multiqc [DEBUG ] No samples found: snpsplit [2021-06-02 09:09:48,451] multiqc [DEBUG ] No samples found: kat [2021-06-02 09:09:48,455] multiqc [DEBUG ] No samples found: leehom [2021-06-02 09:09:48,460] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-02 09:09:48,464] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-02 09:09:48,468] multiqc [DEBUG ] No samples found: cutadapt [2021-06-02 09:09:48,472] multiqc [DEBUG ] No samples found: flexbar [2021-06-02 09:09:48,477] multiqc [DEBUG ] No samples found: kaiju [2021-06-02 09:09:48,481] multiqc [DEBUG ] No samples found: kraken [2021-06-02 09:09:48,486] multiqc [DEBUG ] No samples found: malt [2021-06-02 09:09:48,490] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-02 09:09:48,494] multiqc [DEBUG ] No samples found: sickle [2021-06-02 09:09:48,499] multiqc [DEBUG ] No samples found: skewer [2021-06-02 09:09:48,503] multiqc [DEBUG ] No samples found: sortmerna [2021-06-02 09:09:48,507] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-02 09:09:48,511] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-02 09:09:48,515] multiqc [DEBUG ] No samples found: afterqc [2021-06-02 09:09:48,520] multiqc [DEBUG ] No samples found: fastp [2021-06-02 09:09:48,625] multiqc.modules.fastqc.fastqc [INFO ] Found 13 reports [2021-06-02 09:09:48,966] multiqc [DEBUG ] No samples found: pycoqc [2021-06-02 09:09:48,997] multiqc [DEBUG ] No samples found: minionqc [2021-06-02 09:09:49,001] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-02 09:09:49,006] multiqc [DEBUG ] No samples found: clusterflow [2021-06-02 09:09:49,010] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-02 09:09:49,015] multiqc [DEBUG ] No samples found: interop [2021-06-02 09:09:49,020] multiqc [DEBUG ] No samples found: ivar [2021-06-02 09:09:49,024] multiqc [DEBUG ] No samples found: flash [2021-06-02 09:09:49,028] multiqc [DEBUG ] No samples found: seqyclean [2021-06-02 09:09:49,028] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-06-02 09:09:49,028] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-06-02 09:09:49,028] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-06-02 09:09:49,028] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-06-02 09:09:49,028] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-02 09:09:49,045] multiqc [INFO ] Compressing plot data [2021-06-02 09:09:49,259] multiqc [INFO ] Report : multiqc_report.html [2021-06-02 09:09:49,259] multiqc [INFO ] Data : multiqc_data [2021-06-02 09:09:49,259] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7302697/tmpm75mtmig/multiqc_data' to '/scratch/gencore/logs/html/000000000-JR27G/1/multiqc_data' [2021-06-02 09:09:49,387] multiqc [INFO ] MultiQC complete