[2023-05-17 03:41:21,992] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-17 03:41:21,992] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-17 03:41:21,992] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-17 03:41:21,994] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-17 03:41:21,994] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-05-17 03:41:21,995] 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-KWDDC/1 [2023-05-17 03:41:22,167] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-17 03:41:22,167] multiqc [INFO ] This is MultiQC v1.9 [2023-05-17 03:41:22,167] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KWDDC/1 [2023-05-17 03:41:22,167] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KWDDC/1 [2023-05-17 03:41:22,167] multiqc [INFO ] Template : default [2023-05-17 03:41:22,167] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-17 03:41:22,167] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KWDDC/1 [2023-05-17 03:41:22,168] 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 [2023-05-17 03:41:22,168] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33494115/tmpf3cg_fe_ [2023-05-17 03:41:22,284] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-05-17 03:41:22,286] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-05-17 03:41:22,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_SRF_fastqc.html [2023-05-17 03:41:22,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_SRF_fastqc.html [2023-05-17 03:41:22,522] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_IgG_fastqc.html [2023-05-17 03:41:22,524] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_IgG_fastqc.html [2023-05-17 03:41:22,565] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_BPTF_fastqc.html [2023-05-17 03:41:22,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_BPTF_fastqc.html [2023-05-17 03:41:22,607] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_undetermined_fastqc.html [2023-05-17 03:41:22,609] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_undetermined_fastqc.html [2023-05-17 03:41:22,649] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_H3K4me3_fastqc.html [2023-05-17 03:41:22,651] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_H3K4me3_fastqc.html [2023-05-17 03:41:22,692] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_undetermined_fastqc.html [2023-05-17 03:41:22,694] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_undetermined_fastqc.html [2023-05-17 03:41:22,734] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_H3K4me3_fastqc.html [2023-05-17 03:41:22,736] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_H3K4me3_fastqc.html [2023-05-17 03:41:22,777] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_SRF_fastqc.html [2023-05-17 03:41:22,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_SRF_fastqc.html [2023-05-17 03:41:22,819] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_BPTF_fastqc.html [2023-05-17 03:41:22,821] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_BPTF_fastqc.html [2023-05-17 03:41:22,860] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_IgG_fastqc.html [2023-05-17 03:41:22,862] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_IgG_fastqc.html [2023-05-17 03:41:23,227] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-17 03:41:23,229] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-17 03:41:23,236] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-17 03:41:23,246] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-17 03:41:23,249] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 5 samples (table) [2023-05-17 03:41:23,253] multiqc [DEBUG ] No samples found: conpair [2023-05-17 03:41:23,264] multiqc [DEBUG ] No samples found: peddy [2023-05-17 03:41:23,270] multiqc [DEBUG ] No samples found: somalier [2023-05-17 03:41:23,275] multiqc [DEBUG ] No samples found: methylQA [2023-05-17 03:41:23,286] multiqc [DEBUG ] No samples found: mosdepth [2023-05-17 03:41:23,290] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-17 03:41:23,294] multiqc [DEBUG ] No samples found: qualimap [2023-05-17 03:41:23,304] multiqc [DEBUG ] No samples found: preseq [2023-05-17 03:41:23,308] multiqc [DEBUG ] No samples found: quast [2023-05-17 03:41:23,312] multiqc [DEBUG ] No samples found: qorts [2023-05-17 03:41:23,323] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-17 03:41:23,327] multiqc [DEBUG ] No samples found: rockhopper [2023-05-17 03:41:23,331] multiqc [DEBUG ] No samples found: rsem [2023-05-17 03:41:23,348] multiqc [DEBUG ] No samples found: rseqc [2023-05-17 03:41:23,352] multiqc [DEBUG ] No samples found: busco [2023-05-17 03:41:23,356] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-17 03:41:23,362] multiqc [DEBUG ] No samples found: disambiguate [2023-05-17 03:41:23,370] multiqc [DEBUG ] No samples found: supernova [2023-05-17 03:41:23,388] multiqc [DEBUG ] No samples found: deeptools [2023-05-17 03:41:23,393] multiqc [DEBUG ] No samples found: sargasso [2023-05-17 03:41:23,403] multiqc [DEBUG ] No samples found: verifybamid [2023-05-17 03:41:23,407] multiqc [DEBUG ] No samples found: mirtrace [2023-05-17 03:41:23,412] multiqc [DEBUG ] No samples found: happy [2023-05-17 03:41:23,416] multiqc [DEBUG ] No samples found: mirtop [2023-05-17 03:41:23,424] multiqc [DEBUG ] No samples found: homer [2023-05-17 03:41:23,428] multiqc [DEBUG ] No samples found: macs2 [2023-05-17 03:41:23,432] multiqc [DEBUG ] No samples found: theta2 [2023-05-17 03:41:23,442] multiqc [DEBUG ] No samples found: snpeff [2023-05-17 03:41:23,449] multiqc [DEBUG ] No samples found: gatk [2023-05-17 03:41:23,452] multiqc [DEBUG ] No samples found: htseq [2023-05-17 03:41:23,463] multiqc [DEBUG ] No samples found: bcftools [2023-05-17 03:41:23,467] multiqc [DEBUG ] No samples found: featureCounts [2023-05-17 03:41:23,473] multiqc [DEBUG ] No samples found: fgbio [2023-05-17 03:41:23,491] multiqc [DEBUG ] No samples found: dragen [2023-05-17 03:41:23,495] multiqc [DEBUG ] No samples found: dedup [2023-05-17 03:41:23,503] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-17 03:41:23,528] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-17 03:41:23,532] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-17 03:41:23,534] multiqc [DEBUG ] No samples found: picard [2023-05-17 03:41:23,545] multiqc [DEBUG ] No samples found: prokka [2023-05-17 03:41:23,548] multiqc [DEBUG ] No samples found: samblaster [2023-05-17 03:41:23,563] multiqc [DEBUG ] No samples found: samtools [2023-05-17 03:41:23,567] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-17 03:41:23,572] multiqc [DEBUG ] No samples found: bamtools [2023-05-17 03:41:23,582] multiqc [DEBUG ] No samples found: jellyfish [2023-05-17 03:41:23,591] multiqc [DEBUG ] No samples found: vcftools [2023-05-17 03:41:23,601] multiqc [DEBUG ] No samples found: longranger [2023-05-17 03:41:23,606] multiqc [DEBUG ] No samples found: stacks [2023-05-17 03:41:23,610] multiqc [DEBUG ] No samples found: varscan2 [2023-05-17 03:41:23,628] multiqc [DEBUG ] No samples found: bbmap [2023-05-17 03:41:23,632] multiqc [DEBUG ] No samples found: bismark [2023-05-17 03:41:23,642] multiqc [DEBUG ] No samples found: biscuit [2023-05-17 03:41:23,646] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-17 03:41:23,651] multiqc [DEBUG ] No samples found: hicup [2023-05-17 03:41:23,661] multiqc [DEBUG ] No samples found: hicpro [2023-05-17 03:41:23,665] multiqc [DEBUG ] No samples found: salmon [2023-05-17 03:41:23,669] multiqc [DEBUG ] No samples found: kallisto [2023-05-17 03:41:23,673] multiqc [DEBUG ] No samples found: slamdunk [2023-05-17 03:41:23,685] multiqc [DEBUG ] No samples found: star [2023-05-17 03:41:23,689] multiqc [DEBUG ] No samples found: hisat2 [2023-05-17 03:41:23,693] multiqc [DEBUG ] No samples found: tophat [2023-05-17 03:41:23,701] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-17 03:41:23,705] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-17 03:41:23,710] multiqc [DEBUG ] No samples found: snpsplit [2023-05-17 03:41:23,713] multiqc [DEBUG ] No samples found: kat [2023-05-17 03:41:23,721] multiqc [DEBUG ] No samples found: leehom [2023-05-17 03:41:23,725] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-17 03:41:23,729] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-17 03:41:23,733] multiqc [DEBUG ] No samples found: cutadapt [2023-05-17 03:41:23,741] multiqc [DEBUG ] No samples found: flexbar [2023-05-17 03:41:23,745] multiqc [DEBUG ] No samples found: kaiju [2023-05-17 03:41:23,749] multiqc [DEBUG ] No samples found: kraken [2023-05-17 03:41:23,753] multiqc [DEBUG ] No samples found: malt [2023-05-17 03:41:23,763] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-17 03:41:23,767] multiqc [DEBUG ] No samples found: sickle [2023-05-17 03:41:23,772] multiqc [DEBUG ] No samples found: skewer [2023-05-17 03:41:23,780] multiqc [DEBUG ] No samples found: sortmerna [2023-05-17 03:41:23,784] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-17 03:41:23,788] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-17 03:41:23,792] multiqc [DEBUG ] No samples found: afterqc [2023-05-17 03:41:23,801] multiqc [DEBUG ] No samples found: fastp [2023-05-17 03:41:23,883] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-17 03:41:24,099] multiqc [DEBUG ] No samples found: pycoqc [2023-05-17 03:41:24,103] multiqc [DEBUG ] No samples found: minionqc [2023-05-17 03:41:24,107] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-17 03:41:24,117] multiqc [DEBUG ] No samples found: clusterflow [2023-05-17 03:41:24,123] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-17 03:41:24,127] multiqc [DEBUG ] No samples found: interop [2023-05-17 03:41:24,137] multiqc [DEBUG ] No samples found: ivar [2023-05-17 03:41:24,141] multiqc [DEBUG ] No samples found: flash [2023-05-17 03:41:24,145] multiqc [DEBUG ] No samples found: seqyclean [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-17 03:41:24,145] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-17 03:41:24,146] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-17 03:41:24,159] multiqc [INFO ] Compressing plot data [2023-05-17 03:41:24,338] multiqc [INFO ] Report : multiqc_report.html [2023-05-17 03:41:24,338] multiqc [INFO ] Data : multiqc_data [2023-05-17 03:41:24,338] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33494115/tmpf3cg_fe_/multiqc_data' to '/scratch/gencore/logs/html/000000000-KWDDC/1/multiqc_data' [2023-05-17 03:41:24,479] multiqc [INFO ] MultiQC complete