[2023-05-12 09:22:49,313] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-12 09:22:49,313] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-12 09:22:49,313] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-12 09:22:49,315] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-12 09:22:49,315] 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}} [2023-05-12 09:22:49,316] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5KKWDRX3/merged [2023-05-12 09:22:49,470] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-12 09:22:49,471] multiqc [INFO ] This is MultiQC v1.9 [2023-05-12 09:22:49,471] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5KKWDRX3/merged [2023-05-12 09:22:49,471] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5KKWDRX3/merged [2023-05-12 09:22:49,471] multiqc [INFO ] Template : default [2023-05-12 09:22:49,471] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-12 09:22:49,471] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5KKWDRX3/merged [2023-05-12 09:22:49,471] 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 [2023-05-12 09:22:49,471] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33248000/tmpuylb56ba [2023-05-12 09:22:49,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5KKWDRX3_4_fastqc.html [2023-05-12 09:22:49,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5KKWDRX3_4_fastqc.html [2023-05-12 09:22:49,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5KKWDRX3_2_fastqc.html [2023-05-12 09:22:49,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5KKWDRX3_2_fastqc.html [2023-05-12 09:22:49,696] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5KKWDRX3_1_fastqc.html [2023-05-12 09:22:49,698] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5KKWDRX3_1_fastqc.html [2023-05-12 09:22:49,738] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5KKWDRX3_3_fastqc.html [2023-05-12 09:22:49,740] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5KKWDRX3_3_fastqc.html [2023-05-12 09:22:51,821] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-12 09:22:51,823] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-12 09:22:51,828] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-05-12 09:22:51,829] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-12 09:22:51,835] multiqc [DEBUG ] No samples found: conpair [2023-05-12 09:22:51,841] multiqc [DEBUG ] No samples found: peddy [2023-05-12 09:22:51,846] multiqc [DEBUG ] No samples found: somalier [2023-05-12 09:22:51,852] multiqc [DEBUG ] No samples found: methylQA [2023-05-12 09:22:51,862] multiqc [DEBUG ] No samples found: mosdepth [2023-05-12 09:22:51,867] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-12 09:22:51,871] multiqc [DEBUG ] No samples found: qualimap [2023-05-12 09:22:51,877] multiqc [DEBUG ] No samples found: preseq [2023-05-12 09:22:51,883] multiqc [DEBUG ] No samples found: quast [2023-05-12 09:22:51,888] multiqc [DEBUG ] No samples found: qorts [2023-05-12 09:22:51,894] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-12 09:22:51,899] multiqc [DEBUG ] No samples found: rockhopper [2023-05-12 09:22:51,904] multiqc [DEBUG ] No samples found: rsem [2023-05-12 09:22:51,916] multiqc [DEBUG ] No samples found: rseqc [2023-05-12 09:22:51,921] multiqc [DEBUG ] No samples found: busco [2023-05-12 09:22:51,927] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-12 09:22:51,933] multiqc [DEBUG ] No samples found: disambiguate [2023-05-12 09:22:51,939] multiqc [DEBUG ] No samples found: supernova [2023-05-12 09:22:51,955] multiqc [DEBUG ] No samples found: deeptools [2023-05-12 09:22:51,962] multiqc [DEBUG ] No samples found: sargasso [2023-05-12 09:22:51,967] multiqc [DEBUG ] No samples found: verifybamid [2023-05-12 09:22:51,973] multiqc [DEBUG ] No samples found: mirtrace [2023-05-12 09:22:51,979] multiqc [DEBUG ] No samples found: happy [2023-05-12 09:22:51,984] multiqc [DEBUG ] No samples found: mirtop [2023-05-12 09:22:51,992] multiqc [DEBUG ] No samples found: homer [2023-05-12 09:22:51,998] multiqc [DEBUG ] No samples found: macs2 [2023-05-12 09:22:52,003] multiqc [DEBUG ] No samples found: theta2 [2023-05-12 09:22:52,009] multiqc [DEBUG ] No samples found: snpeff [2023-05-12 09:22:52,017] multiqc [DEBUG ] No samples found: gatk [2023-05-12 09:22:52,022] multiqc [DEBUG ] No samples found: htseq [2023-05-12 09:22:52,028] multiqc [DEBUG ] No samples found: bcftools [2023-05-12 09:22:52,034] multiqc [DEBUG ] No samples found: featureCounts [2023-05-12 09:22:52,042] multiqc [DEBUG ] No samples found: fgbio [2023-05-12 09:22:52,057] multiqc [DEBUG ] No samples found: dragen [2023-05-12 09:22:52,063] multiqc [DEBUG ] No samples found: dedup [2023-05-12 09:22:52,069] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-12 09:22:52,094] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-12 09:22:52,100] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-12 09:22:52,102] multiqc [DEBUG ] No samples found: picard [2023-05-12 09:22:52,107] multiqc [DEBUG ] No samples found: prokka [2023-05-12 09:22:52,112] multiqc [DEBUG ] No samples found: samblaster [2023-05-12 09:22:52,122] multiqc [DEBUG ] No samples found: samtools [2023-05-12 09:22:52,128] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-12 09:22:52,134] multiqc [DEBUG ] No samples found: bamtools [2023-05-12 09:22:52,140] multiqc [DEBUG ] No samples found: jellyfish [2023-05-12 09:22:52,148] multiqc [DEBUG ] No samples found: vcftools [2023-05-12 09:22:52,154] multiqc [DEBUG ] No samples found: longranger [2023-05-12 09:22:52,160] multiqc [DEBUG ] No samples found: stacks [2023-05-12 09:22:52,166] multiqc [DEBUG ] No samples found: varscan2 [2023-05-12 09:22:52,182] multiqc [DEBUG ] No samples found: bbmap [2023-05-12 09:22:52,187] multiqc [DEBUG ] No samples found: bismark [2023-05-12 09:22:52,193] multiqc [DEBUG ] No samples found: biscuit [2023-05-12 09:22:52,199] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-12 09:22:52,205] multiqc [DEBUG ] No samples found: hicup [2023-05-12 09:22:52,211] multiqc [DEBUG ] No samples found: hicpro [2023-05-12 09:22:52,216] multiqc [DEBUG ] No samples found: salmon [2023-05-12 09:22:52,221] multiqc [DEBUG ] No samples found: kallisto [2023-05-12 09:22:52,227] multiqc [DEBUG ] No samples found: slamdunk [2023-05-12 09:22:52,232] multiqc [DEBUG ] No samples found: star [2023-05-12 09:22:52,238] multiqc [DEBUG ] No samples found: hisat2 [2023-05-12 09:22:52,242] multiqc [DEBUG ] No samples found: tophat [2023-05-12 09:22:52,248] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-12 09:22:52,253] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-12 09:22:52,259] multiqc [DEBUG ] No samples found: snpsplit [2023-05-12 09:22:52,264] multiqc [DEBUG ] No samples found: kat [2023-05-12 09:22:52,269] multiqc [DEBUG ] No samples found: leehom [2023-05-12 09:22:52,275] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-12 09:22:52,280] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-12 09:22:52,285] multiqc [DEBUG ] No samples found: cutadapt [2023-05-12 09:22:52,290] multiqc [DEBUG ] No samples found: flexbar [2023-05-12 09:22:52,296] multiqc [DEBUG ] No samples found: kaiju [2023-05-12 09:22:52,301] multiqc [DEBUG ] No samples found: kraken [2023-05-12 09:22:52,306] multiqc [DEBUG ] No samples found: malt [2023-05-12 09:22:52,312] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-12 09:22:52,317] multiqc [DEBUG ] No samples found: sickle [2023-05-12 09:22:52,322] multiqc [DEBUG ] No samples found: skewer [2023-05-12 09:22:52,327] multiqc [DEBUG ] No samples found: sortmerna [2023-05-12 09:22:52,332] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-12 09:22:52,338] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-12 09:22:52,343] multiqc [DEBUG ] No samples found: afterqc [2023-05-12 09:22:52,349] multiqc [DEBUG ] No samples found: fastp [2023-05-12 09:22:52,413] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-05-12 09:22:52,460] multiqc [DEBUG ] No samples found: pycoqc [2023-05-12 09:22:52,465] multiqc [DEBUG ] No samples found: minionqc [2023-05-12 09:22:52,471] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-12 09:22:52,476] multiqc [DEBUG ] No samples found: clusterflow [2023-05-12 09:22:52,482] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-12 09:22:52,488] multiqc [DEBUG ] No samples found: interop [2023-05-12 09:22:52,493] multiqc [DEBUG ] No samples found: ivar [2023-05-12 09:22:52,498] multiqc [DEBUG ] No samples found: flash [2023-05-12 09:22:52,503] multiqc [DEBUG ] No samples found: seqyclean [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-05-12 09:22:52,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-12 09:22:52,504] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-12 09:22:52,510] multiqc [INFO ] Compressing plot data [2023-05-12 09:22:52,579] multiqc [INFO ] Report : multiqc_report.html [2023-05-12 09:22:52,579] multiqc [INFO ] Data : multiqc_data [2023-05-12 09:22:52,579] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33248000/tmpuylb56ba/multiqc_data' to '/scratch/gencore/logs/html/H5KKWDRX3/merged/multiqc_data' [2023-05-12 09:22:52,709] multiqc [INFO ] MultiQC complete