[2024-01-19 16:22:56,362] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-19 16:22:56,362] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-19 16:22:56,362] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-19 16:22:56,365] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2024-01-19 16:22:56,365] 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}} [2024-01-19 16:22:56,365] 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-DNCDK/1 [2024-01-19 16:22:57,731] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-19 16:22:57,731] multiqc [INFO ] This is MultiQC v1.9 [2024-01-19 16:22:57,731] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-DNCDK/1 [2024-01-19 16:22:57,731] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-DNCDK/1 [2024-01-19 16:22:57,731] multiqc [INFO ] Template : default [2024-01-19 16:22:57,731] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-19 16:22:57,731] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-DNCDK/1 [2024-01-19 16:22:57,732] 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 [2024-01-19 16:22:57,732] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42031098/tmpg6r4g9so [2024-01-19 16:22:57,983] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DNCDK_l01.2_fastqc.html [2024-01-19 16:22:57,985] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DNCDK_l01.2_fastqc.html [2024-01-19 16:22:58,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DNCDK_l01.3_fastqc.html [2024-01-19 16:22:58,032] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DNCDK_l01.3_fastqc.html [2024-01-19 16:22:58,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DNCDK_l01.1_fastqc.html [2024-01-19 16:22:58,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DNCDK_l01.1_fastqc.html [2024-01-19 16:22:59,332] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-19 16:22:59,345] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-19 16:22:59,370] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2024-01-19 16:22:59,372] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-19 16:22:59,400] multiqc [DEBUG ] No samples found: conpair [2024-01-19 16:22:59,444] multiqc [DEBUG ] No samples found: peddy [2024-01-19 16:22:59,489] multiqc [DEBUG ] No samples found: somalier [2024-01-19 16:22:59,543] multiqc [DEBUG ] No samples found: methylQA [2024-01-19 16:22:59,734] multiqc [DEBUG ] No samples found: mosdepth [2024-01-19 16:22:59,751] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-19 16:22:59,767] multiqc [DEBUG ] No samples found: qualimap [2024-01-19 16:22:59,803] multiqc [DEBUG ] No samples found: preseq [2024-01-19 16:22:59,856] multiqc [DEBUG ] No samples found: quast [2024-01-19 16:22:59,904] multiqc [DEBUG ] No samples found: qorts [2024-01-19 16:22:59,977] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-19 16:23:00,025] multiqc [DEBUG ] No samples found: rockhopper [2024-01-19 16:23:00,053] multiqc [DEBUG ] No samples found: rsem [2024-01-19 16:23:00,177] multiqc [DEBUG ] No samples found: rseqc [2024-01-19 16:23:00,212] multiqc [DEBUG ] No samples found: busco [2024-01-19 16:23:00,255] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-19 16:23:00,290] multiqc [DEBUG ] No samples found: disambiguate [2024-01-19 16:23:00,333] multiqc [DEBUG ] No samples found: supernova [2024-01-19 16:23:00,503] multiqc [DEBUG ] No samples found: deeptools [2024-01-19 16:23:00,556] multiqc [DEBUG ] No samples found: sargasso [2024-01-19 16:23:00,600] multiqc [DEBUG ] No samples found: verifybamid [2024-01-19 16:23:00,644] multiqc [DEBUG ] No samples found: mirtrace [2024-01-19 16:23:00,687] multiqc [DEBUG ] No samples found: happy [2024-01-19 16:23:00,732] multiqc [DEBUG ] No samples found: mirtop [2024-01-19 16:23:00,802] multiqc [DEBUG ] No samples found: homer [2024-01-19 16:23:00,845] multiqc [DEBUG ] No samples found: macs2 [2024-01-19 16:23:00,878] multiqc [DEBUG ] No samples found: theta2 [2024-01-19 16:23:00,925] multiqc [DEBUG ] No samples found: snpeff [2024-01-19 16:23:01,005] multiqc [DEBUG ] No samples found: gatk [2024-01-19 16:23:01,049] multiqc [DEBUG ] No samples found: htseq [2024-01-19 16:23:01,118] multiqc [DEBUG ] No samples found: bcftools [2024-01-19 16:23:01,167] multiqc [DEBUG ] No samples found: featureCounts [2024-01-19 16:23:01,235] multiqc [DEBUG ] No samples found: fgbio [2024-01-19 16:23:01,428] multiqc [DEBUG ] No samples found: dragen [2024-01-19 16:23:01,472] multiqc [DEBUG ] No samples found: dedup [2024-01-19 16:23:01,516] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-19 16:23:01,890] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-19 16:23:01,936] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-19 16:23:01,939] multiqc [DEBUG ] No samples found: picard [2024-01-19 16:23:01,978] multiqc [DEBUG ] No samples found: prokka [2024-01-19 16:23:02,011] multiqc [DEBUG ] No samples found: samblaster [2024-01-19 16:23:02,131] multiqc [DEBUG ] No samples found: samtools [2024-01-19 16:23:02,172] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-19 16:23:02,217] multiqc [DEBUG ] No samples found: bamtools [2024-01-19 16:23:02,251] multiqc [DEBUG ] No samples found: jellyfish [2024-01-19 16:23:02,338] multiqc [DEBUG ] No samples found: vcftools [2024-01-19 16:23:02,382] multiqc [DEBUG ] No samples found: longranger [2024-01-19 16:23:02,427] multiqc [DEBUG ] No samples found: stacks [2024-01-19 16:23:02,475] multiqc [DEBUG ] No samples found: varscan2 [2024-01-19 16:23:02,678] multiqc [DEBUG ] No samples found: bbmap [2024-01-19 16:23:02,734] multiqc [DEBUG ] No samples found: bismark [2024-01-19 16:23:02,775] multiqc [DEBUG ] No samples found: biscuit [2024-01-19 16:23:02,843] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-19 16:23:02,887] multiqc [DEBUG ] No samples found: hicup [2024-01-19 16:23:02,932] multiqc [DEBUG ] No samples found: hicpro [2024-01-19 16:23:02,951] multiqc [DEBUG ] No samples found: salmon [2024-01-19 16:23:02,994] multiqc [DEBUG ] No samples found: kallisto [2024-01-19 16:23:03,039] multiqc [DEBUG ] No samples found: slamdunk [2024-01-19 16:23:03,084] multiqc [DEBUG ] No samples found: star [2024-01-19 16:23:03,130] multiqc [DEBUG ] No samples found: hisat2 [2024-01-19 16:23:03,185] multiqc [DEBUG ] No samples found: tophat [2024-01-19 16:23:03,216] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-19 16:23:03,259] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-19 16:23:03,292] multiqc [DEBUG ] No samples found: snpsplit [2024-01-19 16:23:03,325] multiqc [DEBUG ] No samples found: kat [2024-01-19 16:23:03,371] multiqc [DEBUG ] No samples found: leehom [2024-01-19 16:23:03,411] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-19 16:23:03,444] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-19 16:23:03,488] multiqc [DEBUG ] No samples found: cutadapt [2024-01-19 16:23:03,521] multiqc [DEBUG ] No samples found: flexbar [2024-01-19 16:23:03,599] multiqc [DEBUG ] No samples found: kaiju [2024-01-19 16:23:03,642] multiqc [DEBUG ] No samples found: kraken [2024-01-19 16:23:03,702] multiqc [DEBUG ] No samples found: malt [2024-01-19 16:23:03,743] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-19 16:23:03,822] multiqc [DEBUG ] No samples found: sickle [2024-01-19 16:23:03,852] multiqc [DEBUG ] No samples found: skewer [2024-01-19 16:23:03,878] multiqc [DEBUG ] No samples found: sortmerna [2024-01-19 16:23:03,941] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-19 16:23:03,985] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-19 16:23:04,020] multiqc [DEBUG ] No samples found: afterqc [2024-01-19 16:23:04,066] multiqc [DEBUG ] No samples found: fastp [2024-01-19 16:23:04,116] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-01-19 16:23:04,268] multiqc [DEBUG ] No samples found: pycoqc [2024-01-19 16:23:04,314] multiqc [DEBUG ] No samples found: minionqc [2024-01-19 16:23:04,357] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-19 16:23:04,402] multiqc [DEBUG ] No samples found: clusterflow [2024-01-19 16:23:04,446] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-19 16:23:04,483] multiqc [DEBUG ] No samples found: interop [2024-01-19 16:23:04,529] multiqc [DEBUG ] No samples found: ivar [2024-01-19 16:23:04,574] multiqc [DEBUG ] No samples found: flash [2024-01-19 16:23:04,605] multiqc [DEBUG ] No samples found: seqyclean [2024-01-19 16:23:04,605] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-19 16:23:04,605] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-01-19 16:23:04,605] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-19 16:23:04,606] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-19 16:23:04,611] multiqc [INFO ] Compressing plot data [2024-01-19 16:23:04,668] multiqc [INFO ] Report : multiqc_report.html [2024-01-19 16:23:04,668] multiqc [INFO ] Data : multiqc_data [2024-01-19 16:23:04,668] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42031098/tmpg6r4g9so/multiqc_data' to '/scratch/gencore/logs/html/000000000-DNCDK/1/multiqc_data' [2024-01-19 16:23:36,053] multiqc [INFO ] MultiQC complete