[2022-05-25 08:09:44,397] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-25 08:09:44,397] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-25 08:09:44,397] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-25 08:09:44,398] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-25 08:09:44,398] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-25 08:09:44,398] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNY5AFX3/merged [2022-05-25 08:09:48,055] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-25 08:09:48,056] multiqc [INFO ] This is MultiQC v1.9 [2022-05-25 08:09:48,056] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNY5AFX3/merged [2022-05-25 08:09:48,056] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLNY5AFX3/merged [2022-05-25 08:09:48,056] multiqc [INFO ] Template : default [2022-05-25 08:09:48,056] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-25 08:09:48,056] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLNY5AFX3/merged [2022-05-25 08:09:48,056] 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 [2022-05-25 08:09:48,056] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20120548/tmpcyjjkro_ [2022-05-25 08:09:48,150] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_C24SPL9_F1a-B_y2_fastqc.html [2022-05-25 08:09:48,153] multiqc [DEBUG ] File ignored by longranger/invocation because it 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hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL9_Col-B_y1_fastqc.html [2022-05-25 08:09:50,644] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL9_Col-B_y1_fastqc.html [2022-05-25 08:09:50,683] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL9_C24-B_y1_fastqc.html [2022-05-25 08:09:50,685] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL9_C24-B_y1_fastqc.html [2022-05-25 08:09:50,723] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL9_F1b-B_y1_fastqc.html [2022-05-25 08:09:50,725] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL9_F1b-B_y1_fastqc.html [2022-05-25 08:09:50,763] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_C24-B_y1_fastqc.html [2022-05-25 08:09:50,765] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_C24-B_y1_fastqc.html [2022-05-25 08:09:50,819] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_ColSPL9_Col-B_y1_fastqc.html [2022-05-25 08:09:50,821] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_ColSPL9_Col-B_y1_fastqc.html [2022-05-25 08:09:50,883] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_F1b-B_y1_fastqc.html [2022-05-25 08:09:50,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_F1b-B_y1_fastqc.html [2022-05-25 08:09:50,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL11_Col-B_y2_fastqc.html [2022-05-25 08:09:50,926] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL11_Col-B_y2_fastqc.html [2022-05-25 08:09:50,965] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_ColSPL9_F1b-B_y2_fastqc.html [2022-05-25 08:09:50,967] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_ColSPL9_F1b-B_y2_fastqc.html [2022-05-25 08:09:51,012] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_pIXHALO_C24-B_y2_fastqc.html [2022-05-25 08:09:51,014] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_pIXHALO_C24-B_y2_fastqc.html [2022-05-25 08:09:51,080] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_F1a-B_y1_fastqc.html [2022-05-25 08:09:51,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_F1a-B_y1_fastqc.html [2022-05-25 08:09:51,122] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL14_Col-B_y2_fastqc.html [2022-05-25 08:09:51,123] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL14_Col-B_y2_fastqc.html [2022-05-25 08:09:51,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL11_Col-B_y1_fastqc.html [2022-05-25 08:09:51,185] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL11_Col-B_y1_fastqc.html [2022-05-25 08:09:51,225] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_C24SPL9_C24-B_y1_fastqc.html [2022-05-25 08:09:51,227] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_C24SPL9_C24-B_y1_fastqc.html [2022-05-25 08:09:51,265] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL9_C24-B_y1_fastqc.html [2022-05-25 08:09:51,267] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_C24SPL9_C24-B_y1_fastqc.html [2022-05-25 08:09:51,306] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_ColSPL11_Colamp-B_y1_fastqc.html [2022-05-25 08:09:51,308] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_ColSPL11_Colamp-B_y1_fastqc.html [2022-05-25 08:09:51,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_undetermined_fastqc.html [2022-05-25 08:09:51,348] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_undetermined_fastqc.html [2022-05-25 08:09:51,387] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_C24SPL11_Colamp-B_y2_fastqc.html [2022-05-25 08:09:51,389] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_C24SPL11_Colamp-B_y2_fastqc.html [2022-05-25 08:09:51,467] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_F1b-B_y2_fastqc.html [2022-05-25 08:09:51,469] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n02_pIXHALO_F1b-B_y2_fastqc.html [2022-05-25 08:09:51,508] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL11_Colamp-B_y2_fastqc.html [2022-05-25 08:09:51,510] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNY5AFX3_n01_ColSPL11_Colamp-B_y2_fastqc.html [2022-05-25 08:09:51,832] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-25 08:09:51,832] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-25 08:09:51,855] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 36 samples (table) [2022-05-25 08:09:51,856] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-25 08:09:51,866] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-25 08:09:51,869] multiqc [DEBUG ] No samples found: conpair [2022-05-25 08:09:51,872] multiqc [DEBUG ] No samples found: peddy [2022-05-25 08:09:51,875] multiqc [DEBUG ] No samples found: somalier [2022-05-25 08:09:51,878] multiqc [DEBUG ] No samples found: methylQA [2022-05-25 08:09:51,882] multiqc [DEBUG ] No samples found: mosdepth [2022-05-25 08:09:51,885] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-25 08:09:51,888] multiqc [DEBUG ] No samples found: qualimap [2022-05-25 08:09:51,891] multiqc [DEBUG ] No samples found: preseq [2022-05-25 08:09:51,894] multiqc [DEBUG ] No samples found: quast [2022-05-25 08:09:51,897] multiqc [DEBUG ] No samples found: qorts [2022-05-25 08:09:51,900] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-25 08:09:51,903] multiqc [DEBUG ] No samples found: rockhopper [2022-05-25 08:09:51,906] multiqc [DEBUG ] No samples found: rsem [2022-05-25 08:09:51,911] multiqc [DEBUG ] No samples found: rseqc [2022-05-25 08:09:51,914] multiqc [DEBUG ] No samples found: busco [2022-05-25 08:09:51,917] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-25 08:09:51,920] multiqc [DEBUG ] No samples found: disambiguate [2022-05-25 08:09:51,923] multiqc [DEBUG ] No samples found: supernova [2022-05-25 08:09:51,929] multiqc [DEBUG ] No samples found: deeptools [2022-05-25 08:09:51,932] multiqc [DEBUG ] No samples found: sargasso [2022-05-25 08:09:51,935] multiqc [DEBUG ] No samples found: verifybamid [2022-05-25 08:09:51,938] multiqc [DEBUG ] No samples found: mirtrace [2022-05-25 08:09:51,941] multiqc [DEBUG ] No samples found: happy [2022-05-25 08:09:51,944] multiqc [DEBUG ] No samples found: mirtop [2022-05-25 08:09:51,947] multiqc [DEBUG ] No samples found: homer [2022-05-25 08:09:51,950] multiqc [DEBUG ] No samples found: macs2 [2022-05-25 08:09:51,953] multiqc [DEBUG ] No samples found: theta2 [2022-05-25 08:09:51,956] multiqc [DEBUG ] No samples found: snpeff [2022-05-25 08:09:51,960] multiqc [DEBUG ] No samples found: gatk [2022-05-25 08:09:51,963] multiqc [DEBUG ] No samples found: htseq [2022-05-25 08:09:51,966] multiqc [DEBUG ] No samples found: bcftools [2022-05-25 08:09:51,969] multiqc [DEBUG ] No samples found: featureCounts [2022-05-25 08:09:51,973] multiqc [DEBUG ] No samples found: fgbio [2022-05-25 08:09:51,979] multiqc [DEBUG ] No samples found: dragen [2022-05-25 08:09:51,982] multiqc [DEBUG ] No samples found: dedup [2022-05-25 08:09:51,985] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-25 08:09:51,994] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-25 08:09:51,997] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-25 08:09:51,999] multiqc [DEBUG ] No samples found: picard [2022-05-25 08:09:52,002] multiqc [DEBUG ] No samples found: prokka [2022-05-25 08:09:52,005] multiqc [DEBUG ] No samples found: samblaster [2022-05-25 08:09:52,009] multiqc [DEBUG ] No samples found: samtools [2022-05-25 08:09:52,012] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-25 08:09:52,015] multiqc [DEBUG ] No samples found: bamtools [2022-05-25 08:09:52,018] multiqc [DEBUG ] No samples found: jellyfish [2022-05-25 08:09:52,022] multiqc [DEBUG ] No samples found: vcftools [2022-05-25 08:09:52,025] multiqc [DEBUG ] No samples found: longranger [2022-05-25 08:09:52,028] multiqc [DEBUG ] No samples found: stacks [2022-05-25 08:09:52,031] multiqc [DEBUG ] No samples found: varscan2 [2022-05-25 08:09:52,037] multiqc [DEBUG ] No samples found: bbmap [2022-05-25 08:09:52,040] multiqc [DEBUG ] No samples found: bismark [2022-05-25 08:09:52,043] multiqc [DEBUG ] No samples found: biscuit [2022-05-25 08:09:52,046] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-25 08:09:52,049] multiqc [DEBUG ] No samples found: hicup [2022-05-25 08:09:52,052] multiqc [DEBUG ] No samples found: hicpro [2022-05-25 08:09:52,055] multiqc [DEBUG ] No samples found: salmon [2022-05-25 08:09:52,058] multiqc [DEBUG ] No samples found: kallisto [2022-05-25 08:09:52,061] multiqc [DEBUG ] No samples found: slamdunk [2022-05-25 08:09:52,064] multiqc [DEBUG ] No samples found: star [2022-05-25 08:09:52,067] multiqc [DEBUG ] No samples found: hisat2 [2022-05-25 08:09:52,070] multiqc [DEBUG ] No samples found: tophat [2022-05-25 08:09:52,073] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-25 08:09:52,075] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-25 08:09:52,079] multiqc [DEBUG ] No samples found: snpsplit [2022-05-25 08:09:52,081] multiqc [DEBUG ] No samples found: kat [2022-05-25 08:09:52,084] multiqc [DEBUG ] No samples found: leehom [2022-05-25 08:09:52,087] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-25 08:09:52,090] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-25 08:09:52,093] multiqc [DEBUG ] No samples found: cutadapt [2022-05-25 08:09:52,096] multiqc [DEBUG ] No samples found: flexbar [2022-05-25 08:09:52,099] multiqc [DEBUG ] No samples found: kaiju [2022-05-25 08:09:52,102] multiqc [DEBUG ] No samples found: kraken [2022-05-25 08:09:52,105] multiqc [DEBUG ] No samples found: malt [2022-05-25 08:09:52,108] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-25 08:09:52,111] multiqc [DEBUG ] No samples found: sickle [2022-05-25 08:09:52,114] multiqc [DEBUG ] No samples found: skewer [2022-05-25 08:09:52,117] multiqc [DEBUG ] No samples found: sortmerna [2022-05-25 08:09:52,119] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-25 08:09:52,122] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-25 08:09:52,125] multiqc [DEBUG ] No samples found: afterqc [2022-05-25 08:09:52,128] multiqc [DEBUG ] No samples found: fastp [2022-05-25 08:09:54,290] multiqc.modules.fastqc.fastqc [INFO ] Found 72 reports [2022-05-25 08:09:55,737] multiqc [DEBUG ] No samples found: pycoqc [2022-05-25 08:09:55,740] multiqc [DEBUG ] No samples found: minionqc [2022-05-25 08:09:55,743] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-25 08:09:55,746] multiqc [DEBUG ] No samples found: clusterflow [2022-05-25 08:09:55,749] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-25 08:09:55,752] multiqc [DEBUG ] No samples found: interop [2022-05-25 08:09:55,755] multiqc [DEBUG ] No samples found: ivar [2022-05-25 08:09:55,758] multiqc [DEBUG ] No samples found: flash [2022-05-25 08:09:55,761] multiqc [DEBUG ] No samples found: seqyclean [2022-05-25 08:09:55,762] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-05-25 08:09:55,762] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-05-25 08:09:55,762] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-25 08:09:55,762] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-25 08:09:55,846] multiqc [INFO ] Compressing plot data [2022-05-25 08:09:57,133] multiqc [INFO ] Report : multiqc_report.html [2022-05-25 08:09:57,134] multiqc [INFO ] Data : multiqc_data [2022-05-25 08:09:57,134] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20120548/tmpcyjjkro_/multiqc_data' to '/scratch/gencore/logs/html/HLNY5AFX3/merged/multiqc_data' [2022-05-25 08:10:23,558] multiqc [INFO ] MultiQC complete