[2022-11-08 22:42:19,617] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-08 22:42:19,617] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-08 22:42:19,617] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-08 22:42:19,618] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-08 22:42:19,618] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-08 22:42:19,618] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TCYBGXN/merged [2022-11-08 22:42:20,251] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-08 22:42:20,252] multiqc [INFO ] This is MultiQC v1.9 [2022-11-08 22:42:20,252] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TCYBGXN/merged [2022-11-08 22:42:20,252] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3TCYBGXN/merged [2022-11-08 22:42:20,252] multiqc [INFO ] Template : default [2022-11-08 22:42:20,252] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-08 22:42:20,252] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3TCYBGXN/merged [2022-11-08 22:42:20,252] 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 [2022-11-08 22:42:20,252] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26838238/tmp1e220wt6 [2022-11-08 22:42:20,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_4BH_fastqc.html [2022-11-08 22:42:20,360] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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H3TCYBGXN_n01_5BH_fastqc.html [2022-11-08 22:42:24,066] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_4AC_fastqc.html [2022-11-08 22:42:24,068] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_4AC_fastqc.html [2022-11-08 22:42:24,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_9AC_fastqc.html [2022-11-08 22:42:24,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_9AC_fastqc.html [2022-11-08 22:42:24,149] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_2AC_fastqc.html [2022-11-08 22:42:24,151] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_2AC_fastqc.html [2022-11-08 22:42:24,191] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_7BC_fastqc.html [2022-11-08 22:42:24,193] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_7BC_fastqc.html [2022-11-08 22:42:24,233] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF4-MYB33-1_fastqc.html [2022-11-08 22:42:24,235] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF4-MYB33-1_fastqc.html [2022-11-08 22:42:24,277] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF1-DIV1-2_fastqc.html [2022-11-08 22:42:24,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF1-DIV1-2_fastqc.html [2022-11-08 22:42:24,320] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_10AH_fastqc.html [2022-11-08 22:42:24,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_10AH_fastqc.html [2022-11-08 22:42:24,362] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_6BH_fastqc.html [2022-11-08 22:42:24,364] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_6BH_fastqc.html [2022-11-08 22:42:24,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_NLP7-GFP2_fastqc.html [2022-11-08 22:42:24,407] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_NLP7-GFP2_fastqc.html [2022-11-08 22:42:24,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_3BH_fastqc.html [2022-11-08 22:42:24,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_3BH_fastqc.html [2022-11-08 22:42:24,490] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_9BC_fastqc.html [2022-11-08 22:42:24,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_9BC_fastqc.html [2022-11-08 22:42:24,532] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly9_fastqc.html [2022-11-08 22:42:24,534] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly9_fastqc.html [2022-11-08 22:42:24,574] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_9BH_fastqc.html [2022-11-08 22:42:24,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_9BH_fastqc.html [2022-11-08 22:42:24,616] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF1-DIV1-3_fastqc.html [2022-11-08 22:42:24,618] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF1-DIV1-3_fastqc.html [2022-11-08 22:42:24,660] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_6AH_fastqc.html [2022-11-08 22:42:24,661] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_6AH_fastqc.html [2022-11-08 22:42:24,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF3-GBF4-2_fastqc.html [2022-11-08 22:42:24,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF3-GBF4-2_fastqc.html [2022-11-08 22:42:24,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_EV-phd-1_fastqc.html [2022-11-08 22:42:24,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_EV-phd-1_fastqc.html [2022-11-08 22:42:24,789] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly12_fastqc.html [2022-11-08 22:42:24,791] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly12_fastqc.html [2022-11-08 22:42:24,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly17_fastqc.html [2022-11-08 22:42:24,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly17_fastqc.html [2022-11-08 22:42:24,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_12BC_fastqc.html [2022-11-08 22:42:24,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_12BC_fastqc.html [2022-11-08 22:42:24,917] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_3AC_fastqc.html [2022-11-08 22:42:24,919] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_3AC_fastqc.html [2022-11-08 22:42:24,960] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_12AC_fastqc.html [2022-11-08 22:42:24,962] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_12AC_fastqc.html [2022-11-08 22:42:25,001] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly6_fastqc.html [2022-11-08 22:42:25,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_carly6_fastqc.html [2022-11-08 22:42:25,045] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF4-MYB33-2_fastqc.html [2022-11-08 22:42:25,046] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_TF4-MYB33-2_fastqc.html [2022-11-08 22:42:25,089] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYBGXN_n01_NLP7-GFP3_fastqc.html [2022-11-08 22:42:25,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYBGXN_n01_NLP7-GFP3_fastqc.html [2022-11-08 22:42:25,458] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-08 22:42:25,460] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-08 22:42:25,468] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-08 22:42:25,478] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-08 22:42:25,519] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 88 samples (table) [2022-11-08 22:42:25,524] multiqc [DEBUG ] No samples found: conpair [2022-11-08 22:42:25,529] multiqc [DEBUG ] No samples found: peddy [2022-11-08 22:42:25,535] multiqc [DEBUG ] No samples found: somalier [2022-11-08 22:42:25,539] multiqc [DEBUG ] No samples found: methylQA [2022-11-08 22:42:25,548] multiqc [DEBUG ] No samples found: mosdepth [2022-11-08 22:42:25,553] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-08 22:42:25,557] multiqc [DEBUG ] No samples found: qualimap [2022-11-08 22:42:25,562] multiqc [DEBUG ] No samples found: preseq [2022-11-08 22:42:25,566] multiqc [DEBUG ] No samples found: quast [2022-11-08 22:42:25,571] multiqc [DEBUG ] No samples found: qorts [2022-11-08 22:42:25,576] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-08 22:42:25,580] multiqc [DEBUG ] No samples found: rockhopper [2022-11-08 22:42:25,585] multiqc [DEBUG ] No samples found: rsem [2022-11-08 22:42:25,596] multiqc [DEBUG ] No samples found: rseqc [2022-11-08 22:42:25,601] multiqc [DEBUG ] No samples found: busco [2022-11-08 22:42:25,606] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-08 22:42:25,610] multiqc [DEBUG ] No samples found: disambiguate [2022-11-08 22:42:25,615] multiqc [DEBUG ] No samples found: supernova [2022-11-08 22:42:25,628] multiqc [DEBUG ] No samples found: deeptools [2022-11-08 22:42:25,632] multiqc [DEBUG ] No samples found: sargasso [2022-11-08 22:42:25,638] multiqc [DEBUG ] No samples found: verifybamid [2022-11-08 22:42:25,642] multiqc [DEBUG ] No samples found: mirtrace [2022-11-08 22:42:25,647] multiqc [DEBUG ] No samples found: happy [2022-11-08 22:42:25,652] multiqc [DEBUG ] No samples found: mirtop [2022-11-08 22:42:25,659] multiqc [DEBUG ] No samples found: homer [2022-11-08 22:42:25,663] multiqc [DEBUG ] No samples found: macs2 [2022-11-08 22:42:25,668] multiqc [DEBUG ] No samples found: theta2 [2022-11-08 22:42:25,673] multiqc [DEBUG ] No samples found: snpeff [2022-11-08 22:42:25,679] multiqc [DEBUG ] No samples found: gatk [2022-11-08 22:42:25,684] multiqc [DEBUG ] No samples found: htseq [2022-11-08 22:42:25,689] multiqc [DEBUG ] No samples found: bcftools [2022-11-08 22:42:25,694] multiqc [DEBUG ] No samples found: featureCounts [2022-11-08 22:42:25,701] multiqc [DEBUG ] No samples found: fgbio [2022-11-08 22:42:25,714] multiqc [DEBUG ] No samples found: dragen [2022-11-08 22:42:25,719] multiqc [DEBUG ] No samples found: dedup [2022-11-08 22:42:25,724] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-08 22:42:25,751] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-08 22:42:25,755] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-08 22:42:25,757] multiqc [DEBUG ] No samples found: picard [2022-11-08 22:42:25,762] multiqc [DEBUG ] No samples found: prokka [2022-11-08 22:42:25,766] multiqc [DEBUG ] No samples found: samblaster [2022-11-08 22:42:25,774] multiqc [DEBUG ] No samples found: samtools [2022-11-08 22:42:25,779] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-08 22:42:25,784] multiqc [DEBUG ] No samples found: bamtools [2022-11-08 22:42:25,788] multiqc [DEBUG ] No samples found: jellyfish [2022-11-08 22:42:25,795] multiqc [DEBUG ] No samples found: vcftools [2022-11-08 22:42:25,800] multiqc [DEBUG ] No samples found: longranger [2022-11-08 22:42:25,805] multiqc [DEBUG ] No samples found: stacks [2022-11-08 22:42:25,810] multiqc [DEBUG ] No samples found: varscan2 [2022-11-08 22:42:25,824] multiqc [DEBUG ] No samples found: bbmap [2022-11-08 22:42:25,828] multiqc [DEBUG ] No samples found: bismark [2022-11-08 22:42:25,833] multiqc [DEBUG ] No samples found: biscuit [2022-11-08 22:42:25,838] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-08 22:42:25,842] multiqc [DEBUG ] No samples found: hicup [2022-11-08 22:42:25,847] multiqc [DEBUG ] No samples found: hicpro [2022-11-08 22:42:25,851] multiqc [DEBUG ] No samples found: salmon [2022-11-08 22:42:25,856] multiqc [DEBUG ] No samples found: kallisto [2022-11-08 22:42:25,861] multiqc [DEBUG ] No samples found: slamdunk [2022-11-08 22:42:25,865] multiqc [DEBUG ] No samples found: star [2022-11-08 22:42:25,870] multiqc [DEBUG ] No samples found: hisat2 [2022-11-08 22:42:25,875] multiqc [DEBUG ] No samples found: tophat [2022-11-08 22:42:25,879] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-08 22:42:25,884] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-08 22:42:25,889] multiqc [DEBUG ] No samples found: snpsplit [2022-11-08 22:42:25,893] multiqc [DEBUG ] No samples found: kat [2022-11-08 22:42:25,897] multiqc [DEBUG ] No samples found: leehom [2022-11-08 22:42:25,902] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-08 22:42:25,906] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-08 22:42:25,911] multiqc [DEBUG ] No samples found: cutadapt [2022-11-08 22:42:25,916] multiqc [DEBUG ] No samples found: flexbar [2022-11-08 22:42:25,920] multiqc [DEBUG ] No samples found: kaiju [2022-11-08 22:42:25,925] multiqc [DEBUG ] No samples found: kraken [2022-11-08 22:42:25,930] multiqc [DEBUG ] No samples found: malt [2022-11-08 22:42:25,934] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-08 22:42:25,938] multiqc [DEBUG ] No samples found: sickle [2022-11-08 22:42:25,947] multiqc [DEBUG ] No samples found: skewer [2022-11-08 22:42:25,952] multiqc [DEBUG ] No samples found: sortmerna [2022-11-08 22:42:25,956] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-08 22:42:25,961] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-08 22:42:25,965] multiqc [DEBUG ] No samples found: afterqc [2022-11-08 22:42:25,970] multiqc [DEBUG ] No samples found: fastp [2022-11-08 22:42:32,108] multiqc.modules.fastqc.fastqc [INFO ] Found 88 reports [2022-11-08 22:42:33,888] multiqc [DEBUG ] No samples found: pycoqc [2022-11-08 22:42:33,893] multiqc [DEBUG ] No samples found: minionqc [2022-11-08 22:42:33,898] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-08 22:42:33,903] multiqc [DEBUG ] No samples found: clusterflow [2022-11-08 22:42:33,908] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-08 22:42:33,915] multiqc [DEBUG ] No samples found: interop [2022-11-08 22:42:33,919] multiqc [DEBUG ] No samples found: ivar [2022-11-08 22:42:33,924] multiqc [DEBUG ] No samples found: flash [2022-11-08 22:42:33,929] multiqc [DEBUG ] No samples found: seqyclean [2022-11-08 22:42:33,929] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-08 22:42:33,929] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-08 22:42:33,929] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-08 22:42:33,930] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-08 22:42:34,031] multiqc [INFO ] Compressing plot data [2022-11-08 22:42:35,477] multiqc [INFO ] Report : multiqc_report.html [2022-11-08 22:42:35,477] multiqc [INFO ] Data : multiqc_data [2022-11-08 22:42:35,477] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26838238/tmp1e220wt6/multiqc_data' to '/scratch/gencore/logs/html/H3TCYBGXN/merged/multiqc_data' [2022-11-08 22:42:35,611] multiqc [INFO ] MultiQC complete