[2021-07-08 04:27:00,806] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-07-08 04:27:00,807] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-07-08 04:27:00,807] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-07-08 04:27:00,807] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-07-08 04:27:00,808] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-07-08 04:27:00,808] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H325JDMXY/merged [2021-07-08 04:27:02,629] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-07-08 04:27:02,629] multiqc [INFO ] This is MultiQC v1.9 [2021-07-08 04:27:02,629] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H325JDMXY/merged [2021-07-08 04:27:02,629] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H325JDMXY/merged [2021-07-08 04:27:02,629] multiqc [INFO ] Template : default [2021-07-08 04:27:02,629] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-07-08 04:27:02,629] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H325JDMXY/merged [2021-07-08 04:27:02,630] 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 [2021-07-08 04:27:02,630] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8445202/tmp1rvevbyz [2021-07-08 04:27:02,752] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n01_GDO_A_210622_fastqc.html [2021-07-08 04:27:02,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n02_cDNA_C4_210622_fastqc.html [2021-07-08 04:27:06,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H325JDMXY_n02_cDNA_C4_210622_fastqc.html [2021-07-08 04:27:06,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n02_cDNA_C1_210622_fastqc.html [2021-07-08 04:27:06,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H325JDMXY_n02_cDNA_C1_210622_fastqc.html [2021-07-08 04:27:06,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n01_cDNA_C1_210622_fastqc.html [2021-07-08 04:27:06,866] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H325JDMXY_n01_cDNA_C1_210622_fastqc.html [2021-07-08 04:27:06,919] multiqc [DEBUG ] File 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File ignored by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n01_cDNA_C3_210622_fastqc.html [2021-07-08 04:27:07,107] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H325JDMXY_n01_cDNA_C3_210622_fastqc.html [2021-07-08 04:27:07,155] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n01_HTO_A_210622_fastqc.html [2021-07-08 04:27:07,156] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H325JDMXY_n01_HTO_A_210622_fastqc.html [2021-07-08 04:27:07,211] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n02_GDO_D_210622_fastqc.html [2021-07-08 04:27:07,213] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H325JDMXY_n02_GDO_D_210622_fastqc.html [2021-07-08 04:27:07,297] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H325JDMXY_n01_cDNA_A2_210622_fastqc.html [2021-07-08 04:27:07,299] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H325JDMXY_n01_cDNA_A2_210622_fastqc.html [2021-07-08 04:27:07,750] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-08 04:27:07,751] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-08 04:27:07,771] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2021-07-08 04:27:07,781] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-07-08 04:27:07,782] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-07-08 04:27:07,787] multiqc [DEBUG ] No samples found: conpair [2021-07-08 04:27:07,792] multiqc [DEBUG ] No samples found: peddy [2021-07-08 04:27:07,796] multiqc [DEBUG ] No samples found: somalier [2021-07-08 04:27:07,800] multiqc [DEBUG ] No samples found: methylQA [2021-07-08 04:27:07,808] multiqc [DEBUG ] No samples found: mosdepth [2021-07-08 04:27:07,812] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-07-08 04:27:07,815] multiqc [DEBUG ] No samples found: qualimap [2021-07-08 04:27:07,819] multiqc [DEBUG ] No samples found: preseq [2021-07-08 04:27:07,823] multiqc [DEBUG ] No samples found: quast [2021-07-08 04:27:07,828] multiqc [DEBUG ] No samples found: qorts [2021-07-08 04:27:07,832] multiqc [DEBUG ] No samples found: rna_seqc [2021-07-08 04:27:07,837] multiqc [DEBUG ] No samples found: rockhopper [2021-07-08 04:27:07,841] multiqc [DEBUG ] No samples found: rsem [2021-07-08 04:27:07,851] multiqc [DEBUG ] No samples found: rseqc [2021-07-08 04:27:07,856] multiqc [DEBUG ] No samples found: busco [2021-07-08 04:27:07,860] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-07-08 04:27:07,866] multiqc [DEBUG ] No samples found: disambiguate [2021-07-08 04:27:07,871] multiqc [DEBUG ] No samples found: supernova [2021-07-08 04:27:07,883] multiqc [DEBUG ] No samples found: deeptools [2021-07-08 04:27:07,887] multiqc [DEBUG ] No samples found: sargasso [2021-07-08 04:27:07,892] multiqc [DEBUG ] No samples found: verifybamid [2021-07-08 04:27:07,896] multiqc [DEBUG ] No samples found: mirtrace [2021-07-08 04:27:07,900] multiqc [DEBUG ] No samples found: happy [2021-07-08 04:27:07,905] multiqc [DEBUG ] No samples found: mirtop [2021-07-08 04:27:07,911] multiqc [DEBUG ] No samples found: homer [2021-07-08 04:27:07,915] multiqc [DEBUG ] No samples found: macs2 [2021-07-08 04:27:07,919] multiqc [DEBUG ] No samples found: theta2 [2021-07-08 04:27:07,924] multiqc [DEBUG ] No samples found: snpeff [2021-07-08 04:27:07,930] multiqc [DEBUG ] No samples found: gatk [2021-07-08 04:27:07,934] multiqc [DEBUG ] No samples found: htseq [2021-07-08 04:27:07,939] multiqc [DEBUG ] No samples found: bcftools [2021-07-08 04:27:07,943] multiqc [DEBUG ] No samples found: featureCounts [2021-07-08 04:27:07,949] multiqc [DEBUG ] No samples found: fgbio [2021-07-08 04:27:07,961] multiqc [DEBUG ] No samples found: dragen [2021-07-08 04:27:07,965] multiqc [DEBUG ] No samples found: dedup [2021-07-08 04:27:07,970] multiqc [DEBUG ] No samples found: damageprofiler [2021-07-08 04:27:07,989] multiqc [DEBUG ] No samples found: biobambam2 [2021-07-08 04:27:07,993] multiqc [DEBUG ] No samples found: mtnucratio [2021-07-08 04:27:07,995] multiqc [DEBUG ] No samples found: picard [2021-07-08 04:27:07,999] multiqc [DEBUG ] No samples found: prokka [2021-07-08 04:27:08,003] multiqc [DEBUG ] No samples found: samblaster [2021-07-08 04:27:08,010] multiqc [DEBUG ] No samples found: samtools [2021-07-08 04:27:08,015] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-07-08 04:27:08,019] multiqc [DEBUG ] No samples found: bamtools [2021-07-08 04:27:08,023] multiqc [DEBUG ] No samples found: jellyfish [2021-07-08 04:27:08,032] multiqc [DEBUG ] No samples found: vcftools [2021-07-08 04:27:08,039] multiqc [DEBUG ] No samples found: longranger [2021-07-08 04:27:08,044] multiqc [DEBUG ] No samples found: stacks [2021-07-08 04:27:08,048] multiqc [DEBUG ] No samples found: varscan2 [2021-07-08 04:27:08,062] multiqc [DEBUG ] No samples found: bbmap [2021-07-08 04:27:08,067] multiqc [DEBUG ] No samples found: bismark [2021-07-08 04:27:08,071] multiqc [DEBUG ] No samples found: biscuit [2021-07-08 04:27:08,076] multiqc [DEBUG ] No samples found: hicexplorer [2021-07-08 04:27:08,080] multiqc [DEBUG ] No samples found: hicup [2021-07-08 04:27:08,084] multiqc [DEBUG ] No samples found: hicpro [2021-07-08 04:27:08,088] multiqc [DEBUG ] No samples found: salmon [2021-07-08 04:27:08,093] multiqc [DEBUG ] No samples found: kallisto [2021-07-08 04:27:08,097] multiqc [DEBUG ] No samples found: slamdunk [2021-07-08 04:27:08,102] multiqc [DEBUG ] No samples found: star [2021-07-08 04:27:08,106] multiqc [DEBUG ] No samples found: hisat2 [2021-07-08 04:27:08,110] multiqc [DEBUG ] No samples found: tophat [2021-07-08 04:27:08,116] multiqc [DEBUG ] No samples found: bowtie2 [2021-07-08 04:27:08,122] multiqc [DEBUG ] No samples found: bowtie1 [2021-07-08 04:27:08,126] multiqc [DEBUG ] No samples found: snpsplit [2021-07-08 04:27:08,132] multiqc [DEBUG ] No samples found: kat [2021-07-08 04:27:08,136] multiqc [DEBUG ] No samples found: leehom [2021-07-08 04:27:08,140] multiqc [DEBUG ] No samples found: adapterRemoval [2021-07-08 04:27:08,144] multiqc [DEBUG ] No samples found: clipandmerge [2021-07-08 04:27:08,148] multiqc [DEBUG ] No samples found: cutadapt [2021-07-08 04:27:08,152] multiqc [DEBUG ] No samples found: flexbar [2021-07-08 04:27:08,157] multiqc [DEBUG ] No samples found: kaiju [2021-07-08 04:27:08,161] multiqc [DEBUG ] No samples found: kraken [2021-07-08 04:27:08,165] multiqc [DEBUG ] No samples found: malt [2021-07-08 04:27:08,169] multiqc [DEBUG ] No samples found: trimmomatic [2021-07-08 04:27:08,173] multiqc [DEBUG ] No samples found: sickle [2021-07-08 04:27:08,178] multiqc [DEBUG ] No samples found: skewer [2021-07-08 04:27:08,182] multiqc [DEBUG ] No samples found: sortmerna [2021-07-08 04:27:08,186] multiqc [DEBUG ] No samples found: biobloomtools [2021-07-08 04:27:08,190] multiqc [DEBUG ] No samples found: fastq_screen [2021-07-08 04:27:08,194] multiqc [DEBUG ] No samples found: afterqc [2021-07-08 04:27:08,199] multiqc [DEBUG ] No samples found: fastp [2021-07-08 04:27:16,060] multiqc.modules.fastqc.fastqc [INFO ] Found 58 reports [2021-07-08 04:27:16,502] multiqc [DEBUG ] No samples found: pycoqc [2021-07-08 04:27:16,507] multiqc [DEBUG ] No samples found: minionqc [2021-07-08 04:27:16,512] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-07-08 04:27:16,516] multiqc [DEBUG ] No samples found: clusterflow [2021-07-08 04:27:16,520] multiqc [DEBUG ] No samples found: bcl2fastq [2021-07-08 04:27:16,525] multiqc [DEBUG ] No samples found: interop [2021-07-08 04:27:16,529] multiqc [DEBUG ] No samples found: ivar [2021-07-08 04:27:16,533] multiqc [DEBUG ] No samples found: flash [2021-07-08 04:27:16,539] multiqc [DEBUG ] No samples found: seqyclean [2021-07-08 04:27:16,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-07-08 04:27:16,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-07-08 04:27:16,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-07-08 04:27:16,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-07-08 04:27:16,606] multiqc [INFO ] Compressing plot data [2021-07-08 04:27:17,515] multiqc [INFO ] Report : multiqc_report.html [2021-07-08 04:27:17,515] multiqc [INFO ] Data : multiqc_data [2021-07-08 04:27:17,515] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8445202/tmp1rvevbyz/multiqc_data' to '/scratch/gencore/logs/html/H325JDMXY/merged/multiqc_data' [2021-07-08 04:27:17,880] multiqc [INFO ] MultiQC complete