[2021-09-23 01:45:32,113] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-23 01:45:32,113] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-23 01:45:32,113] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-23 01:45:32,114] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-23 01:45:32,114] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-23 01:45:32,114] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGTMKDRXY/merged [2021-09-23 01:45:33,474] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-23 01:45:33,474] multiqc [INFO ] This is MultiQC v1.9 [2021-09-23 01:45:33,475] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGTMKDRXY/merged [2021-09-23 01:45:33,475] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGTMKDRXY/merged [2021-09-23 01:45:33,475] multiqc [INFO ] Template : default [2021-09-23 01:45:33,475] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-23 01:45:33,475] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGTMKDRXY/merged [2021-09-23 01:45:33,475] 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 [2021-09-23 01:45:33,475] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10228797/tmpmokl2rk_ [2021-09-23 01:45:33,578] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei073_1_fastqc.html [2021-09-23 01:45:33,580] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei073_1_fastqc.html [2021-09-23 01:45:33,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-23 01:45:33,622] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-23 01:45:33,703] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei069_1_fastqc.html [2021-09-23 01:45:33,705] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei069_1_fastqc.html [2021-09-23 01:45:33,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei070_1_fastqc.html [2021-09-23 01:45:33,747] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei070_1_fastqc.html [2021-09-23 01:45:33,787] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei056_1_fastqc.html [2021-09-23 01:45:33,789] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei056_1_fastqc.html [2021-09-23 01:45:33,829] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei080_fastqc.html [2021-09-23 01:45:33,831] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei080_fastqc.html [2021-09-23 01:45:33,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei075_1_fastqc.html [2021-09-23 01:45:33,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei075_1_fastqc.html [2021-09-23 01:45:33,917] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei085_fastqc.html [2021-09-23 01:45:33,919] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei085_fastqc.html [2021-09-23 01:45:33,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei074_1_fastqc.html [2021-09-23 01:45:33,960] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei074_1_fastqc.html [2021-09-23 01:45:34,003] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei082_fastqc.html [2021-09-23 01:45:34,005] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei082_fastqc.html [2021-09-23 01:45:34,044] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei064_1_fastqc.html [2021-09-23 01:45:34,046] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei064_1_fastqc.html [2021-09-23 01:45:34,086] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei076_1_fastqc.html [2021-09-23 01:45:34,088] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei076_1_fastqc.html [2021-09-23 01:45:34,127] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei084_fastqc.html [2021-09-23 01:45:34,129] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei084_fastqc.html [2021-09-23 01:45:34,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei083_fastqc.html [2021-09-23 01:45:34,171] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei083_fastqc.html [2021-09-23 01:45:34,210] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei081_fastqc.html [2021-09-23 01:45:34,212] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_dei081_fastqc.html [2021-09-23 01:45:34,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTMKDRXY_n01_undetermined_fastqc.html [2021-09-23 01:45:34,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTMKDRXY_n01_undetermined_fastqc.html [2021-09-23 01:45:34,780] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-23 01:45:34,782] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-23 01:45:34,791] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-23 01:45:34,801] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-23 01:45:34,808] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 15 samples (table) [2021-09-23 01:45:34,812] multiqc [DEBUG ] No samples found: conpair [2021-09-23 01:45:34,817] multiqc [DEBUG ] No samples found: peddy [2021-09-23 01:45:34,823] multiqc [DEBUG ] No samples found: somalier [2021-09-23 01:45:34,829] multiqc [DEBUG ] No samples found: methylQA [2021-09-23 01:45:34,839] multiqc [DEBUG ] No samples found: mosdepth [2021-09-23 01:45:34,843] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-23 01:45:34,846] multiqc [DEBUG ] No samples found: qualimap [2021-09-23 01:45:34,851] multiqc [DEBUG ] No samples found: preseq [2021-09-23 01:45:34,855] multiqc [DEBUG ] No samples found: quast [2021-09-23 01:45:34,860] multiqc [DEBUG ] No samples found: qorts [2021-09-23 01:45:34,864] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-23 01:45:34,869] multiqc [DEBUG ] No samples found: rockhopper [2021-09-23 01:45:34,875] multiqc [DEBUG ] No samples found: rsem [2021-09-23 01:45:34,887] multiqc [DEBUG ] No samples found: rseqc [2021-09-23 01:45:34,892] multiqc [DEBUG ] No samples found: busco [2021-09-23 01:45:34,896] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-23 01:45:34,901] multiqc [DEBUG ] No samples found: disambiguate [2021-09-23 01:45:34,905] multiqc [DEBUG ] No samples found: supernova [2021-09-23 01:45:34,918] multiqc [DEBUG ] No samples found: deeptools [2021-09-23 01:45:34,923] multiqc [DEBUG ] No samples found: sargasso [2021-09-23 01:45:34,927] multiqc [DEBUG ] No samples found: verifybamid [2021-09-23 01:45:34,932] multiqc [DEBUG ] No samples found: mirtrace [2021-09-23 01:45:34,936] multiqc [DEBUG ] No samples found: happy [2021-09-23 01:45:34,941] multiqc [DEBUG ] No samples found: mirtop [2021-09-23 01:45:34,947] multiqc [DEBUG ] No samples found: homer [2021-09-23 01:45:34,952] multiqc [DEBUG ] No samples found: macs2 [2021-09-23 01:45:34,956] multiqc [DEBUG ] No samples found: theta2 [2021-09-23 01:45:34,960] multiqc [DEBUG ] No samples found: snpeff [2021-09-23 01:45:34,968] multiqc [DEBUG ] No samples found: gatk [2021-09-23 01:45:34,972] multiqc [DEBUG ] No samples found: htseq [2021-09-23 01:45:34,978] multiqc [DEBUG ] No samples found: bcftools [2021-09-23 01:45:34,983] multiqc [DEBUG ] No samples found: featureCounts [2021-09-23 01:45:34,989] multiqc [DEBUG ] No samples found: fgbio [2021-09-23 01:45:35,002] multiqc [DEBUG ] No samples found: dragen [2021-09-23 01:45:35,006] multiqc [DEBUG ] No samples found: dedup [2021-09-23 01:45:35,010] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-23 01:45:35,033] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-23 01:45:35,037] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-23 01:45:35,040] multiqc [DEBUG ] No samples found: picard [2021-09-23 01:45:35,044] multiqc [DEBUG ] No samples found: prokka [2021-09-23 01:45:35,048] multiqc [DEBUG ] No samples found: samblaster [2021-09-23 01:45:35,058] multiqc [DEBUG ] No samples found: samtools [2021-09-23 01:45:35,062] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-23 01:45:35,067] multiqc [DEBUG ] No samples found: bamtools [2021-09-23 01:45:35,071] multiqc [DEBUG ] No samples found: jellyfish [2021-09-23 01:45:35,079] multiqc [DEBUG ] No samples found: vcftools [2021-09-23 01:45:35,084] multiqc [DEBUG ] No samples found: longranger [2021-09-23 01:45:35,088] multiqc [DEBUG ] No samples found: stacks [2021-09-23 01:45:35,093] multiqc [DEBUG ] No samples found: varscan2 [2021-09-23 01:45:35,107] multiqc [DEBUG ] No samples found: bbmap [2021-09-23 01:45:35,111] multiqc [DEBUG ] No samples found: bismark [2021-09-23 01:45:35,116] multiqc [DEBUG ] No samples found: biscuit [2021-09-23 01:45:35,121] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-23 01:45:35,125] multiqc [DEBUG ] No samples found: hicup [2021-09-23 01:45:35,130] multiqc [DEBUG ] No samples found: hicpro [2021-09-23 01:45:35,135] multiqc [DEBUG ] No samples found: salmon [2021-09-23 01:45:35,140] multiqc [DEBUG ] No samples found: kallisto [2021-09-23 01:45:35,144] multiqc [DEBUG ] No samples found: slamdunk [2021-09-23 01:45:35,149] multiqc [DEBUG ] No samples found: star [2021-09-23 01:45:35,155] multiqc [DEBUG ] No samples found: hisat2 [2021-09-23 01:45:35,159] multiqc [DEBUG ] No samples found: tophat [2021-09-23 01:45:35,163] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-23 01:45:35,167] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-23 01:45:35,172] multiqc [DEBUG ] No samples found: snpsplit [2021-09-23 01:45:35,176] multiqc [DEBUG ] No samples found: kat [2021-09-23 01:45:35,181] multiqc [DEBUG ] No samples found: leehom [2021-09-23 01:45:35,185] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-23 01:45:35,190] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-23 01:45:35,196] multiqc [DEBUG ] No samples found: cutadapt [2021-09-23 01:45:35,200] multiqc [DEBUG ] No samples found: flexbar [2021-09-23 01:45:35,204] multiqc [DEBUG ] No samples found: kaiju [2021-09-23 01:45:35,209] multiqc [DEBUG ] No samples found: kraken [2021-09-23 01:45:35,213] multiqc [DEBUG ] No samples found: malt [2021-09-23 01:45:35,217] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-23 01:45:35,222] multiqc [DEBUG ] No samples found: sickle [2021-09-23 01:45:35,226] multiqc [DEBUG ] No samples found: skewer [2021-09-23 01:45:35,230] multiqc [DEBUG ] No samples found: sortmerna [2021-09-23 01:45:35,234] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-23 01:45:35,240] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-23 01:45:35,244] multiqc [DEBUG ] No samples found: afterqc [2021-09-23 01:45:35,249] multiqc [DEBUG ] No samples found: fastp [2021-09-23 01:45:35,801] multiqc.modules.fastqc.fastqc [INFO ] Found 15 reports [2021-09-23 01:45:36,014] multiqc [DEBUG ] No samples found: pycoqc [2021-09-23 01:45:36,019] multiqc [DEBUG ] No samples found: minionqc [2021-09-23 01:45:36,023] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-23 01:45:36,028] multiqc [DEBUG ] No samples found: clusterflow [2021-09-23 01:45:36,033] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-23 01:45:36,039] multiqc [DEBUG ] No samples found: interop [2021-09-23 01:45:36,044] multiqc [DEBUG ] No samples found: ivar [2021-09-23 01:45:36,049] multiqc [DEBUG ] No samples found: flash [2021-09-23 01:45:36,053] multiqc [DEBUG ] No samples found: seqyclean [2021-09-23 01:45:36,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-09-23 01:45:36,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-09-23 01:45:36,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-23 01:45:36,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-23 01:45:36,073] multiqc [INFO ] Compressing plot data [2021-09-23 01:45:36,364] multiqc [INFO ] Report : multiqc_report.html [2021-09-23 01:45:36,365] multiqc [INFO ] Data : multiqc_data [2021-09-23 01:45:36,365] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10228797/tmpmokl2rk_/multiqc_data' to '/scratch/gencore/logs/html/HGTMKDRXY/merged/multiqc_data' [2021-09-23 01:45:36,572] multiqc [INFO ] MultiQC complete