[2022-07-22 15:14:03,631] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-22 15:14:03,631] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-22 15:14:03,631] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-22 15:14:03,632] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-22 15:14:03,632] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-22 15:14:03,632] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HT5W2AFX3/merged [2022-07-22 15:14:04,043] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-22 15:14:04,044] multiqc [INFO ] This is MultiQC v1.9 [2022-07-22 15:14:04,044] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HT5W2AFX3/merged [2022-07-22 15:14:04,044] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HT5W2AFX3/merged [2022-07-22 15:14:04,044] multiqc [INFO ] Template : default [2022-07-22 15:14:04,044] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-22 15:14:04,044] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HT5W2AFX3/merged [2022-07-22 15:14:04,044] 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 [2022-07-22 15:14:04,044] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22654834/tmp5qsl5gvo [2022-07-22 15:14:04,160] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n02_11757e-spike_fastqc.html [2022-07-22 15:14:04,163] multiqc [DEBUG ] File ignored by longranger/invocation because it 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HT5W2AFX3_n02_12014in_fastqc.html [2022-07-22 15:14:05,805] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n01_12016-in-spike_fastqc.html [2022-07-22 15:14:05,806] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n01_12016-in-spike_fastqc.html [2022-07-22 15:14:05,848] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n01_11757in-spike_fastqc.html [2022-07-22 15:14:05,850] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n01_11757in-spike_fastqc.html [2022-07-22 15:14:05,889] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n02_12016e_fastqc.html [2022-07-22 15:14:05,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n02_12016e_fastqc.html [2022-07-22 15:14:05,930] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n02_12016-e-spike_fastqc.html [2022-07-22 15:14:05,932] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n02_12016-e-spike_fastqc.html [2022-07-22 15:14:05,971] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n02_11757e_fastqc.html [2022-07-22 15:14:05,973] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n02_11757e_fastqc.html [2022-07-22 15:14:06,012] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n01_11758in-spike_fastqc.html [2022-07-22 15:14:06,014] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n01_11758in-spike_fastqc.html [2022-07-22 15:14:06,054] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n01_12012e_fastqc.html [2022-07-22 15:14:06,055] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n01_12012e_fastqc.html [2022-07-22 15:14:06,102] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n01_12012e-spike_fastqc.html [2022-07-22 15:14:06,105] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n01_12012e-spike_fastqc.html [2022-07-22 15:14:06,150] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n02_11757in-spike_fastqc.html [2022-07-22 15:14:06,152] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n02_11757in-spike_fastqc.html [2022-07-22 15:14:06,192] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5W2AFX3_n01_11758e-spike_fastqc.html [2022-07-22 15:14:06,193] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5W2AFX3_n01_11758e-spike_fastqc.html [2022-07-22 15:14:06,544] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-22 15:14:06,546] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-22 15:14:06,554] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-22 15:14:06,565] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2022-07-22 15:14:06,574] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-22 15:14:06,579] multiqc [DEBUG ] No samples found: conpair [2022-07-22 15:14:06,584] multiqc [DEBUG ] No samples found: peddy [2022-07-22 15:14:06,590] multiqc [DEBUG ] No samples found: somalier [2022-07-22 15:14:06,594] multiqc [DEBUG ] No samples found: methylQA [2022-07-22 15:14:06,602] multiqc [DEBUG ] No samples found: mosdepth [2022-07-22 15:14:06,606] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-22 15:14:06,609] multiqc [DEBUG ] No samples found: qualimap [2022-07-22 15:14:06,614] multiqc [DEBUG ] No samples found: preseq [2022-07-22 15:14:06,618] multiqc [DEBUG ] No samples found: quast [2022-07-22 15:14:06,622] multiqc [DEBUG ] No samples found: qorts [2022-07-22 15:14:06,627] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-22 15:14:06,632] multiqc [DEBUG ] No samples found: rockhopper [2022-07-22 15:14:06,636] multiqc [DEBUG ] No samples found: rsem [2022-07-22 15:14:06,647] multiqc [DEBUG ] No samples found: rseqc [2022-07-22 15:14:06,651] multiqc [DEBUG ] No samples found: busco [2022-07-22 15:14:06,656] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-22 15:14:06,660] multiqc [DEBUG ] No samples found: disambiguate [2022-07-22 15:14:06,665] multiqc [DEBUG ] No samples found: supernova [2022-07-22 15:14:06,678] multiqc [DEBUG ] No samples found: deeptools [2022-07-22 15:14:06,683] multiqc [DEBUG ] No samples found: sargasso [2022-07-22 15:14:06,687] multiqc [DEBUG ] No samples found: verifybamid [2022-07-22 15:14:06,692] multiqc [DEBUG ] No samples found: mirtrace [2022-07-22 15:14:06,696] multiqc [DEBUG ] No samples found: happy [2022-07-22 15:14:06,700] multiqc [DEBUG ] No samples found: mirtop [2022-07-22 15:14:06,706] multiqc [DEBUG ] No samples found: homer [2022-07-22 15:14:06,711] multiqc [DEBUG ] No samples found: macs2 [2022-07-22 15:14:06,716] multiqc [DEBUG ] No samples found: theta2 [2022-07-22 15:14:06,722] multiqc [DEBUG ] No samples found: snpeff [2022-07-22 15:14:06,728] multiqc [DEBUG ] No samples found: gatk [2022-07-22 15:14:06,732] multiqc [DEBUG ] No samples found: htseq [2022-07-22 15:14:06,739] multiqc [DEBUG ] No samples found: bcftools [2022-07-22 15:14:06,745] multiqc [DEBUG ] No samples found: featureCounts [2022-07-22 15:14:06,751] multiqc [DEBUG ] No samples found: fgbio [2022-07-22 15:14:06,767] multiqc [DEBUG ] No samples found: dragen [2022-07-22 15:14:06,774] multiqc [DEBUG ] No samples found: dedup [2022-07-22 15:14:06,778] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-22 15:14:06,804] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-22 15:14:06,808] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-22 15:14:06,811] multiqc [DEBUG ] No samples found: picard [2022-07-22 15:14:06,817] multiqc [DEBUG ] No samples found: prokka [2022-07-22 15:14:06,821] multiqc [DEBUG ] No samples found: samblaster [2022-07-22 15:14:06,831] multiqc [DEBUG ] No samples found: samtools [2022-07-22 15:14:06,835] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-22 15:14:06,841] multiqc [DEBUG ] No samples found: bamtools [2022-07-22 15:14:06,846] multiqc [DEBUG ] No samples found: jellyfish [2022-07-22 15:14:06,854] multiqc [DEBUG ] No samples found: vcftools [2022-07-22 15:14:06,859] multiqc [DEBUG ] No samples found: longranger [2022-07-22 15:14:06,864] multiqc [DEBUG ] No samples found: stacks [2022-07-22 15:14:06,871] multiqc [DEBUG ] No samples found: varscan2 [2022-07-22 15:14:06,887] multiqc [DEBUG ] No samples found: bbmap [2022-07-22 15:14:06,891] multiqc [DEBUG ] No samples found: bismark [2022-07-22 15:14:06,898] multiqc [DEBUG ] No samples found: biscuit [2022-07-22 15:14:06,902] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-22 15:14:06,907] multiqc [DEBUG ] No samples found: hicup [2022-07-22 15:14:06,911] multiqc [DEBUG ] No samples found: hicpro [2022-07-22 15:14:06,915] multiqc [DEBUG ] No samples found: salmon [2022-07-22 15:14:06,920] multiqc [DEBUG ] No samples found: kallisto [2022-07-22 15:14:06,924] multiqc [DEBUG ] No samples found: slamdunk [2022-07-22 15:14:06,929] multiqc [DEBUG ] No samples found: star [2022-07-22 15:14:06,935] multiqc [DEBUG ] No samples found: hisat2 [2022-07-22 15:14:06,939] multiqc [DEBUG ] No samples found: tophat [2022-07-22 15:14:06,944] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-22 15:14:06,949] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-22 15:14:06,953] multiqc [DEBUG ] No samples found: snpsplit [2022-07-22 15:14:06,957] multiqc [DEBUG ] No samples found: kat [2022-07-22 15:14:06,961] multiqc [DEBUG ] No samples found: leehom [2022-07-22 15:14:06,966] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-22 15:14:06,970] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-22 15:14:06,974] multiqc [DEBUG ] No samples found: cutadapt [2022-07-22 15:14:06,980] multiqc [DEBUG ] No samples found: flexbar [2022-07-22 15:14:06,984] multiqc [DEBUG ] No samples found: kaiju [2022-07-22 15:14:06,989] multiqc [DEBUG ] No samples found: kraken [2022-07-22 15:14:06,993] multiqc [DEBUG ] No samples found: malt [2022-07-22 15:14:06,997] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-22 15:14:07,003] multiqc [DEBUG ] No samples found: sickle [2022-07-22 15:14:07,009] multiqc [DEBUG ] No samples found: skewer [2022-07-22 15:14:07,013] multiqc [DEBUG ] No samples found: sortmerna [2022-07-22 15:14:07,017] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-22 15:14:07,021] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-22 15:14:07,026] multiqc [DEBUG ] No samples found: afterqc [2022-07-22 15:14:07,030] multiqc [DEBUG ] No samples found: fastp [2022-07-22 15:14:08,016] multiqc.modules.fastqc.fastqc [INFO ] Found 46 reports [2022-07-22 15:14:08,383] multiqc [DEBUG ] No samples found: pycoqc [2022-07-22 15:14:08,395] multiqc [DEBUG ] No samples found: minionqc [2022-07-22 15:14:08,413] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-22 15:14:08,418] multiqc [DEBUG ] No samples found: clusterflow [2022-07-22 15:14:08,429] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-22 15:14:08,434] multiqc [DEBUG ] No samples found: interop [2022-07-22 15:14:08,440] multiqc [DEBUG ] No samples found: ivar [2022-07-22 15:14:08,446] multiqc [DEBUG ] No samples found: flash [2022-07-22 15:14:08,457] multiqc [DEBUG ] No samples found: seqyclean [2022-07-22 15:14:08,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-22 15:14:08,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-22 15:14:08,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-22 15:14:08,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-22 15:14:08,512] multiqc [INFO ] Compressing plot data [2022-07-22 15:14:09,258] multiqc [INFO ] Report : multiqc_report.html [2022-07-22 15:14:09,258] multiqc [INFO ] Data : multiqc_data [2022-07-22 15:14:09,258] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22654834/tmp5qsl5gvo/multiqc_data' to '/scratch/gencore/logs/html/HT5W2AFX3/merged/multiqc_data' [2022-07-22 15:14:09,442] multiqc [INFO ] MultiQC complete