[2021-06-28 16:50:57,895] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-28 16:50:57,895] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-28 16:50:57,895] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-28 16:50:57,896] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-28 16:50:57,896] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-28 16:50:57,896] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H53C5BGXJ/merged [2021-06-28 16:50:59,244] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-28 16:50:59,244] multiqc [INFO ] This is MultiQC v1.9 [2021-06-28 16:50:59,244] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H53C5BGXJ/merged [2021-06-28 16:50:59,244] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H53C5BGXJ/merged [2021-06-28 16:50:59,244] multiqc [INFO ] Template : default [2021-06-28 16:50:59,244] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-28 16:50:59,244] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H53C5BGXJ/merged [2021-06-28 16:50:59,245] 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 [2021-06-28 16:50:59,245] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8165522/tmphyk8f32h [2021-06-28 16:50:59,349] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3385_fastqc.html [2021-06-28 16:50:59,352] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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filesize limit: H53C5BGXJ_n02_3QG3382_fastqc.html [2021-06-28 16:51:08,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3394_fastqc.html [2021-06-28 16:51:08,688] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3394_fastqc.html [2021-06-28 16:51:08,728] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3377_fastqc.html [2021-06-28 16:51:08,730] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3377_fastqc.html [2021-06-28 16:51:08,768] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3284_fastqc.html [2021-06-28 16:51:08,770] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3284_fastqc.html [2021-06-28 16:51:08,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3420_fastqc.html [2021-06-28 16:51:08,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3420_fastqc.html [2021-06-28 16:51:08,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3288_fastqc.html [2021-06-28 16:51:08,868] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3288_fastqc.html [2021-06-28 16:51:08,907] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3335_fastqc.html [2021-06-28 16:51:08,909] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3335_fastqc.html [2021-06-28 16:51:08,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3470_fastqc.html [2021-06-28 16:51:08,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3470_fastqc.html [2021-06-28 16:51:09,008] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3137_fastqc.html [2021-06-28 16:51:09,010] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3137_fastqc.html [2021-06-28 16:51:09,049] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3431_fastqc.html [2021-06-28 16:51:09,051] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3431_fastqc.html [2021-06-28 16:51:09,109] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3234_fastqc.html [2021-06-28 16:51:09,111] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3234_fastqc.html [2021-06-28 16:51:09,150] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3188_fastqc.html [2021-06-28 16:51:09,151] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n01_3QG3188_fastqc.html [2021-06-28 16:51:09,190] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3218_fastqc.html [2021-06-28 16:51:09,192] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53C5BGXJ_n02_3QG3218_fastqc.html [2021-06-28 16:51:09,537] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-28 16:51:09,538] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-28 16:51:09,588] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 96 samples (table) [2021-06-28 16:51:09,590] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-28 16:51:09,599] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-06-28 16:51:09,603] multiqc [DEBUG ] No samples found: conpair [2021-06-28 16:51:09,607] multiqc [DEBUG ] No samples found: peddy [2021-06-28 16:51:09,612] multiqc [DEBUG ] No samples found: somalier [2021-06-28 16:51:09,616] multiqc [DEBUG ] No samples found: methylQA [2021-06-28 16:51:09,623] multiqc [DEBUG ] No samples found: mosdepth [2021-06-28 16:51:09,627] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-28 16:51:09,630] multiqc [DEBUG ] No samples found: qualimap [2021-06-28 16:51:09,634] multiqc [DEBUG ] No samples found: preseq [2021-06-28 16:51:09,638] multiqc [DEBUG ] No samples found: quast [2021-06-28 16:51:09,642] multiqc [DEBUG ] No samples found: qorts [2021-06-28 16:51:09,647] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-28 16:51:09,652] multiqc [DEBUG ] No samples found: rockhopper [2021-06-28 16:51:09,656] multiqc [DEBUG ] No samples found: rsem [2021-06-28 16:51:09,666] multiqc [DEBUG ] No samples found: rseqc [2021-06-28 16:51:09,670] multiqc [DEBUG ] No samples found: busco [2021-06-28 16:51:09,675] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-28 16:51:09,679] multiqc [DEBUG ] No samples found: disambiguate [2021-06-28 16:51:09,684] multiqc [DEBUG ] No samples found: supernova [2021-06-28 16:51:09,696] multiqc [DEBUG ] No samples found: deeptools [2021-06-28 16:51:09,701] multiqc [DEBUG ] No samples found: sargasso [2021-06-28 16:51:09,705] multiqc [DEBUG ] No samples found: verifybamid [2021-06-28 16:51:09,709] multiqc [DEBUG ] No samples found: mirtrace [2021-06-28 16:51:09,713] multiqc [DEBUG ] No samples found: happy [2021-06-28 16:51:09,717] multiqc [DEBUG ] No samples found: mirtop [2021-06-28 16:51:09,723] multiqc [DEBUG ] No samples found: homer [2021-06-28 16:51:09,727] multiqc [DEBUG ] No samples found: macs2 [2021-06-28 16:51:09,731] multiqc [DEBUG ] No samples found: theta2 [2021-06-28 16:51:09,736] multiqc [DEBUG ] No samples found: snpeff [2021-06-28 16:51:09,742] multiqc [DEBUG ] No samples found: gatk [2021-06-28 16:51:09,746] multiqc [DEBUG ] No samples found: htseq [2021-06-28 16:51:09,751] multiqc [DEBUG ] No samples found: bcftools [2021-06-28 16:51:09,755] multiqc [DEBUG ] No samples found: featureCounts [2021-06-28 16:51:09,760] multiqc [DEBUG ] No samples found: fgbio [2021-06-28 16:51:09,771] multiqc [DEBUG ] No samples found: dragen [2021-06-28 16:51:09,775] multiqc [DEBUG ] No samples found: dedup [2021-06-28 16:51:09,779] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-28 16:51:09,798] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-28 16:51:09,802] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-28 16:51:09,804] multiqc [DEBUG ] No samples found: picard [2021-06-28 16:51:09,809] multiqc [DEBUG ] No samples found: prokka [2021-06-28 16:51:09,813] multiqc [DEBUG ] No samples found: samblaster [2021-06-28 16:51:09,820] multiqc [DEBUG ] No samples found: samtools [2021-06-28 16:51:09,824] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-28 16:51:09,828] multiqc [DEBUG ] No samples found: bamtools [2021-06-28 16:51:09,832] multiqc [DEBUG ] No samples found: jellyfish [2021-06-28 16:51:09,839] multiqc [DEBUG ] No samples found: vcftools [2021-06-28 16:51:09,844] multiqc [DEBUG ] No samples found: longranger [2021-06-28 16:51:09,848] multiqc [DEBUG ] No samples found: stacks [2021-06-28 16:51:09,852] multiqc [DEBUG ] No samples found: varscan2 [2021-06-28 16:51:09,864] multiqc [DEBUG ] No samples found: bbmap [2021-06-28 16:51:09,868] multiqc [DEBUG ] No samples found: bismark [2021-06-28 16:51:09,872] multiqc [DEBUG ] No samples found: biscuit [2021-06-28 16:51:09,877] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-28 16:51:09,881] multiqc [DEBUG ] No samples found: hicup [2021-06-28 16:51:09,885] multiqc [DEBUG ] No samples found: hicpro [2021-06-28 16:51:09,889] multiqc [DEBUG ] No samples found: salmon [2021-06-28 16:51:09,893] multiqc [DEBUG ] No samples found: kallisto [2021-06-28 16:51:09,897] multiqc [DEBUG ] No samples found: slamdunk [2021-06-28 16:51:09,901] multiqc [DEBUG ] No samples found: star [2021-06-28 16:51:09,905] multiqc [DEBUG ] No samples found: hisat2 [2021-06-28 16:51:09,910] multiqc [DEBUG ] No samples found: tophat [2021-06-28 16:51:09,914] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-28 16:51:09,918] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-28 16:51:09,922] multiqc [DEBUG ] No samples found: snpsplit [2021-06-28 16:51:09,926] multiqc [DEBUG ] No samples found: kat [2021-06-28 16:51:09,930] multiqc [DEBUG ] No samples found: leehom [2021-06-28 16:51:09,934] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-28 16:51:09,938] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-28 16:51:09,942] multiqc [DEBUG ] No samples found: cutadapt [2021-06-28 16:51:09,947] multiqc [DEBUG ] No samples found: flexbar [2021-06-28 16:51:09,951] multiqc [DEBUG ] No samples found: kaiju [2021-06-28 16:51:09,955] multiqc [DEBUG ] No samples found: kraken [2021-06-28 16:51:09,960] multiqc [DEBUG ] No samples found: malt [2021-06-28 16:51:09,964] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-28 16:51:09,968] multiqc [DEBUG ] No samples found: sickle [2021-06-28 16:51:09,973] multiqc [DEBUG ] No samples found: skewer [2021-06-28 16:51:09,978] multiqc [DEBUG ] No samples found: sortmerna [2021-06-28 16:51:09,982] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-28 16:51:09,986] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-28 16:51:09,991] multiqc [DEBUG ] No samples found: afterqc [2021-06-28 16:51:09,995] multiqc [DEBUG ] No samples found: fastp [2021-06-28 16:51:24,870] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2021-06-28 16:51:45,977] multiqc [DEBUG ] No samples found: pycoqc [2021-06-28 16:51:45,982] multiqc [DEBUG ] No samples found: minionqc [2021-06-28 16:51:45,987] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-28 16:51:45,991] multiqc [DEBUG ] No samples found: clusterflow [2021-06-28 16:51:45,996] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-28 16:51:46,001] multiqc [DEBUG ] No samples found: interop [2021-06-28 16:51:46,006] multiqc [DEBUG ] No samples found: ivar [2021-06-28 16:51:46,011] multiqc [DEBUG ] No samples found: flash [2021-06-28 16:51:46,016] multiqc [DEBUG ] No samples found: seqyclean [2021-06-28 16:51:46,016] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-06-28 16:51:46,016] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-06-28 16:51:46,016] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-06-28 16:51:46,016] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-28 16:51:46,231] multiqc [INFO ] Compressing plot data [2021-06-28 16:51:46,293] multiqc [INFO ] Report : multiqc_report.html [2021-06-28 16:51:46,293] multiqc [INFO ] Data : multiqc_data [2021-06-28 16:51:46,293] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8165522/tmphyk8f32h/multiqc_data' to '/scratch/gencore/logs/html/H53C5BGXJ/merged/multiqc_data' [2021-06-28 16:51:46,431] multiqc [INFO ] MultiQC complete