[2021-04-05 23:45:32,102] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-04-05 23:45:32,103] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-04-05 23:45:32,103] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-04-05 23:45:32,103] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-04-05 23:45:32,104] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-04-05 23:45:32,104] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HYCCVBGXG/merged [2021-04-05 23:45:33,179] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-04-05 23:45:33,179] multiqc [INFO ] This is MultiQC v1.9 [2021-04-05 23:45:33,179] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HYCCVBGXG/merged [2021-04-05 23:45:33,179] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HYCCVBGXG/merged [2021-04-05 23:45:33,179] multiqc [INFO ] Template : default [2021-04-05 23:45:33,179] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-04-05 23:45:33,179] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HYCCVBGXG/merged [2021-04-05 23:45:33,180] 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 [2021-04-05 23:45:33,180] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-4858552/tmpx23rmk2x [2021-04-05 23:45:33,283] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM230_fastqc.html [2021-04-05 23:45:33,286] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM230_fastqc.html [2021-04-05 23:45:33,326] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM232_fastqc.html [2021-04-05 23:45:33,327] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM232_fastqc.html [2021-04-05 23:45:33,366] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM201_fastqc.html [2021-04-05 23:45:33,367] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM201_fastqc.html [2021-04-05 23:45:33,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-04-05 23:45:33,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-04-05 23:45:33,505] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM210_fastqc.html [2021-04-05 23:45:33,506] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM210_fastqc.html [2021-04-05 23:45:33,546] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM231_fastqc.html [2021-04-05 23:45:33,547] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM231_fastqc.html [2021-04-05 23:45:33,585] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM239_fastqc.html [2021-04-05 23:45:33,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM239_fastqc.html [2021-04-05 23:45:33,625] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM242_fastqc.html [2021-04-05 23:45:33,626] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM242_fastqc.html [2021-04-05 23:45:33,664] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_undetermined_fastqc.html [2021-04-05 23:45:33,666] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_undetermined_fastqc.html [2021-04-05 23:45:33,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM233_fastqc.html [2021-04-05 23:45:33,706] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM233_fastqc.html [2021-04-05 23:45:33,744] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM235_fastqc.html [2021-04-05 23:45:33,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM235_fastqc.html [2021-04-05 23:45:33,783] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_JK26_fastqc.html [2021-04-05 23:45:33,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_JK26_fastqc.html [2021-04-05 23:45:33,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM240_fastqc.html [2021-04-05 23:45:33,831] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM240_fastqc.html [2021-04-05 23:45:33,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_JK27_fastqc.html [2021-04-05 23:45:33,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_JK27_fastqc.html [2021-04-05 23:45:33,913] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM229_fastqc.html [2021-04-05 23:45:33,915] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM229_fastqc.html [2021-04-05 23:45:33,953] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM236_fastqc.html [2021-04-05 23:45:33,955] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM236_fastqc.html [2021-04-05 23:45:33,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM237_fastqc.html [2021-04-05 23:45:33,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM237_fastqc.html [2021-04-05 23:45:34,034] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM203_fastqc.html [2021-04-05 23:45:34,036] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM203_fastqc.html [2021-04-05 23:45:34,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM234_fastqc.html [2021-04-05 23:45:34,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM234_fastqc.html [2021-04-05 23:45:34,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_JK25_fastqc.html [2021-04-05 23:45:34,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_JK25_fastqc.html [2021-04-05 23:45:34,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM241_fastqc.html [2021-04-05 23:45:34,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM241_fastqc.html [2021-04-05 23:45:34,196] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM211_fastqc.html [2021-04-05 23:45:34,198] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM211_fastqc.html [2021-04-05 23:45:34,238] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM238_fastqc.html [2021-04-05 23:45:34,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM238_fastqc.html [2021-04-05 23:45:34,277] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM202_fastqc.html [2021-04-05 23:45:34,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYCCVBGXG_n01_AKM202_fastqc.html [2021-04-05 23:45:35,089] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-05 23:45:35,090] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-05 23:45:35,097] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-04-05 23:45:35,108] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2021-04-05 23:45:35,118] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-04-05 23:45:35,122] multiqc [DEBUG ] No samples found: conpair [2021-04-05 23:45:35,127] multiqc [DEBUG ] No samples found: peddy [2021-04-05 23:45:35,132] multiqc [DEBUG ] No samples found: somalier [2021-04-05 23:45:35,137] multiqc [DEBUG ] No samples found: methylQA [2021-04-05 23:45:35,145] multiqc [DEBUG ] No samples found: mosdepth [2021-04-05 23:45:35,149] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-04-05 23:45:35,153] multiqc [DEBUG ] No samples found: qualimap [2021-04-05 23:45:35,157] multiqc [DEBUG ] No samples found: preseq [2021-04-05 23:45:35,162] multiqc [DEBUG ] No samples found: quast [2021-04-05 23:45:35,167] multiqc [DEBUG ] No samples found: qorts [2021-04-05 23:45:35,171] multiqc [DEBUG ] No samples found: rna_seqc [2021-04-05 23:45:35,176] multiqc [DEBUG ] No samples found: rockhopper [2021-04-05 23:45:35,180] multiqc [DEBUG ] No samples found: rsem [2021-04-05 23:45:35,191] multiqc [DEBUG ] No samples found: rseqc [2021-04-05 23:45:35,195] multiqc [DEBUG ] No samples found: busco [2021-04-05 23:45:35,200] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-04-05 23:45:35,204] multiqc [DEBUG ] No samples found: disambiguate [2021-04-05 23:45:35,209] multiqc [DEBUG ] No samples found: supernova [2021-04-05 23:45:35,222] multiqc [DEBUG ] No samples found: deeptools [2021-04-05 23:45:35,226] multiqc [DEBUG ] No samples found: sargasso [2021-04-05 23:45:35,230] multiqc [DEBUG ] No samples found: verifybamid [2021-04-05 23:45:35,235] multiqc [DEBUG ] No samples found: mirtrace [2021-04-05 23:45:35,239] multiqc [DEBUG ] No samples found: happy [2021-04-05 23:45:35,243] multiqc [DEBUG ] No samples found: mirtop [2021-04-05 23:45:35,250] multiqc [DEBUG ] No samples found: homer [2021-04-05 23:45:35,254] multiqc [DEBUG ] No samples found: macs2 [2021-04-05 23:45:35,259] multiqc [DEBUG ] No samples found: theta2 [2021-04-05 23:45:35,263] multiqc [DEBUG ] No samples found: snpeff [2021-04-05 23:45:35,270] multiqc [DEBUG ] No samples found: gatk [2021-04-05 23:45:35,274] multiqc [DEBUG ] No samples found: htseq [2021-04-05 23:45:35,279] multiqc [DEBUG ] No samples found: bcftools [2021-04-05 23:45:35,283] multiqc [DEBUG ] No samples found: featureCounts [2021-04-05 23:45:35,289] multiqc [DEBUG ] No samples found: fgbio [2021-04-05 23:45:35,301] multiqc [DEBUG ] No samples found: dragen [2021-04-05 23:45:35,306] multiqc [DEBUG ] No samples found: dedup [2021-04-05 23:45:35,311] multiqc [DEBUG ] No samples found: damageprofiler [2021-04-05 23:45:35,329] multiqc [DEBUG ] No samples found: biobambam2 [2021-04-05 23:45:35,332] multiqc [DEBUG ] No samples found: mtnucratio [2021-04-05 23:45:35,335] multiqc [DEBUG ] No samples found: picard [2021-04-05 23:45:35,339] multiqc [DEBUG ] No samples found: prokka [2021-04-05 23:45:35,343] multiqc [DEBUG ] No samples found: samblaster [2021-04-05 23:45:35,350] multiqc [DEBUG ] No samples found: samtools [2021-04-05 23:45:35,355] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-04-05 23:45:35,360] multiqc [DEBUG ] No samples found: bamtools [2021-04-05 23:45:35,364] multiqc [DEBUG ] No samples found: jellyfish [2021-04-05 23:45:35,371] multiqc [DEBUG ] No samples found: vcftools [2021-04-05 23:45:35,375] multiqc [DEBUG ] No samples found: longranger [2021-04-05 23:45:35,379] multiqc [DEBUG ] No samples found: stacks [2021-04-05 23:45:35,384] multiqc [DEBUG ] No samples found: varscan2 [2021-04-05 23:45:35,398] multiqc [DEBUG ] No samples found: bbmap [2021-04-05 23:45:35,402] multiqc [DEBUG ] No samples found: bismark [2021-04-05 23:45:35,407] multiqc [DEBUG ] No samples found: biscuit [2021-04-05 23:45:35,412] multiqc [DEBUG ] No samples found: hicexplorer [2021-04-05 23:45:35,416] multiqc [DEBUG ] No samples found: hicup [2021-04-05 23:45:35,421] multiqc [DEBUG ] No samples found: hicpro [2021-04-05 23:45:35,425] multiqc [DEBUG ] No samples found: salmon [2021-04-05 23:45:35,429] multiqc [DEBUG ] No samples found: kallisto [2021-04-05 23:45:35,434] multiqc [DEBUG ] No samples found: slamdunk [2021-04-05 23:45:35,438] multiqc [DEBUG ] No samples found: star [2021-04-05 23:45:35,442] multiqc [DEBUG ] No samples found: hisat2 [2021-04-05 23:45:35,446] multiqc [DEBUG ] No samples found: tophat [2021-04-05 23:45:35,451] multiqc [DEBUG ] No samples found: bowtie2 [2021-04-05 23:45:35,456] multiqc [DEBUG ] No samples found: bowtie1 [2021-04-05 23:45:35,461] multiqc [DEBUG ] No samples found: snpsplit [2021-04-05 23:45:35,465] multiqc [DEBUG ] No samples found: kat [2021-04-05 23:45:35,469] multiqc [DEBUG ] No samples found: leehom [2021-04-05 23:45:35,473] multiqc [DEBUG ] No samples found: adapterRemoval [2021-04-05 23:45:35,477] multiqc [DEBUG ] No samples found: clipandmerge [2021-04-05 23:45:35,481] multiqc [DEBUG ] No samples found: cutadapt [2021-04-05 23:45:35,485] multiqc [DEBUG ] No samples found: flexbar [2021-04-05 23:45:35,490] multiqc [DEBUG ] No samples found: kaiju [2021-04-05 23:45:35,494] multiqc [DEBUG ] No samples found: kraken [2021-04-05 23:45:35,499] multiqc [DEBUG ] No samples found: malt [2021-04-05 23:45:35,503] multiqc [DEBUG ] No samples found: trimmomatic [2021-04-05 23:45:35,507] multiqc [DEBUG ] No samples found: sickle [2021-04-05 23:45:35,512] multiqc [DEBUG ] No samples found: skewer [2021-04-05 23:45:35,516] multiqc [DEBUG ] No samples found: sortmerna [2021-04-05 23:45:35,520] multiqc [DEBUG ] No samples found: biobloomtools [2021-04-05 23:45:35,525] multiqc [DEBUG ] No samples found: fastq_screen [2021-04-05 23:45:35,529] multiqc [DEBUG ] No samples found: afterqc [2021-04-05 23:45:35,534] multiqc [DEBUG ] No samples found: fastp [2021-04-05 23:45:37,117] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2021-04-05 23:45:37,605] multiqc [DEBUG ] No samples found: pycoqc [2021-04-05 23:45:37,610] multiqc [DEBUG ] No samples found: minionqc [2021-04-05 23:45:37,615] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-04-05 23:45:37,619] multiqc [DEBUG ] No samples found: clusterflow [2021-04-05 23:45:37,624] multiqc [DEBUG ] No samples found: bcl2fastq [2021-04-05 23:45:37,628] multiqc [DEBUG ] No samples found: interop [2021-04-05 23:45:37,633] multiqc [DEBUG ] No samples found: ivar [2021-04-05 23:45:37,638] multiqc [DEBUG ] No samples found: flash [2021-04-05 23:45:37,642] multiqc [DEBUG ] No samples found: seqyclean [2021-04-05 23:45:37,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-04-05 23:45:37,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-04-05 23:45:37,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-04-05 23:45:37,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-04-05 23:45:37,669] multiqc [INFO ] Compressing plot data [2021-04-05 23:45:38,083] multiqc [INFO ] Report : multiqc_report.html [2021-04-05 23:45:38,083] multiqc [INFO ] Data : multiqc_data [2021-04-05 23:45:38,083] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4858552/tmpx23rmk2x/multiqc_data' to '/scratch/gencore/logs/html/HYCCVBGXG/merged/multiqc_data' [2021-04-05 23:45:38,193] multiqc [INFO ] MultiQC complete