[2022-03-18 05:19:15,629] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-18 05:19:15,629] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-18 05:19:15,629] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-18 05:19:15,630] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-18 05:19:15,630] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-18 05:19:15,630] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJKC5AFX3/merged [2022-03-18 05:19:16,988] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-18 05:19:16,989] multiqc [INFO ] This is MultiQC v1.9 [2022-03-18 05:19:16,989] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJKC5AFX3/merged [2022-03-18 05:19:16,989] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJKC5AFX3/merged [2022-03-18 05:19:16,989] multiqc [INFO ] Template : default [2022-03-18 05:19:16,989] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-18 05:19:16,989] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJKC5AFX3/merged [2022-03-18 05:19:16,990] 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 [2022-03-18 05:19:16,990] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16207170/tmpbdou_i41 [2022-03-18 05:19:17,110] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:17,112] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:17,112] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:17,112] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:17,112] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:17,112] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:17,113] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:17,138] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-18 05:19:18,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T18_Rep1_fastqc.html [2022-03-18 05:19:18,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T18_Rep1_fastqc.html [2022-03-18 05:19:18,236] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T0_Rep2_fastqc.html [2022-03-18 05:19:18,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T0_Rep2_fastqc.html [2022-03-18 05:19:18,283] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T0_Rep1_fastqc.html [2022-03-18 05:19:18,285] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T0_Rep1_fastqc.html [2022-03-18 05:19:18,330] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T6_Rep2_fastqc.html [2022-03-18 05:19:18,332] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T6_Rep2_fastqc.html [2022-03-18 05:19:18,375] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_undetermined_fastqc.html [2022-03-18 05:19:18,376] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_undetermined_fastqc.html [2022-03-18 05:19:18,422] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T12_Rep2_fastqc.html [2022-03-18 05:19:18,423] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T12_Rep2_fastqc.html [2022-03-18 05:19:18,472] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T12_Rep1_fastqc.html [2022-03-18 05:19:18,474] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T12_Rep1_fastqc.html [2022-03-18 05:19:18,523] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T6_Rep1_fastqc.html [2022-03-18 05:19:18,524] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T6_Rep1_fastqc.html [2022-03-18 05:19:18,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T18_Rep2_fastqc.html [2022-03-18 05:19:18,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJKC5AFX3_n01_T18_Rep2_fastqc.html [2022-03-18 05:19:18,940] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-18 05:19:18,942] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-18 05:19:18,951] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-18 05:19:18,956] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2022-03-18 05:19:18,965] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-18 05:19:18,971] multiqc [DEBUG ] No samples found: conpair [2022-03-18 05:19:18,976] multiqc [DEBUG ] No samples found: peddy [2022-03-18 05:19:18,981] multiqc [DEBUG ] No samples found: somalier [2022-03-18 05:19:18,987] multiqc [DEBUG ] No samples found: methylQA [2022-03-18 05:19:18,996] multiqc [DEBUG ] No samples found: mosdepth [2022-03-18 05:19:19,001] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-18 05:19:19,005] multiqc [DEBUG ] No samples found: qualimap [2022-03-18 05:19:19,010] multiqc [DEBUG ] No samples found: preseq [2022-03-18 05:19:19,015] multiqc [DEBUG ] No samples found: quast [2022-03-18 05:19:19,020] multiqc [DEBUG ] No samples found: qorts [2022-03-18 05:19:19,025] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-18 05:19:19,031] multiqc [DEBUG ] No samples found: rockhopper [2022-03-18 05:19:19,036] multiqc [DEBUG ] No samples found: rsem [2022-03-18 05:19:19,048] multiqc [DEBUG ] No samples found: rseqc [2022-03-18 05:19:19,053] multiqc [DEBUG ] No samples found: busco [2022-03-18 05:19:19,058] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-18 05:19:19,063] multiqc [DEBUG ] No samples found: disambiguate [2022-03-18 05:19:19,068] multiqc [DEBUG ] No samples found: supernova [2022-03-18 05:19:19,081] multiqc [DEBUG ] No samples found: deeptools [2022-03-18 05:19:19,087] multiqc [DEBUG ] No samples found: sargasso [2022-03-18 05:19:19,092] multiqc [DEBUG ] No samples found: verifybamid [2022-03-18 05:19:19,097] multiqc [DEBUG ] No samples found: mirtrace [2022-03-18 05:19:19,103] multiqc [DEBUG ] No samples found: happy [2022-03-18 05:19:19,108] multiqc [DEBUG ] No samples found: mirtop [2022-03-18 05:19:19,115] multiqc [DEBUG ] No samples found: homer [2022-03-18 05:19:19,120] multiqc [DEBUG ] No samples found: macs2 [2022-03-18 05:19:19,126] multiqc [DEBUG ] No samples found: theta2 [2022-03-18 05:19:19,131] multiqc [DEBUG ] No samples found: snpeff [2022-03-18 05:19:19,145] multiqc [DEBUG ] No samples found: gatk [2022-03-18 05:19:19,153] multiqc [DEBUG ] No samples found: htseq [2022-03-18 05:19:19,159] multiqc [DEBUG ] No samples found: bcftools [2022-03-18 05:19:19,167] multiqc [DEBUG ] No samples found: featureCounts [2022-03-18 05:19:19,174] multiqc [DEBUG ] No samples found: fgbio [2022-03-18 05:19:19,189] multiqc [DEBUG ] No samples found: dragen [2022-03-18 05:19:19,195] multiqc [DEBUG ] No samples found: dedup [2022-03-18 05:19:19,200] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-18 05:19:19,225] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-18 05:19:19,232] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-18 05:19:19,234] multiqc [DEBUG ] No samples found: picard [2022-03-18 05:19:19,239] multiqc [DEBUG ] No samples found: prokka [2022-03-18 05:19:19,244] multiqc [DEBUG ] No samples found: samblaster [2022-03-18 05:19:19,253] multiqc [DEBUG ] No samples found: samtools [2022-03-18 05:19:19,258] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-18 05:19:19,264] multiqc [DEBUG ] No samples found: bamtools [2022-03-18 05:19:19,268] multiqc [DEBUG ] No samples found: jellyfish [2022-03-18 05:19:19,276] multiqc [DEBUG ] No samples found: vcftools [2022-03-18 05:19:19,281] multiqc [DEBUG ] No samples found: longranger [2022-03-18 05:19:19,287] multiqc [DEBUG ] No samples found: stacks [2022-03-18 05:19:19,292] multiqc [DEBUG ] No samples found: varscan2 [2022-03-18 05:19:19,307] multiqc [DEBUG ] No samples found: bbmap [2022-03-18 05:19:19,312] multiqc [DEBUG ] No samples found: bismark [2022-03-18 05:19:19,318] multiqc [DEBUG ] No samples found: biscuit [2022-03-18 05:19:19,323] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-18 05:19:19,328] multiqc [DEBUG ] No samples found: hicup [2022-03-18 05:19:19,333] multiqc [DEBUG ] No samples found: hicpro [2022-03-18 05:19:19,338] multiqc [DEBUG ] No samples found: salmon [2022-03-18 05:19:19,343] multiqc [DEBUG ] No samples found: kallisto [2022-03-18 05:19:19,348] multiqc [DEBUG ] No samples found: slamdunk [2022-03-18 05:19:19,353] multiqc [DEBUG ] No samples found: star [2022-03-18 05:19:19,358] multiqc [DEBUG ] No samples found: hisat2 [2022-03-18 05:19:19,366] multiqc [DEBUG ] No samples found: tophat [2022-03-18 05:19:19,371] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-18 05:19:19,376] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-18 05:19:19,381] multiqc [DEBUG ] No samples found: snpsplit [2022-03-18 05:19:19,386] multiqc [DEBUG ] No samples found: kat [2022-03-18 05:19:19,390] multiqc [DEBUG ] No samples found: leehom [2022-03-18 05:19:19,396] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-18 05:19:19,401] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-18 05:19:19,408] multiqc [DEBUG ] No samples found: cutadapt [2022-03-18 05:19:19,415] multiqc [DEBUG ] No samples found: flexbar [2022-03-18 05:19:19,425] multiqc [DEBUG ] No samples found: kaiju [2022-03-18 05:19:19,435] multiqc [DEBUG ] No samples found: kraken [2022-03-18 05:19:19,445] multiqc [DEBUG ] No samples found: malt [2022-03-18 05:19:19,455] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-18 05:19:19,466] multiqc [DEBUG ] No samples found: sickle [2022-03-18 05:19:19,473] multiqc [DEBUG ] No samples found: skewer [2022-03-18 05:19:19,478] multiqc [DEBUG ] No samples found: sortmerna [2022-03-18 05:19:19,483] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-18 05:19:19,488] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-18 05:19:19,493] multiqc [DEBUG ] No samples found: afterqc [2022-03-18 05:19:19,499] multiqc [DEBUG ] No samples found: fastp [2022-03-18 05:19:19,536] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports [2022-03-18 05:19:19,628] multiqc [DEBUG ] No samples found: pycoqc [2022-03-18 05:19:19,633] multiqc [DEBUG ] No samples found: minionqc [2022-03-18 05:19:19,638] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-18 05:19:19,643] multiqc [DEBUG ] No samples found: clusterflow [2022-03-18 05:19:19,648] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-18 05:19:19,653] multiqc [DEBUG ] No samples found: interop [2022-03-18 05:19:19,658] multiqc [DEBUG ] No samples found: ivar [2022-03-18 05:19:19,663] multiqc [DEBUG ] No samples found: flash [2022-03-18 05:19:19,667] multiqc [DEBUG ] No samples found: seqyclean [2022-03-18 05:19:19,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-18 05:19:19,668] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-18 05:19:19,668] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-18 05:19:19,668] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-18 05:19:19,679] multiqc [INFO ] Compressing plot data [2022-03-18 05:19:19,783] multiqc [INFO ] Report : multiqc_report.html [2022-03-18 05:19:19,783] multiqc [INFO ] Data : multiqc_data [2022-03-18 05:19:19,783] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16207170/tmpbdou_i41/multiqc_data' to '/scratch/gencore/logs/html/HJKC5AFX3/merged/multiqc_data' [2022-03-18 05:19:19,916] multiqc [INFO ] MultiQC complete