[2022-07-02 04:33:35,224] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-02 04:33:35,225] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-02 04:33:35,225] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-02 04:33:35,226] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-02 04:33:35,226] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-02 04:33:35,226] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFCVLBGXM/merged [2022-07-02 04:33:35,728] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-02 04:33:35,728] multiqc [INFO ] This is MultiQC v1.9 [2022-07-02 04:33:35,728] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFCVLBGXM/merged [2022-07-02 04:33:35,728] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFCVLBGXM/merged [2022-07-02 04:33:35,728] multiqc [INFO ] Template : default [2022-07-02 04:33:35,729] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-02 04:33:35,729] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFCVLBGXM/merged [2022-07-02 04:33:35,730] 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 [2022-07-02 04:33:35,730] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-21810303/tmp9wamar7h [2022-07-02 04:33:35,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFCVLBGXM_2_fastqc.html [2022-07-02 04:33:35,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFCVLBGXM_2_fastqc.html [2022-07-02 04:33:35,887] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFCVLBGXM_3_fastqc.html [2022-07-02 04:33:35,889] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFCVLBGXM_3_fastqc.html [2022-07-02 04:33:35,928] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFCVLBGXM_4_fastqc.html [2022-07-02 04:33:35,930] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFCVLBGXM_4_fastqc.html [2022-07-02 04:33:35,970] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFCVLBGXM_1_fastqc.html [2022-07-02 04:33:35,972] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFCVLBGXM_1_fastqc.html [2022-07-02 04:33:36,370] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-02 04:33:36,374] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-02 04:33:36,378] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-07-02 04:33:36,380] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-02 04:33:36,386] multiqc [DEBUG ] No samples found: conpair [2022-07-02 04:33:36,393] multiqc [DEBUG ] No samples found: peddy [2022-07-02 04:33:36,404] multiqc [DEBUG ] No samples found: somalier [2022-07-02 04:33:36,412] multiqc [DEBUG ] No samples found: methylQA [2022-07-02 04:33:36,425] multiqc [DEBUG ] No samples found: mosdepth [2022-07-02 04:33:36,431] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-02 04:33:36,436] multiqc [DEBUG ] No samples found: qualimap [2022-07-02 04:33:36,442] multiqc [DEBUG ] No samples found: preseq [2022-07-02 04:33:36,449] multiqc [DEBUG ] No samples found: quast [2022-07-02 04:33:36,455] multiqc [DEBUG ] No samples found: qorts [2022-07-02 04:33:36,461] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-02 04:33:36,467] multiqc [DEBUG ] No samples found: rockhopper [2022-07-02 04:33:36,473] multiqc [DEBUG ] No samples found: rsem [2022-07-02 04:33:36,488] multiqc [DEBUG ] No samples found: rseqc [2022-07-02 04:33:36,493] multiqc [DEBUG ] No samples found: busco [2022-07-02 04:33:36,499] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-02 04:33:36,505] multiqc [DEBUG ] No samples found: disambiguate [2022-07-02 04:33:36,511] multiqc [DEBUG ] No samples found: supernova [2022-07-02 04:33:36,530] multiqc [DEBUG ] No samples found: deeptools [2022-07-02 04:33:36,536] multiqc [DEBUG ] No samples found: sargasso [2022-07-02 04:33:36,543] multiqc [DEBUG ] No samples found: verifybamid [2022-07-02 04:33:36,551] multiqc [DEBUG ] No samples found: mirtrace [2022-07-02 04:33:36,556] multiqc [DEBUG ] No samples found: happy [2022-07-02 04:33:36,562] multiqc [DEBUG ] No samples found: mirtop [2022-07-02 04:33:36,569] multiqc [DEBUG ] No samples found: homer [2022-07-02 04:33:36,575] multiqc [DEBUG ] No samples found: macs2 [2022-07-02 04:33:36,580] multiqc [DEBUG ] No samples found: theta2 [2022-07-02 04:33:36,585] multiqc [DEBUG ] No samples found: snpeff [2022-07-02 04:33:36,593] multiqc [DEBUG ] No samples found: gatk [2022-07-02 04:33:36,599] multiqc [DEBUG ] No samples found: htseq [2022-07-02 04:33:36,605] multiqc [DEBUG ] No samples found: bcftools [2022-07-02 04:33:36,610] multiqc [DEBUG ] No samples found: featureCounts [2022-07-02 04:33:36,619] multiqc [DEBUG ] No samples found: fgbio [2022-07-02 04:33:36,633] multiqc [DEBUG ] No samples found: dragen [2022-07-02 04:33:36,639] multiqc [DEBUG ] No samples found: dedup [2022-07-02 04:33:36,644] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-02 04:33:36,677] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-02 04:33:36,685] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-02 04:33:36,687] multiqc [DEBUG ] No samples found: picard [2022-07-02 04:33:36,693] multiqc [DEBUG ] No samples found: prokka [2022-07-02 04:33:36,699] multiqc [DEBUG ] No samples found: samblaster [2022-07-02 04:33:36,712] multiqc [DEBUG ] No samples found: samtools [2022-07-02 04:33:36,718] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-02 04:33:36,724] multiqc [DEBUG ] No samples found: bamtools [2022-07-02 04:33:36,729] multiqc [DEBUG ] No samples found: jellyfish [2022-07-02 04:33:36,737] multiqc [DEBUG ] No samples found: vcftools [2022-07-02 04:33:36,743] multiqc [DEBUG ] No samples found: longranger [2022-07-02 04:33:36,750] multiqc [DEBUG ] No samples found: stacks [2022-07-02 04:33:36,756] multiqc [DEBUG ] No samples found: varscan2 [2022-07-02 04:33:36,786] multiqc [DEBUG ] No samples found: bbmap [2022-07-02 04:33:36,793] multiqc [DEBUG ] No samples found: bismark [2022-07-02 04:33:36,802] multiqc [DEBUG ] No samples found: biscuit [2022-07-02 04:33:36,808] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-02 04:33:36,813] multiqc [DEBUG ] No samples found: hicup [2022-07-02 04:33:36,821] multiqc [DEBUG ] No samples found: hicpro [2022-07-02 04:33:36,826] multiqc [DEBUG ] No samples found: salmon [2022-07-02 04:33:36,832] multiqc [DEBUG ] No samples found: kallisto [2022-07-02 04:33:36,839] multiqc [DEBUG ] No samples found: slamdunk [2022-07-02 04:33:36,845] multiqc [DEBUG ] No samples found: star [2022-07-02 04:33:36,850] multiqc [DEBUG ] No samples found: hisat2 [2022-07-02 04:33:36,856] multiqc [DEBUG ] No samples found: tophat [2022-07-02 04:33:36,862] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-02 04:33:36,867] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-02 04:33:36,873] multiqc [DEBUG ] No samples found: snpsplit [2022-07-02 04:33:36,881] multiqc [DEBUG ] No samples found: kat [2022-07-02 04:33:36,885] multiqc [DEBUG ] No samples found: leehom [2022-07-02 04:33:36,891] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-02 04:33:36,896] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-02 04:33:36,903] multiqc [DEBUG ] No samples found: cutadapt [2022-07-02 04:33:36,908] multiqc [DEBUG ] No samples found: flexbar [2022-07-02 04:33:36,913] multiqc [DEBUG ] No samples found: kaiju [2022-07-02 04:33:36,921] multiqc [DEBUG ] No samples found: kraken [2022-07-02 04:33:36,926] multiqc [DEBUG ] No samples found: malt [2022-07-02 04:33:36,931] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-02 04:33:36,936] multiqc [DEBUG ] No samples found: sickle [2022-07-02 04:33:36,941] multiqc [DEBUG ] No samples found: skewer [2022-07-02 04:33:36,946] multiqc [DEBUG ] No samples found: sortmerna [2022-07-02 04:33:36,951] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-02 04:33:36,956] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-02 04:33:36,962] multiqc [DEBUG ] No samples found: afterqc [2022-07-02 04:33:36,967] multiqc [DEBUG ] No samples found: fastp [2022-07-02 04:33:37,136] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-07-02 04:33:37,185] multiqc [DEBUG ] No samples found: pycoqc [2022-07-02 04:33:37,191] multiqc [DEBUG ] No samples found: minionqc [2022-07-02 04:33:37,196] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-02 04:33:37,201] multiqc [DEBUG ] No samples found: clusterflow [2022-07-02 04:33:37,207] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-02 04:33:37,212] multiqc [DEBUG ] No samples found: interop [2022-07-02 04:33:37,220] multiqc [DEBUG ] No samples found: ivar [2022-07-02 04:33:37,225] multiqc [DEBUG ] No samples found: flash [2022-07-02 04:33:37,230] multiqc [DEBUG ] No samples found: seqyclean [2022-07-02 04:33:37,230] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-07-02 04:33:37,230] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-02 04:33:37,230] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-02 04:33:37,236] multiqc [INFO ] Compressing plot data [2022-07-02 04:33:37,306] multiqc [INFO ] Report : multiqc_report.html [2022-07-02 04:33:37,306] multiqc [INFO ] Data : multiqc_data [2022-07-02 04:33:37,306] multiqc [DEBUG ] Moving data file from '/state/partition1/job-21810303/tmp9wamar7h/multiqc_data' to '/scratch/gencore/logs/html/HFCVLBGXM/merged/multiqc_data' [2022-07-02 04:33:37,441] multiqc [INFO ] MultiQC complete