[2022-08-03 18:30:17,482] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-08-03 18:30:17,482] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-08-03 18:30:17,482] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-08-03 18:30:17,484] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-08-03 18:30:17,484] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-08-03 18:30:17,484] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGGMHDRX2/merged [2022-08-03 18:30:18,101] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-08-03 18:30:18,102] multiqc [INFO ] This is MultiQC v1.9 [2022-08-03 18:30:18,102] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGGMHDRX2/merged [2022-08-03 18:30:18,102] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGGMHDRX2/merged [2022-08-03 18:30:18,102] multiqc [INFO ] Template : default [2022-08-03 18:30:18,102] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-08-03 18:30:18,102] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGGMHDRX2/merged [2022-08-03 18:30:18,103] 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 [2022-08-03 18:30:18,104] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-23183157/tmpmiayui45 [2022-08-03 18:30:18,223] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_CDC944_fastqc.html [2022-08-03 18:30:18,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_CDC944_fastqc.html [2022-08-03 18:30:18,268] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_FTG328_fastqc.html [2022-08-03 18:30:18,270] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_FTG328_fastqc.html [2022-08-03 18:30:18,311] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_CDC944_fastqc.html [2022-08-03 18:30:18,313] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_CDC944_fastqc.html [2022-08-03 18:30:18,353] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_BUSH04_fastqc.html [2022-08-03 18:30:18,355] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_BUSH04_fastqc.html [2022-08-03 18:30:18,396] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_BUSH20_fastqc.html [2022-08-03 18:30:18,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_BUSH20_fastqc.html [2022-08-03 18:30:18,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_JAM20_fastqc.html [2022-08-03 18:30:18,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_JAM20_fastqc.html [2022-08-03 18:30:18,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_CDC888_fastqc.html [2022-08-03 18:30:18,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_CDC888_fastqc.html [2022-08-03 18:30:18,522] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_CDC888_fastqc.html [2022-08-03 18:30:18,524] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_CDC888_fastqc.html [2022-08-03 18:30:18,565] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_CDC1080_fastqc.html [2022-08-03 18:30:18,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_CDC1080_fastqc.html [2022-08-03 18:30:18,623] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_undetermined_fastqc.html [2022-08-03 18:30:18,625] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_undetermined_fastqc.html [2022-08-03 18:30:18,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_JAM20_fastqc.html [2022-08-03 18:30:18,666] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_JAM20_fastqc.html [2022-08-03 18:30:18,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_CDC1080_fastqc.html [2022-08-03 18:30:18,709] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_CDC1080_fastqc.html [2022-08-03 18:30:18,767] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_FTG328_fastqc.html [2022-08-03 18:30:18,769] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_FTG328_fastqc.html [2022-08-03 18:30:18,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_BUSH20_fastqc.html [2022-08-03 18:30:18,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_BUSH20_fastqc.html [2022-08-03 18:30:18,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n01_BUSH04_fastqc.html [2022-08-03 18:30:18,855] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n01_BUSH04_fastqc.html [2022-08-03 18:30:18,896] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGMHDRX2_n02_undetermined_fastqc.html [2022-08-03 18:30:18,897] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGMHDRX2_n02_undetermined_fastqc.html [2022-08-03 18:30:19,672] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-03 18:30:19,674] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-03 18:30:19,685] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2022-08-03 18:30:19,686] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-08-03 18:30:19,696] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-08-03 18:30:19,701] multiqc [DEBUG ] No samples found: conpair [2022-08-03 18:30:19,707] multiqc [DEBUG ] No samples found: peddy [2022-08-03 18:30:19,714] multiqc [DEBUG ] No samples found: somalier [2022-08-03 18:30:19,720] multiqc [DEBUG ] No samples found: methylQA [2022-08-03 18:30:19,730] multiqc [DEBUG ] No samples found: mosdepth [2022-08-03 18:30:19,737] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-08-03 18:30:19,746] multiqc [DEBUG ] No samples found: qualimap [2022-08-03 18:30:19,753] multiqc [DEBUG ] No samples found: preseq [2022-08-03 18:30:19,760] multiqc [DEBUG ] No samples found: quast [2022-08-03 18:30:19,766] multiqc [DEBUG ] No samples found: qorts [2022-08-03 18:30:19,771] multiqc [DEBUG ] No samples found: rna_seqc [2022-08-03 18:30:19,778] multiqc [DEBUG ] No samples found: rockhopper [2022-08-03 18:30:19,784] multiqc [DEBUG ] No samples found: rsem [2022-08-03 18:30:19,802] multiqc [DEBUG ] No samples found: rseqc [2022-08-03 18:30:19,809] multiqc [DEBUG ] No samples found: busco [2022-08-03 18:30:19,815] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-08-03 18:30:19,821] multiqc [DEBUG ] No samples found: disambiguate [2022-08-03 18:30:19,826] multiqc [DEBUG ] No samples found: supernova [2022-08-03 18:30:19,842] multiqc [DEBUG ] No samples found: deeptools [2022-08-03 18:30:19,848] multiqc [DEBUG ] No samples found: sargasso [2022-08-03 18:30:19,853] multiqc [DEBUG ] No samples found: verifybamid [2022-08-03 18:30:19,858] multiqc [DEBUG ] No samples found: mirtrace [2022-08-03 18:30:19,863] multiqc [DEBUG ] No samples found: happy [2022-08-03 18:30:19,868] multiqc [DEBUG ] No samples found: mirtop [2022-08-03 18:30:19,875] multiqc [DEBUG ] No samples found: homer [2022-08-03 18:30:19,881] multiqc [DEBUG ] No samples found: macs2 [2022-08-03 18:30:19,886] multiqc [DEBUG ] No samples found: theta2 [2022-08-03 18:30:19,894] multiqc [DEBUG ] No samples found: snpeff [2022-08-03 18:30:19,909] multiqc [DEBUG ] No samples found: gatk [2022-08-03 18:30:19,915] multiqc [DEBUG ] No samples found: htseq [2022-08-03 18:30:19,923] multiqc [DEBUG ] No samples found: bcftools [2022-08-03 18:30:19,929] multiqc [DEBUG ] No samples found: featureCounts [2022-08-03 18:30:19,936] multiqc [DEBUG ] No samples found: fgbio [2022-08-03 18:30:19,956] multiqc [DEBUG ] No samples found: dragen [2022-08-03 18:30:19,966] multiqc [DEBUG ] No samples found: dedup [2022-08-03 18:30:19,974] multiqc [DEBUG ] No samples found: damageprofiler [2022-08-03 18:30:20,014] multiqc [DEBUG ] No samples found: biobambam2 [2022-08-03 18:30:20,023] multiqc [DEBUG ] No samples found: mtnucratio [2022-08-03 18:30:20,026] multiqc [DEBUG ] No samples found: picard [2022-08-03 18:30:20,032] multiqc [DEBUG ] No samples found: prokka [2022-08-03 18:30:20,038] multiqc [DEBUG ] No samples found: samblaster [2022-08-03 18:30:20,049] multiqc [DEBUG ] No samples found: samtools [2022-08-03 18:30:20,055] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-08-03 18:30:20,062] multiqc [DEBUG ] No samples found: bamtools [2022-08-03 18:30:20,068] multiqc [DEBUG ] No samples found: jellyfish [2022-08-03 18:30:20,078] multiqc [DEBUG ] No samples found: vcftools [2022-08-03 18:30:20,084] multiqc [DEBUG ] No samples found: longranger [2022-08-03 18:30:20,091] multiqc [DEBUG ] No samples found: stacks [2022-08-03 18:30:20,098] multiqc [DEBUG ] No samples found: varscan2 [2022-08-03 18:30:20,115] multiqc [DEBUG ] No samples found: bbmap [2022-08-03 18:30:20,121] multiqc [DEBUG ] No samples found: bismark [2022-08-03 18:30:20,129] multiqc [DEBUG ] No samples found: biscuit [2022-08-03 18:30:20,135] multiqc [DEBUG ] No samples found: hicexplorer [2022-08-03 18:30:20,142] multiqc [DEBUG ] No samples found: hicup [2022-08-03 18:30:20,149] multiqc [DEBUG ] No samples found: hicpro [2022-08-03 18:30:20,155] multiqc [DEBUG ] No samples found: salmon [2022-08-03 18:30:20,161] multiqc [DEBUG ] No samples found: kallisto [2022-08-03 18:30:20,168] multiqc [DEBUG ] No samples found: slamdunk [2022-08-03 18:30:20,174] multiqc [DEBUG ] No samples found: star [2022-08-03 18:30:20,180] multiqc [DEBUG ] No samples found: hisat2 [2022-08-03 18:30:20,186] multiqc [DEBUG ] No samples found: tophat [2022-08-03 18:30:20,192] multiqc [DEBUG ] No samples found: bowtie2 [2022-08-03 18:30:20,198] multiqc [DEBUG ] No samples found: bowtie1 [2022-08-03 18:30:20,204] multiqc [DEBUG ] No samples found: snpsplit [2022-08-03 18:30:20,209] multiqc [DEBUG ] No samples found: kat [2022-08-03 18:30:20,215] multiqc [DEBUG ] No samples found: leehom [2022-08-03 18:30:20,221] multiqc [DEBUG ] No samples found: adapterRemoval [2022-08-03 18:30:20,226] multiqc [DEBUG ] No samples found: clipandmerge [2022-08-03 18:30:20,231] multiqc [DEBUG ] No samples found: cutadapt [2022-08-03 18:30:20,236] multiqc [DEBUG ] No samples found: flexbar [2022-08-03 18:30:20,242] multiqc [DEBUG ] No samples found: kaiju [2022-08-03 18:30:20,248] multiqc [DEBUG ] No samples found: kraken [2022-08-03 18:30:20,255] multiqc [DEBUG ] No samples found: malt [2022-08-03 18:30:20,260] multiqc [DEBUG ] No samples found: trimmomatic [2022-08-03 18:30:20,266] multiqc [DEBUG ] No samples found: sickle [2022-08-03 18:30:20,272] multiqc [DEBUG ] No samples found: skewer [2022-08-03 18:30:20,278] multiqc [DEBUG ] No samples found: sortmerna [2022-08-03 18:30:20,284] multiqc [DEBUG ] No samples found: biobloomtools [2022-08-03 18:30:20,290] multiqc [DEBUG ] No samples found: fastq_screen [2022-08-03 18:30:20,296] multiqc [DEBUG ] No samples found: afterqc [2022-08-03 18:30:20,308] multiqc [DEBUG ] No samples found: fastp [2022-08-03 18:30:20,821] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2022-08-03 18:30:21,090] multiqc [DEBUG ] No samples found: pycoqc [2022-08-03 18:30:21,097] multiqc [DEBUG ] No samples found: minionqc [2022-08-03 18:30:21,103] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-08-03 18:30:21,110] multiqc [DEBUG ] No samples found: clusterflow [2022-08-03 18:30:21,117] multiqc [DEBUG ] No samples found: bcl2fastq [2022-08-03 18:30:21,124] multiqc [DEBUG ] No samples found: interop [2022-08-03 18:30:21,130] multiqc [DEBUG ] No samples found: ivar [2022-08-03 18:30:21,136] multiqc [DEBUG ] No samples found: flash [2022-08-03 18:30:21,143] multiqc [DEBUG ] No samples found: seqyclean [2022-08-03 18:30:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-08-03 18:30:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-08-03 18:30:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-08-03 18:30:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-08-03 18:30:21,162] multiqc [INFO ] Compressing plot data [2022-08-03 18:30:21,461] multiqc [INFO ] Report : multiqc_report.html [2022-08-03 18:30:21,462] multiqc [INFO ] Data : multiqc_data [2022-08-03 18:30:21,462] multiqc [DEBUG ] Moving data file from '/state/partition1/job-23183157/tmpmiayui45/multiqc_data' to '/scratch/gencore/logs/html/HGGMHDRX2/merged/multiqc_data' [2022-08-03 18:30:21,617] multiqc [INFO ] MultiQC complete