[2022-10-07 02:05:06,842] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-07 02:05:06,843] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-07 02:05:06,843] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-07 02:05:06,844] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-07 02:05:06,844] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-07 02:05:06,844] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLH7LBGXM/merged [2022-10-07 02:05:07,548] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-07 02:05:07,548] multiqc [INFO ] This is MultiQC v1.9 [2022-10-07 02:05:07,548] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLH7LBGXM/merged [2022-10-07 02:05:07,548] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLH7LBGXM/merged [2022-10-07 02:05:07,548] multiqc [INFO ] Template : default [2022-10-07 02:05:07,548] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-07 02:05:07,548] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLH7LBGXM/merged [2022-10-07 02:05:07,549] 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 [2022-10-07 02:05:07,549] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-25707298/tmphwf1wsi1 [2022-10-07 02:05:07,688] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-10-07 02:05:07,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-10-07 02:05:07,818] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK138_fastqc.html [2022-10-07 02:05:07,819] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK138_fastqc.html [2022-10-07 02:05:07,859] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK151_fastqc.html [2022-10-07 02:05:07,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK151_fastqc.html [2022-10-07 02:05:07,905] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK148_fastqc.html [2022-10-07 02:05:07,907] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK148_fastqc.html [2022-10-07 02:05:07,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM424_fastqc.html [2022-10-07 02:05:07,952] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM424_fastqc.html [2022-10-07 02:05:07,992] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM417_fastqc.html [2022-10-07 02:05:07,994] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM417_fastqc.html [2022-10-07 02:05:08,033] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK137_fastqc.html [2022-10-07 02:05:08,035] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK137_fastqc.html [2022-10-07 02:05:08,074] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_undetermined_fastqc.html [2022-10-07 02:05:08,076] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_undetermined_fastqc.html [2022-10-07 02:05:08,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK140_fastqc.html [2022-10-07 02:05:08,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK140_fastqc.html [2022-10-07 02:05:08,155] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK139_fastqc.html [2022-10-07 02:05:08,157] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK139_fastqc.html [2022-10-07 02:05:08,196] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM421_fastqc.html [2022-10-07 02:05:08,197] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM421_fastqc.html [2022-10-07 02:05:08,236] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM425_fastqc.html [2022-10-07 02:05:08,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM425_fastqc.html [2022-10-07 02:05:08,277] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK147_fastqc.html [2022-10-07 02:05:08,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK147_fastqc.html [2022-10-07 02:05:08,320] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK149_fastqc.html [2022-10-07 02:05:08,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK149_fastqc.html [2022-10-07 02:05:08,364] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK145_fastqc.html [2022-10-07 02:05:08,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK145_fastqc.html [2022-10-07 02:05:08,407] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM418_fastqc.html [2022-10-07 02:05:08,409] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM418_fastqc.html [2022-10-07 02:05:08,449] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM420_fastqc.html [2022-10-07 02:05:08,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM420_fastqc.html [2022-10-07 02:05:08,490] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK143_fastqc.html [2022-10-07 02:05:08,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK143_fastqc.html [2022-10-07 02:05:08,535] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM423_fastqc.html [2022-10-07 02:05:08,537] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM423_fastqc.html [2022-10-07 02:05:08,575] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM419_fastqc.html [2022-10-07 02:05:08,577] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM419_fastqc.html [2022-10-07 02:05:08,617] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK150_fastqc.html [2022-10-07 02:05:08,618] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK150_fastqc.html [2022-10-07 02:05:08,661] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK142_fastqc.html [2022-10-07 02:05:08,663] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK142_fastqc.html [2022-10-07 02:05:08,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK144_fastqc.html [2022-10-07 02:05:08,709] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK144_fastqc.html [2022-10-07 02:05:08,751] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK146_fastqc.html [2022-10-07 02:05:08,752] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK146_fastqc.html [2022-10-07 02:05:08,795] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM422_fastqc.html [2022-10-07 02:05:08,797] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_AKM422_fastqc.html [2022-10-07 02:05:08,835] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK141_fastqc.html [2022-10-07 02:05:08,837] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLH7LBGXM_n01_JK141_fastqc.html [2022-10-07 02:05:09,206] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-07 02:05:09,208] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-07 02:05:09,226] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2022-10-07 02:05:09,227] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-07 02:05:09,237] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-10-07 02:05:09,242] multiqc [DEBUG ] No samples found: conpair [2022-10-07 02:05:09,247] multiqc [DEBUG ] No samples found: peddy [2022-10-07 02:05:09,252] multiqc [DEBUG ] No samples found: somalier [2022-10-07 02:05:09,257] multiqc [DEBUG ] No samples found: methylQA [2022-10-07 02:05:09,266] multiqc [DEBUG ] No samples found: mosdepth [2022-10-07 02:05:09,270] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-07 02:05:09,274] multiqc [DEBUG ] No samples found: qualimap [2022-10-07 02:05:09,279] multiqc [DEBUG ] No samples found: preseq [2022-10-07 02:05:09,284] multiqc [DEBUG ] No samples found: quast [2022-10-07 02:05:09,290] multiqc [DEBUG ] No samples found: qorts [2022-10-07 02:05:09,294] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-07 02:05:09,300] multiqc [DEBUG ] No samples found: rockhopper [2022-10-07 02:05:09,305] multiqc [DEBUG ] No samples found: rsem [2022-10-07 02:05:09,316] multiqc [DEBUG ] No samples found: rseqc [2022-10-07 02:05:09,321] multiqc [DEBUG ] No samples found: busco [2022-10-07 02:05:09,326] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-07 02:05:09,330] multiqc [DEBUG ] No samples found: disambiguate [2022-10-07 02:05:09,335] multiqc [DEBUG ] No samples found: supernova [2022-10-07 02:05:09,349] multiqc [DEBUG ] No samples found: deeptools [2022-10-07 02:05:09,354] multiqc [DEBUG ] No samples found: sargasso [2022-10-07 02:05:09,360] multiqc [DEBUG ] No samples found: verifybamid [2022-10-07 02:05:09,365] multiqc [DEBUG ] No samples found: mirtrace [2022-10-07 02:05:09,370] multiqc [DEBUG ] No samples found: happy [2022-10-07 02:05:09,376] multiqc [DEBUG ] No samples found: mirtop [2022-10-07 02:05:09,383] multiqc [DEBUG ] No samples found: homer [2022-10-07 02:05:09,388] multiqc [DEBUG ] No samples found: macs2 [2022-10-07 02:05:09,392] multiqc [DEBUG ] No samples found: theta2 [2022-10-07 02:05:09,397] multiqc [DEBUG ] No samples found: snpeff [2022-10-07 02:05:09,404] multiqc [DEBUG ] No samples found: gatk [2022-10-07 02:05:09,408] multiqc [DEBUG ] No samples found: htseq [2022-10-07 02:05:09,414] multiqc [DEBUG ] No samples found: bcftools [2022-10-07 02:05:09,418] multiqc [DEBUG ] No samples found: featureCounts [2022-10-07 02:05:09,425] multiqc [DEBUG ] No samples found: fgbio [2022-10-07 02:05:09,440] multiqc [DEBUG ] No samples found: dragen [2022-10-07 02:05:09,446] multiqc [DEBUG ] No samples found: dedup [2022-10-07 02:05:09,451] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-07 02:05:09,475] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-07 02:05:09,479] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-07 02:05:09,482] multiqc [DEBUG ] No samples found: picard [2022-10-07 02:05:09,486] multiqc [DEBUG ] No samples found: prokka [2022-10-07 02:05:09,490] multiqc [DEBUG ] No samples found: samblaster [2022-10-07 02:05:09,499] multiqc [DEBUG ] No samples found: samtools [2022-10-07 02:05:09,504] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-07 02:05:09,510] multiqc [DEBUG ] No samples found: bamtools [2022-10-07 02:05:09,514] multiqc [DEBUG ] No samples found: jellyfish [2022-10-07 02:05:09,521] multiqc [DEBUG ] No samples found: vcftools [2022-10-07 02:05:09,526] multiqc [DEBUG ] No samples found: longranger [2022-10-07 02:05:09,531] multiqc [DEBUG ] No samples found: stacks [2022-10-07 02:05:09,536] multiqc [DEBUG ] No samples found: varscan2 [2022-10-07 02:05:09,551] multiqc [DEBUG ] No samples found: bbmap [2022-10-07 02:05:09,556] multiqc [DEBUG ] No samples found: bismark [2022-10-07 02:05:09,561] multiqc [DEBUG ] No samples found: biscuit [2022-10-07 02:05:09,566] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-07 02:05:09,571] multiqc [DEBUG ] No samples found: hicup [2022-10-07 02:05:09,576] multiqc [DEBUG ] No samples found: hicpro [2022-10-07 02:05:09,581] multiqc [DEBUG ] No samples found: salmon [2022-10-07 02:05:09,586] multiqc [DEBUG ] No samples found: kallisto [2022-10-07 02:05:09,591] multiqc [DEBUG ] No samples found: slamdunk [2022-10-07 02:05:09,596] multiqc [DEBUG ] No samples found: star [2022-10-07 02:05:09,600] multiqc [DEBUG ] No samples found: hisat2 [2022-10-07 02:05:09,605] multiqc [DEBUG ] No samples found: tophat [2022-10-07 02:05:09,610] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-07 02:05:09,615] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-07 02:05:09,620] multiqc [DEBUG ] No samples found: snpsplit [2022-10-07 02:05:09,624] multiqc [DEBUG ] No samples found: kat [2022-10-07 02:05:09,629] multiqc [DEBUG ] No samples found: leehom [2022-10-07 02:05:09,633] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-07 02:05:09,638] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-07 02:05:09,642] multiqc [DEBUG ] No samples found: cutadapt [2022-10-07 02:05:09,647] multiqc [DEBUG ] No samples found: flexbar [2022-10-07 02:05:09,652] multiqc [DEBUG ] No samples found: kaiju [2022-10-07 02:05:09,657] multiqc [DEBUG ] No samples found: kraken [2022-10-07 02:05:09,662] multiqc [DEBUG ] No samples found: malt [2022-10-07 02:05:09,666] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-07 02:05:09,671] multiqc [DEBUG ] No samples found: sickle [2022-10-07 02:05:09,677] multiqc [DEBUG ] No samples found: skewer [2022-10-07 02:05:09,681] multiqc [DEBUG ] No samples found: sortmerna [2022-10-07 02:05:09,685] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-07 02:05:09,691] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-07 02:05:09,695] multiqc [DEBUG ] No samples found: afterqc [2022-10-07 02:05:09,700] multiqc [DEBUG ] No samples found: fastp [2022-10-07 02:05:11,383] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2022-10-07 02:05:11,909] multiqc [DEBUG ] No samples found: pycoqc [2022-10-07 02:05:11,914] multiqc [DEBUG ] No samples found: minionqc [2022-10-07 02:05:11,919] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-07 02:05:11,924] multiqc [DEBUG ] No samples found: clusterflow [2022-10-07 02:05:11,928] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-07 02:05:11,933] multiqc [DEBUG ] No samples found: interop [2022-10-07 02:05:11,938] multiqc [DEBUG ] No samples found: ivar [2022-10-07 02:05:11,942] multiqc [DEBUG ] No samples found: flash [2022-10-07 02:05:11,947] multiqc [DEBUG ] No samples found: seqyclean [2022-10-07 02:05:11,947] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-10-07 02:05:11,947] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-10-07 02:05:11,947] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-10-07 02:05:11,947] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-07 02:05:11,979] multiqc [INFO ] Compressing plot data [2022-10-07 02:05:12,434] multiqc [INFO ] Report : multiqc_report.html [2022-10-07 02:05:12,434] multiqc [INFO ] Data : multiqc_data [2022-10-07 02:05:12,434] multiqc [DEBUG ] Moving data file from '/state/partition1/job-25707298/tmphwf1wsi1/multiqc_data' to '/scratch/gencore/logs/html/HLH7LBGXM/merged/multiqc_data' [2022-10-07 02:05:12,567] multiqc [INFO ] MultiQC complete