[2021-08-14 00:16:37,627] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-14 00:16:37,627] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-14 00:16:37,627] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-14 00:16:37,628] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-14 00:16:37,628] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-14 00:16:37,628] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNVGBGXJ/merged [2021-08-14 00:16:39,186] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-14 00:16:39,186] multiqc [INFO ] This is MultiQC v1.9 [2021-08-14 00:16:39,186] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNVGBGXJ/merged [2021-08-14 00:16:39,186] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLNVGBGXJ/merged [2021-08-14 00:16:39,186] multiqc [INFO ] Template : default [2021-08-14 00:16:39,186] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-14 00:16:39,186] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLNVGBGXJ/merged [2021-08-14 00:16:39,187] 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 [2021-08-14 00:16:39,187] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9393457/tmp44pofe7y [2021-08-14 00:16:39,305] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-14 00:16:39,307] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-14 00:16:39,307] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-14 00:16:39,307] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-14 00:16:39,307] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-14 00:16:39,307] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-14 00:16:39,308] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-14 00:16:40,013] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep1_day22_fastqc.html [2021-08-14 00:16:40,014] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep1_day22_fastqc.html [2021-08-14 00:16:40,067] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep1_day1_fastqc.html [2021-08-14 00:16:40,069] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep1_day1_fastqc.html [2021-08-14 00:16:40,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep1_day22_fastqc.html [2021-08-14 00:16:40,124] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep1_day22_fastqc.html [2021-08-14 00:16:40,179] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep3_day22_fastqc.html [2021-08-14 00:16:40,180] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep3_day22_fastqc.html [2021-08-14 00:16:40,233] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_undetermined_fastqc.html [2021-08-14 00:16:40,234] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_undetermined_fastqc.html [2021-08-14 00:16:40,289] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep3_day22_fastqc.html [2021-08-14 00:16:40,291] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep3_day22_fastqc.html [2021-08-14 00:16:40,345] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep2_day22_fastqc.html [2021-08-14 00:16:40,347] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep2_day22_fastqc.html [2021-08-14 00:16:40,399] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep2_day22_fastqc.html [2021-08-14 00:16:40,401] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep2_day22_fastqc.html [2021-08-14 00:16:40,454] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep3_day1_fastqc.html [2021-08-14 00:16:40,457] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep3_day1_fastqc.html [2021-08-14 00:16:40,510] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep2_day1_fastqc.html [2021-08-14 00:16:40,511] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_HCT116_rep2_day1_fastqc.html [2021-08-14 00:16:40,565] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep1_day7_fastqc.html [2021-08-14 00:16:40,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep1_day7_fastqc.html [2021-08-14 00:16:40,622] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep3_day11_fastqc.html [2021-08-14 00:16:40,624] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep3_day11_fastqc.html [2021-08-14 00:16:40,677] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep2_day11_fastqc.html [2021-08-14 00:16:40,678] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGBGXJ_n01_MCF7_rep2_day11_fastqc.html [2021-08-14 00:16:41,184] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-14 00:16:41,189] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-14 00:16:41,199] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-14 00:16:41,206] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 13 samples (table) [2021-08-14 00:16:41,215] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-14 00:16:41,225] multiqc [DEBUG ] No samples found: conpair [2021-08-14 00:16:41,231] multiqc [DEBUG ] No samples found: peddy [2021-08-14 00:16:41,240] multiqc [DEBUG ] No samples found: somalier [2021-08-14 00:16:41,247] multiqc [DEBUG ] No samples found: methylQA [2021-08-14 00:16:41,268] multiqc [DEBUG ] No samples found: mosdepth [2021-08-14 00:16:41,275] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-14 00:16:41,282] multiqc [DEBUG ] No samples found: qualimap [2021-08-14 00:16:41,292] multiqc [DEBUG ] No samples found: preseq [2021-08-14 00:16:41,301] multiqc [DEBUG ] No samples found: quast [2021-08-14 00:16:41,310] multiqc [DEBUG ] No samples found: qorts [2021-08-14 00:16:41,318] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-14 00:16:41,323] multiqc [DEBUG ] No samples found: rockhopper [2021-08-14 00:16:41,331] multiqc [DEBUG ] No samples found: rsem [2021-08-14 00:16:41,349] multiqc [DEBUG ] No samples found: rseqc [2021-08-14 00:16:41,356] multiqc [DEBUG ] No samples found: busco [2021-08-14 00:16:41,363] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-14 00:16:41,372] multiqc [DEBUG ] No samples found: disambiguate [2021-08-14 00:16:41,381] multiqc [DEBUG ] No samples found: supernova [2021-08-14 00:16:41,412] multiqc [DEBUG ] No samples found: deeptools [2021-08-14 00:16:41,420] multiqc [DEBUG ] No samples found: sargasso [2021-08-14 00:16:41,430] multiqc [DEBUG ] No samples found: verifybamid [2021-08-14 00:16:41,439] multiqc [DEBUG ] No samples found: mirtrace [2021-08-14 00:16:41,449] multiqc [DEBUG ] No samples found: happy [2021-08-14 00:16:41,458] multiqc [DEBUG ] No samples found: mirtop [2021-08-14 00:16:41,468] multiqc [DEBUG ] No samples found: homer [2021-08-14 00:16:41,477] multiqc [DEBUG ] No samples found: macs2 [2021-08-14 00:16:41,485] multiqc [DEBUG ] No samples found: theta2 [2021-08-14 00:16:41,493] multiqc [DEBUG ] No samples found: snpeff [2021-08-14 00:16:41,512] multiqc [DEBUG ] No samples found: gatk [2021-08-14 00:16:41,519] multiqc [DEBUG ] No samples found: htseq [2021-08-14 00:16:41,526] multiqc [DEBUG ] No samples found: bcftools [2021-08-14 00:16:41,535] multiqc [DEBUG ] No samples found: featureCounts [2021-08-14 00:16:41,544] multiqc [DEBUG ] No samples found: fgbio [2021-08-14 00:16:41,571] multiqc [DEBUG ] No samples found: dragen [2021-08-14 00:16:41,580] multiqc [DEBUG ] No samples found: dedup [2021-08-14 00:16:41,585] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-14 00:16:41,656] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-14 00:16:41,665] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-14 00:16:41,667] multiqc [DEBUG ] No samples found: picard [2021-08-14 00:16:41,680] multiqc [DEBUG ] No samples found: prokka [2021-08-14 00:16:41,686] multiqc [DEBUG ] No samples found: samblaster [2021-08-14 00:16:41,717] multiqc [DEBUG ] No samples found: samtools [2021-08-14 00:16:41,722] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-14 00:16:41,733] multiqc [DEBUG ] No samples found: bamtools [2021-08-14 00:16:41,737] multiqc [DEBUG ] No samples found: jellyfish [2021-08-14 00:16:41,755] multiqc [DEBUG ] No samples found: vcftools [2021-08-14 00:16:41,766] multiqc [DEBUG ] No samples found: longranger [2021-08-14 00:16:41,777] multiqc [DEBUG ] No samples found: stacks [2021-08-14 00:16:41,786] multiqc [DEBUG ] No samples found: varscan2 [2021-08-14 00:16:41,821] multiqc [DEBUG ] No samples found: bbmap [2021-08-14 00:16:41,826] multiqc [DEBUG ] No samples found: bismark [2021-08-14 00:16:41,838] multiqc [DEBUG ] No samples found: biscuit [2021-08-14 00:16:41,848] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-14 00:16:41,858] multiqc [DEBUG ] No samples found: hicup [2021-08-14 00:16:41,867] multiqc [DEBUG ] No samples found: hicpro [2021-08-14 00:16:41,876] multiqc [DEBUG ] No samples found: salmon [2021-08-14 00:16:41,885] multiqc [DEBUG ] No samples found: kallisto [2021-08-14 00:16:41,893] multiqc [DEBUG ] No samples found: slamdunk [2021-08-14 00:16:41,905] multiqc [DEBUG ] No samples found: star [2021-08-14 00:16:41,922] multiqc [DEBUG ] No samples found: hisat2 [2021-08-14 00:16:41,928] multiqc [DEBUG ] No samples found: tophat [2021-08-14 00:16:41,939] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-14 00:16:41,945] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-14 00:16:41,958] multiqc [DEBUG ] No samples found: snpsplit [2021-08-14 00:16:41,971] multiqc [DEBUG ] No samples found: kat [2021-08-14 00:16:41,977] multiqc [DEBUG ] No samples found: leehom [2021-08-14 00:16:41,983] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-14 00:16:41,989] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-14 00:16:41,995] multiqc [DEBUG ] No samples found: cutadapt [2021-08-14 00:16:42,003] multiqc [DEBUG ] No samples found: flexbar [2021-08-14 00:16:42,008] multiqc [DEBUG ] No samples found: kaiju [2021-08-14 00:16:42,014] multiqc [DEBUG ] No samples found: kraken [2021-08-14 00:16:42,023] multiqc [DEBUG ] No samples found: malt [2021-08-14 00:16:42,035] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-14 00:16:42,044] multiqc [DEBUG ] No samples found: sickle [2021-08-14 00:16:42,052] multiqc [DEBUG ] No samples found: skewer [2021-08-14 00:16:42,059] multiqc [DEBUG ] No samples found: sortmerna [2021-08-14 00:16:42,065] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-14 00:16:42,070] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-14 00:16:42,074] multiqc [DEBUG ] No samples found: afterqc [2021-08-14 00:16:42,084] multiqc [DEBUG ] No samples found: fastp [2021-08-14 00:16:42,976] multiqc.modules.fastqc.fastqc [INFO ] Found 13 reports [2021-08-14 00:16:43,256] multiqc [DEBUG ] No samples found: pycoqc [2021-08-14 00:16:43,262] multiqc [DEBUG ] No samples found: minionqc [2021-08-14 00:16:43,270] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-14 00:16:43,277] multiqc [DEBUG ] No samples found: clusterflow [2021-08-14 00:16:43,286] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-14 00:16:43,294] multiqc [DEBUG ] No samples found: interop [2021-08-14 00:16:43,299] multiqc [DEBUG ] No samples found: ivar [2021-08-14 00:16:43,308] multiqc [DEBUG ] No samples found: flash [2021-08-14 00:16:43,312] multiqc [DEBUG ] No samples found: seqyclean [2021-08-14 00:16:43,312] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-08-14 00:16:43,312] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-08-14 00:16:43,312] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-14 00:16:43,312] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-14 00:16:43,328] multiqc [INFO ] Compressing plot data [2021-08-14 00:16:43,512] multiqc [INFO ] Report : multiqc_report.html [2021-08-14 00:16:43,512] multiqc [INFO ] Data : multiqc_data [2021-08-14 00:16:43,512] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9393457/tmp44pofe7y/multiqc_data' to '/scratch/gencore/logs/html/HLNVGBGXJ/merged/multiqc_data' [2021-08-14 00:16:43,753] multiqc [INFO ] MultiQC complete