[2021-09-08 02:16:01,351] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-08 02:16:01,351] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-08 02:16:01,351] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-08 02:16:01,352] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-08 02:16:01,352] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-08 02:16:01,353] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52GVBGXK/merged [2021-09-08 02:16:02,827] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-08 02:16:02,827] multiqc [INFO ] This is MultiQC v1.9 [2021-09-08 02:16:02,827] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52GVBGXK/merged [2021-09-08 02:16:02,827] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H52GVBGXK/merged [2021-09-08 02:16:02,828] multiqc [INFO ] Template : default [2021-09-08 02:16:02,828] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-08 02:16:02,828] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H52GVBGXK/merged [2021-09-08 02:16:02,828] 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 [2021-09-08 02:16:02,828] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9828112/tmpbue7uurg [2021-09-08 02:16:02,939] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-08 02:16:02,941] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-08 02:16:03,353] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_11_fastqc.html [2021-09-08 02:16:03,355] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_11_fastqc.html [2021-09-08 02:16:03,398] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_8_fastqc.html [2021-09-08 02:16:03,400] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_8_fastqc.html [2021-09-08 02:16:03,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52GVBGXK_n01_undetermined_fastqc.html [2021-09-08 02:16:03,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52GVBGXK_n01_undetermined_fastqc.html [2021-09-08 02:16:03,487] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_10_fastqc.html [2021-09-08 02:16:03,489] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_10_fastqc.html [2021-09-08 02:16:03,531] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_9_fastqc.html [2021-09-08 02:16:03,533] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52GVBGXK_n01_ATAC_Tcell_S_9_fastqc.html [2021-09-08 02:16:03,866] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-08 02:16:03,867] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-08 02:16:03,878] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-08 02:16:03,881] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2021-09-08 02:16:03,891] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-08 02:16:03,899] multiqc [DEBUG ] No samples found: conpair [2021-09-08 02:16:03,904] multiqc [DEBUG ] No samples found: peddy [2021-09-08 02:16:03,912] multiqc [DEBUG ] No samples found: somalier [2021-09-08 02:16:03,921] multiqc [DEBUG ] No samples found: methylQA [2021-09-08 02:16:03,933] multiqc [DEBUG ] No samples found: mosdepth [2021-09-08 02:16:03,937] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-08 02:16:03,941] multiqc [DEBUG ] No samples found: qualimap [2021-09-08 02:16:03,948] multiqc [DEBUG ] No samples found: preseq [2021-09-08 02:16:03,953] multiqc [DEBUG ] No samples found: quast [2021-09-08 02:16:03,962] multiqc [DEBUG ] No samples found: qorts [2021-09-08 02:16:03,970] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-08 02:16:03,975] multiqc [DEBUG ] No samples found: rockhopper [2021-09-08 02:16:03,979] multiqc [DEBUG ] No samples found: rsem [2021-09-08 02:16:03,992] multiqc [DEBUG ] No samples found: rseqc [2021-09-08 02:16:03,997] multiqc [DEBUG ] No samples found: busco [2021-09-08 02:16:04,004] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-08 02:16:04,010] multiqc [DEBUG ] No samples found: disambiguate [2021-09-08 02:16:04,016] multiqc [DEBUG ] No samples found: supernova [2021-09-08 02:16:04,034] multiqc [DEBUG ] No samples found: deeptools [2021-09-08 02:16:04,038] multiqc [DEBUG ] No samples found: sargasso [2021-09-08 02:16:04,043] multiqc [DEBUG ] No samples found: verifybamid [2021-09-08 02:16:04,047] multiqc [DEBUG ] No samples found: mirtrace [2021-09-08 02:16:04,052] multiqc [DEBUG ] No samples found: happy [2021-09-08 02:16:04,056] multiqc [DEBUG ] No samples found: mirtop [2021-09-08 02:16:04,064] multiqc [DEBUG ] No samples found: homer [2021-09-08 02:16:04,068] multiqc [DEBUG ] No samples found: macs2 [2021-09-08 02:16:04,072] multiqc [DEBUG ] No samples found: theta2 [2021-09-08 02:16:04,080] multiqc [DEBUG ] No samples found: snpeff [2021-09-08 02:16:04,094] multiqc [DEBUG ] No samples found: gatk [2021-09-08 02:16:04,098] multiqc [DEBUG ] No samples found: htseq [2021-09-08 02:16:04,105] multiqc [DEBUG ] No samples found: bcftools [2021-09-08 02:16:04,109] multiqc [DEBUG ] No samples found: featureCounts [2021-09-08 02:16:04,115] multiqc [DEBUG ] No samples found: fgbio [2021-09-08 02:16:04,129] multiqc [DEBUG ] No samples found: dragen [2021-09-08 02:16:04,137] multiqc [DEBUG ] No samples found: dedup [2021-09-08 02:16:04,141] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-08 02:16:04,170] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-08 02:16:04,177] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-08 02:16:04,179] multiqc [DEBUG ] No samples found: picard [2021-09-08 02:16:04,190] multiqc [DEBUG ] No samples found: prokka [2021-09-08 02:16:04,194] multiqc [DEBUG ] No samples found: samblaster [2021-09-08 02:16:04,206] multiqc [DEBUG ] No samples found: samtools [2021-09-08 02:16:04,210] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-08 02:16:04,215] multiqc [DEBUG ] No samples found: bamtools [2021-09-08 02:16:04,219] multiqc [DEBUG ] No samples found: jellyfish [2021-09-08 02:16:04,227] multiqc [DEBUG ] No samples found: vcftools [2021-09-08 02:16:04,235] multiqc [DEBUG ] No samples found: longranger [2021-09-08 02:16:04,240] multiqc [DEBUG ] No samples found: stacks [2021-09-08 02:16:04,244] multiqc [DEBUG ] No samples found: varscan2 [2021-09-08 02:16:04,261] multiqc [DEBUG ] No samples found: bbmap [2021-09-08 02:16:04,266] multiqc [DEBUG ] No samples found: bismark [2021-09-08 02:16:04,271] multiqc [DEBUG ] No samples found: biscuit [2021-09-08 02:16:04,277] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-08 02:16:04,286] multiqc [DEBUG ] No samples found: hicup [2021-09-08 02:16:04,292] multiqc [DEBUG ] No samples found: hicpro [2021-09-08 02:16:04,296] multiqc [DEBUG ] No samples found: salmon [2021-09-08 02:16:04,301] multiqc [DEBUG ] No samples found: kallisto [2021-09-08 02:16:04,307] multiqc [DEBUG ] No samples found: slamdunk [2021-09-08 02:16:04,315] multiqc [DEBUG ] No samples found: star [2021-09-08 02:16:04,329] multiqc [DEBUG ] No samples found: hisat2 [2021-09-08 02:16:04,335] multiqc [DEBUG ] No samples found: tophat [2021-09-08 02:16:04,339] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-08 02:16:04,343] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-08 02:16:04,348] multiqc [DEBUG ] No samples found: snpsplit [2021-09-08 02:16:04,353] multiqc [DEBUG ] No samples found: kat [2021-09-08 02:16:04,357] multiqc [DEBUG ] No samples found: leehom [2021-09-08 02:16:04,361] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-08 02:16:04,367] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-08 02:16:04,372] multiqc [DEBUG ] No samples found: cutadapt [2021-09-08 02:16:04,376] multiqc [DEBUG ] No samples found: flexbar [2021-09-08 02:16:04,380] multiqc [DEBUG ] No samples found: kaiju [2021-09-08 02:16:04,386] multiqc [DEBUG ] No samples found: kraken [2021-09-08 02:16:04,390] multiqc [DEBUG ] No samples found: malt [2021-09-08 02:16:04,394] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-08 02:16:04,398] multiqc [DEBUG ] No samples found: sickle [2021-09-08 02:16:04,404] multiqc [DEBUG ] No samples found: skewer [2021-09-08 02:16:04,407] multiqc [DEBUG ] No samples found: sortmerna [2021-09-08 02:16:04,411] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-08 02:16:04,417] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-08 02:16:04,421] multiqc [DEBUG ] No samples found: afterqc [2021-09-08 02:16:04,427] multiqc [DEBUG ] No samples found: fastp [2021-09-08 02:16:04,776] multiqc.modules.fastqc.fastqc [INFO ] Found 5 reports [2021-09-08 02:16:04,907] multiqc [DEBUG ] No samples found: pycoqc [2021-09-08 02:16:04,912] multiqc [DEBUG ] No samples found: minionqc [2021-09-08 02:16:04,916] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-08 02:16:04,920] multiqc [DEBUG ] No samples found: clusterflow [2021-09-08 02:16:04,925] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-08 02:16:04,932] multiqc [DEBUG ] No samples found: interop [2021-09-08 02:16:04,937] multiqc [DEBUG ] No samples found: ivar [2021-09-08 02:16:04,941] multiqc [DEBUG ] No samples found: flash [2021-09-08 02:16:04,945] multiqc [DEBUG ] No samples found: seqyclean [2021-09-08 02:16:04,945] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-09-08 02:16:04,945] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-09-08 02:16:04,945] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-08 02:16:04,945] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-08 02:16:04,952] multiqc [INFO ] Compressing plot data [2021-09-08 02:16:05,058] multiqc [INFO ] Report : multiqc_report.html [2021-09-08 02:16:05,058] multiqc [INFO ] Data : multiqc_data [2021-09-08 02:16:05,058] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9828112/tmpbue7uurg/multiqc_data' to '/scratch/gencore/logs/html/H52GVBGXK/merged/multiqc_data' [2021-09-08 02:16:05,203] multiqc [INFO ] MultiQC complete