[2021-02-17 08:49:13,001] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-02-17 08:49:13,001] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-02-17 08:49:13,001] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-17 08:49:13,002] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-02-17 08:49:13,002] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-02-17 08:49:13,002] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVHT2DRXX/2 [2021-02-17 08:49:14,301] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-17 08:49:14,301] multiqc [INFO ] This is MultiQC v1.9 [2021-02-17 08:49:14,301] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVHT2DRXX/2 [2021-02-17 08:49:14,301] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVHT2DRXX/2 [2021-02-17 08:49:14,301] multiqc [INFO ] Template : default [2021-02-17 08:49:14,301] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-02-17 08:49:14,301] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVHT2DRXX/2 [2021-02-17 08:49:14,302] 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 [2021-02-17 08:49:14,302] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-2876432/tmpndxma6rr [2021-02-17 08:49:14,392] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb391_fastqc.html [2021-02-17 08:49:14,395] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb391_fastqc.html [2021-02-17 08:49:14,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei044_fastqc.html [2021-02-17 08:49:14,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei044_fastqc.html [2021-02-17 08:49:14,478] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-02-17 08:49:14,479] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-02-17 08:49:14,572] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei046_fastqc.html [2021-02-17 08:49:14,574] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei046_fastqc.html [2021-02-17 08:49:14,615] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb410_fastqc.html [2021-02-17 08:49:14,617] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb410_fastqc.html [2021-02-17 08:49:14,657] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb407_fastqc.html [2021-02-17 08:49:14,659] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb407_fastqc.html [2021-02-17 08:49:14,699] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei040_fastqc.html [2021-02-17 08:49:14,701] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei040_fastqc.html [2021-02-17 08:49:14,742] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb412_fastqc.html [2021-02-17 08:49:14,743] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb412_fastqc.html [2021-02-17 08:49:14,783] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei050_fastqc.html [2021-02-17 08:49:14,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei050_fastqc.html [2021-02-17 08:49:14,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb406_fastqc.html [2021-02-17 08:49:14,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb406_fastqc.html [2021-02-17 08:49:14,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei038_fastqc.html [2021-02-17 08:49:14,868] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei038_fastqc.html [2021-02-17 08:49:14,908] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei047_fastqc.html [2021-02-17 08:49:14,910] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei047_fastqc.html [2021-02-17 08:49:14,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb393_fastqc.html [2021-02-17 08:49:14,952] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb393_fastqc.html [2021-02-17 08:49:14,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb405_fastqc.html [2021-02-17 08:49:14,994] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb405_fastqc.html [2021-02-17 08:49:15,036] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb392_fastqc.html [2021-02-17 08:49:15,038] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb392_fastqc.html [2021-02-17 08:49:15,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei055_fastqc.html [2021-02-17 08:49:15,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei055_fastqc.html [2021-02-17 08:49:15,121] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb411_fastqc.html [2021-02-17 08:49:15,122] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb411_fastqc.html [2021-02-17 08:49:15,163] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei041_fastqc.html [2021-02-17 08:49:15,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei041_fastqc.html [2021-02-17 08:49:15,206] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei049_fastqc.html [2021-02-17 08:49:15,207] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei049_fastqc.html [2021-02-17 08:49:15,249] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb409_fastqc.html [2021-02-17 08:49:15,251] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb409_fastqc.html [2021-02-17 08:49:15,291] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei043_fastqc.html [2021-02-17 08:49:15,293] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei043_fastqc.html [2021-02-17 08:49:15,334] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei052_fastqc.html [2021-02-17 08:49:15,336] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei052_fastqc.html [2021-02-17 08:49:15,376] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb408_fastqc.html [2021-02-17 08:49:15,378] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb408_fastqc.html [2021-02-17 08:49:15,419] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_undetermined_fastqc.html [2021-02-17 08:49:15,420] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_undetermined_fastqc.html [2021-02-17 08:49:15,459] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb394_fastqc.html [2021-02-17 08:49:15,461] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_mb394_fastqc.html [2021-02-17 08:49:15,501] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei053_fastqc.html [2021-02-17 08:49:15,503] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVHT2DRXX_l02_n01_dei053_fastqc.html [2021-02-17 08:49:15,798] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-17 08:49:15,799] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-17 08:49:15,805] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-02-17 08:49:15,815] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-02-17 08:49:15,827] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 25 samples (table) [2021-02-17 08:49:15,829] multiqc [DEBUG ] No samples found: conpair [2021-02-17 08:49:15,832] multiqc [DEBUG ] No samples found: peddy [2021-02-17 08:49:15,835] multiqc [DEBUG ] No samples found: somalier [2021-02-17 08:49:15,838] multiqc [DEBUG ] No samples found: methylQA [2021-02-17 08:49:15,841] multiqc [DEBUG ] No samples found: mosdepth [2021-02-17 08:49:15,844] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-17 08:49:15,846] multiqc [DEBUG ] No samples found: qualimap [2021-02-17 08:49:15,849] multiqc [DEBUG ] No samples found: preseq [2021-02-17 08:49:15,852] multiqc [DEBUG ] No samples found: quast [2021-02-17 08:49:15,854] multiqc [DEBUG ] No samples found: qorts [2021-02-17 08:49:15,857] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-17 08:49:15,860] multiqc [DEBUG ] No samples found: rockhopper [2021-02-17 08:49:15,862] multiqc [DEBUG ] No samples found: rsem [2021-02-17 08:49:15,867] multiqc [DEBUG ] No samples found: rseqc [2021-02-17 08:49:15,869] multiqc [DEBUG ] No samples found: busco [2021-02-17 08:49:15,872] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-17 08:49:15,875] multiqc [DEBUG ] No samples found: disambiguate [2021-02-17 08:49:15,877] multiqc [DEBUG ] No samples found: supernova [2021-02-17 08:49:15,882] multiqc [DEBUG ] No samples found: deeptools [2021-02-17 08:49:15,885] multiqc [DEBUG ] No samples found: sargasso [2021-02-17 08:49:15,887] multiqc [DEBUG ] No samples found: verifybamid [2021-02-17 08:49:15,890] multiqc [DEBUG ] No samples found: mirtrace [2021-02-17 08:49:15,893] multiqc [DEBUG ] No samples found: happy [2021-02-17 08:49:15,895] multiqc [DEBUG ] No samples found: mirtop [2021-02-17 08:49:15,899] multiqc [DEBUG ] No samples found: homer [2021-02-17 08:49:15,901] multiqc [DEBUG ] No samples found: macs2 [2021-02-17 08:49:15,904] multiqc [DEBUG ] No samples found: theta2 [2021-02-17 08:49:15,906] multiqc [DEBUG ] No samples found: snpeff [2021-02-17 08:49:15,910] multiqc [DEBUG ] No samples found: gatk [2021-02-17 08:49:15,912] multiqc [DEBUG ] No samples found: htseq [2021-02-17 08:49:15,915] multiqc [DEBUG ] No samples found: bcftools [2021-02-17 08:49:15,918] multiqc [DEBUG ] No samples found: featureCounts [2021-02-17 08:49:15,921] multiqc [DEBUG ] No samples found: fgbio [2021-02-17 08:49:15,926] multiqc [DEBUG ] No samples found: dragen [2021-02-17 08:49:15,928] multiqc [DEBUG ] No samples found: dedup [2021-02-17 08:49:15,931] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-17 08:49:15,938] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-17 08:49:15,941] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-17 08:49:15,943] multiqc [DEBUG ] No samples found: picard [2021-02-17 08:49:15,946] multiqc [DEBUG ] No samples found: prokka [2021-02-17 08:49:15,948] multiqc [DEBUG ] No samples found: samblaster [2021-02-17 08:49:15,952] multiqc [DEBUG ] No samples found: samtools [2021-02-17 08:49:15,955] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-17 08:49:15,957] multiqc [DEBUG ] No samples found: bamtools [2021-02-17 08:49:15,960] multiqc [DEBUG ] No samples found: jellyfish [2021-02-17 08:49:15,963] multiqc [DEBUG ] No samples found: vcftools [2021-02-17 08:49:15,966] multiqc [DEBUG ] No samples found: longranger [2021-02-17 08:49:15,969] multiqc [DEBUG ] No samples found: stacks [2021-02-17 08:49:15,971] multiqc [DEBUG ] No samples found: varscan2 [2021-02-17 08:49:15,976] multiqc [DEBUG ] No samples found: bbmap [2021-02-17 08:49:15,979] multiqc [DEBUG ] No samples found: bismark [2021-02-17 08:49:15,982] multiqc [DEBUG ] No samples found: biscuit [2021-02-17 08:49:15,985] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-17 08:49:15,987] multiqc [DEBUG ] No samples found: hicup [2021-02-17 08:49:15,990] multiqc [DEBUG ] No samples found: hicpro [2021-02-17 08:49:15,993] multiqc [DEBUG ] No samples found: salmon [2021-02-17 08:49:15,995] multiqc [DEBUG ] No samples found: kallisto [2021-02-17 08:49:15,998] multiqc [DEBUG ] No samples found: slamdunk [2021-02-17 08:49:16,001] multiqc [DEBUG ] No samples found: star [2021-02-17 08:49:16,003] multiqc [DEBUG ] No samples found: hisat2 [2021-02-17 08:49:16,006] multiqc [DEBUG ] No samples found: tophat [2021-02-17 08:49:16,008] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-17 08:49:16,011] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-17 08:49:16,014] multiqc [DEBUG ] No samples found: snpsplit [2021-02-17 08:49:16,016] multiqc [DEBUG ] No samples found: kat [2021-02-17 08:49:16,019] multiqc [DEBUG ] No samples found: leehom [2021-02-17 08:49:16,022] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-17 08:49:16,024] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-17 08:49:16,027] multiqc [DEBUG ] No samples found: cutadapt [2021-02-17 08:49:16,030] multiqc [DEBUG ] No samples found: flexbar [2021-02-17 08:49:16,032] multiqc [DEBUG ] No samples found: kaiju [2021-02-17 08:49:16,035] multiqc [DEBUG ] No samples found: kraken [2021-02-17 08:49:16,037] multiqc [DEBUG ] No samples found: malt [2021-02-17 08:49:16,040] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-17 08:49:16,043] multiqc [DEBUG ] No samples found: sickle [2021-02-17 08:49:16,045] multiqc [DEBUG ] No samples found: skewer [2021-02-17 08:49:16,048] multiqc [DEBUG ] No samples found: sortmerna [2021-02-17 08:49:16,051] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-17 08:49:16,053] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-17 08:49:16,056] multiqc [DEBUG ] No samples found: afterqc [2021-02-17 08:49:16,059] multiqc [DEBUG ] No samples found: fastp [2021-02-17 08:49:17,633] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2021-02-17 08:49:17,984] multiqc [DEBUG ] No samples found: pycoqc [2021-02-17 08:49:17,987] multiqc [DEBUG ] No samples found: minionqc [2021-02-17 08:49:17,990] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-17 08:49:17,993] multiqc [DEBUG ] No samples found: clusterflow [2021-02-17 08:49:17,995] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-17 08:49:17,998] multiqc [DEBUG ] No samples found: interop [2021-02-17 08:49:18,001] multiqc [DEBUG ] No samples found: ivar [2021-02-17 08:49:18,003] multiqc [DEBUG ] No samples found: flash [2021-02-17 08:49:18,006] multiqc [DEBUG ] No samples found: seqyclean [2021-02-17 08:49:18,006] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-02-17 08:49:18,006] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-02-17 08:49:18,006] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-02-17 08:49:18,006] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2021-02-17 08:49:18,006] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-02-17 08:49:18,035] multiqc [INFO ] Compressing plot data [2021-02-17 08:49:18,493] multiqc [INFO ] Report : multiqc_report.html [2021-02-17 08:49:18,493] multiqc [INFO ] Data : multiqc_data [2021-02-17 08:49:18,493] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2876432/tmpndxma6rr/multiqc_data' to '/scratch/gencore/logs/html/HVHT2DRXX/2/multiqc_data' [2021-02-17 08:49:18,584] multiqc [INFO ] MultiQC complete