[2022-03-22 16:18:27,797] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-22 16:18:27,797] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-22 16:18:27,797] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-22 16:18:27,798] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-22 16:18:27,798] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-22 16:18:27,798] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVNNCDRXY/merged [2022-03-22 16:18:28,289] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-22 16:18:28,289] multiqc [INFO ] This is MultiQC v1.9 [2022-03-22 16:18:28,289] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVNNCDRXY/merged [2022-03-22 16:18:28,289] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVNNCDRXY/merged [2022-03-22 16:18:28,289] multiqc [INFO ] Template : default [2022-03-22 16:18:28,289] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-22 16:18:28,289] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVNNCDRXY/merged [2022-03-22 16:18:28,289] 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 [2022-03-22 16:18:28,290] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16507447/tmpuh5sdics [2022-03-22 16:18:28,402] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK91_fastqc.html [2022-03-22 16:18:28,405] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK91_fastqc.html [2022-03-22 16:18:28,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK88_fastqc.html [2022-03-22 16:18:28,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK88_fastqc.html [2022-03-22 16:18:28,486] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:28,488] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:18:33,394] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK89_fastqc.html [2022-03-22 16:18:33,396] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK89_fastqc.html [2022-03-22 16:18:33,436] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK88_fastqc.html [2022-03-22 16:18:33,438] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK88_fastqc.html [2022-03-22 16:18:33,477] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK13_2_hic_fastqc.html [2022-03-22 16:18:33,479] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK13_2_hic_fastqc.html [2022-03-22 16:18:33,518] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK13_2_hic_fastqc.html [2022-03-22 16:18:33,519] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK13_2_hic_fastqc.html [2022-03-22 16:18:33,561] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK90_fastqc.html [2022-03-22 16:18:33,563] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK90_fastqc.html [2022-03-22 16:18:33,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n01_undetermined_fastqc.html [2022-03-22 16:18:33,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n01_undetermined_fastqc.html [2022-03-22 16:18:33,644] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK90_fastqc.html [2022-03-22 16:18:33,646] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK90_fastqc.html [2022-03-22 16:18:33,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n02_undetermined_fastqc.html [2022-03-22 16:18:33,689] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n02_undetermined_fastqc.html [2022-03-22 16:18:33,728] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK91_fastqc.html [2022-03-22 16:18:33,729] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n01_JK91_fastqc.html [2022-03-22 16:18:33,768] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK89_fastqc.html [2022-03-22 16:18:33,770] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVNNCDRXY_n02_JK89_fastqc.html [2022-03-22 16:18:34,116] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-22 16:18:34,118] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-22 16:18:34,126] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-22 16:18:34,136] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-22 16:18:34,139] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2022-03-22 16:18:34,143] multiqc [DEBUG ] No samples found: conpair [2022-03-22 16:18:34,148] multiqc [DEBUG ] No samples found: peddy [2022-03-22 16:18:34,152] multiqc [DEBUG ] No samples found: somalier [2022-03-22 16:18:34,157] multiqc [DEBUG ] No samples found: methylQA [2022-03-22 16:18:34,164] multiqc [DEBUG ] No samples found: mosdepth [2022-03-22 16:18:34,168] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-22 16:18:34,172] multiqc [DEBUG ] No samples found: qualimap [2022-03-22 16:18:34,176] multiqc [DEBUG ] No samples found: preseq [2022-03-22 16:18:34,180] multiqc [DEBUG ] No samples found: quast [2022-03-22 16:18:34,184] multiqc [DEBUG ] No samples found: qorts [2022-03-22 16:18:34,189] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-22 16:18:34,193] multiqc [DEBUG ] No samples found: rockhopper [2022-03-22 16:18:34,197] multiqc [DEBUG ] No samples found: rsem [2022-03-22 16:18:34,207] multiqc [DEBUG ] No samples found: rseqc [2022-03-22 16:18:34,211] multiqc [DEBUG ] No samples found: busco [2022-03-22 16:18:34,216] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-22 16:18:34,220] multiqc [DEBUG ] No samples found: disambiguate [2022-03-22 16:18:34,224] multiqc [DEBUG ] No samples found: supernova [2022-03-22 16:18:34,235] multiqc [DEBUG ] No samples found: deeptools [2022-03-22 16:18:34,240] multiqc [DEBUG ] No samples found: sargasso [2022-03-22 16:18:34,244] multiqc [DEBUG ] No samples found: verifybamid [2022-03-22 16:18:34,248] multiqc [DEBUG ] No samples found: mirtrace [2022-03-22 16:18:34,252] multiqc [DEBUG ] No samples found: happy [2022-03-22 16:18:34,256] multiqc [DEBUG ] No samples found: mirtop [2022-03-22 16:18:34,262] multiqc [DEBUG ] No samples found: homer [2022-03-22 16:18:34,266] multiqc [DEBUG ] No samples found: macs2 [2022-03-22 16:18:34,270] multiqc [DEBUG ] No samples found: theta2 [2022-03-22 16:18:34,276] multiqc [DEBUG ] No samples found: snpeff [2022-03-22 16:18:34,282] multiqc [DEBUG ] No samples found: gatk [2022-03-22 16:18:34,287] multiqc [DEBUG ] No samples found: htseq [2022-03-22 16:18:34,292] multiqc [DEBUG ] No samples found: bcftools [2022-03-22 16:18:34,296] multiqc [DEBUG ] No samples found: featureCounts [2022-03-22 16:18:34,302] multiqc [DEBUG ] No samples found: fgbio [2022-03-22 16:18:34,313] multiqc [DEBUG ] No samples found: dragen [2022-03-22 16:18:34,317] multiqc [DEBUG ] No samples found: dedup [2022-03-22 16:18:34,322] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-22 16:18:34,341] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-22 16:18:34,345] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-22 16:18:34,348] multiqc [DEBUG ] No samples found: picard [2022-03-22 16:18:34,352] multiqc [DEBUG ] No samples found: prokka [2022-03-22 16:18:34,356] multiqc [DEBUG ] No samples found: samblaster [2022-03-22 16:18:34,363] multiqc [DEBUG ] No samples found: samtools [2022-03-22 16:18:34,367] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-22 16:18:34,372] multiqc [DEBUG ] No samples found: bamtools [2022-03-22 16:18:34,376] multiqc [DEBUG ] No samples found: jellyfish [2022-03-22 16:18:34,383] multiqc [DEBUG ] No samples found: vcftools [2022-03-22 16:18:34,387] multiqc [DEBUG ] No samples found: longranger [2022-03-22 16:18:34,391] multiqc [DEBUG ] No samples found: stacks [2022-03-22 16:18:34,395] multiqc [DEBUG ] No samples found: varscan2 [2022-03-22 16:18:34,409] multiqc [DEBUG ] No samples found: bbmap [2022-03-22 16:18:34,413] multiqc [DEBUG ] No samples found: bismark [2022-03-22 16:18:34,418] multiqc [DEBUG ] No samples found: biscuit [2022-03-22 16:18:34,423] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-22 16:18:34,427] multiqc [DEBUG ] No samples found: hicup [2022-03-22 16:18:34,431] multiqc [DEBUG ] No samples found: hicpro [2022-03-22 16:18:34,435] multiqc [DEBUG ] No samples found: salmon [2022-03-22 16:18:34,439] multiqc [DEBUG ] No samples found: kallisto [2022-03-22 16:18:34,444] multiqc [DEBUG ] No samples found: slamdunk [2022-03-22 16:18:34,448] multiqc [DEBUG ] No samples found: star [2022-03-22 16:18:34,452] multiqc [DEBUG ] No samples found: hisat2 [2022-03-22 16:18:34,456] multiqc [DEBUG ] No samples found: tophat [2022-03-22 16:18:34,460] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-22 16:18:34,465] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-22 16:18:34,469] multiqc [DEBUG ] No samples found: snpsplit [2022-03-22 16:18:34,473] multiqc [DEBUG ] No samples found: kat [2022-03-22 16:18:34,477] multiqc [DEBUG ] No samples found: leehom [2022-03-22 16:18:34,481] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-22 16:18:34,485] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-22 16:18:34,489] multiqc [DEBUG ] No samples found: cutadapt [2022-03-22 16:18:34,493] multiqc [DEBUG ] No samples found: flexbar [2022-03-22 16:18:34,497] multiqc [DEBUG ] No samples found: kaiju [2022-03-22 16:18:34,502] multiqc [DEBUG ] No samples found: kraken [2022-03-22 16:18:34,506] multiqc [DEBUG ] No samples found: malt [2022-03-22 16:18:34,510] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-22 16:18:34,514] multiqc [DEBUG ] No samples found: sickle [2022-03-22 16:18:34,518] multiqc [DEBUG ] No samples found: skewer [2022-03-22 16:18:34,522] multiqc [DEBUG ] No samples found: sortmerna [2022-03-22 16:18:34,528] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-22 16:18:34,532] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-22 16:18:34,536] multiqc [DEBUG ] No samples found: afterqc [2022-03-22 16:18:34,540] multiqc [DEBUG ] No samples found: fastp [2022-03-22 16:18:34,936] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2022-03-22 16:18:35,141] multiqc [DEBUG ] No samples found: pycoqc [2022-03-22 16:18:35,148] multiqc [DEBUG ] No samples found: minionqc [2022-03-22 16:18:35,153] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-22 16:18:35,158] multiqc [DEBUG ] No samples found: clusterflow [2022-03-22 16:18:35,163] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-22 16:18:35,168] multiqc [DEBUG ] No samples found: interop [2022-03-22 16:18:35,177] multiqc [DEBUG ] No samples found: ivar [2022-03-22 16:18:35,183] multiqc [DEBUG ] No samples found: flash [2022-03-22 16:18:35,189] multiqc [DEBUG ] No samples found: seqyclean [2022-03-22 16:18:35,189] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-22 16:18:35,189] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-22 16:18:35,189] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-22 16:18:35,189] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-22 16:18:35,204] multiqc [INFO ] Compressing plot data [2022-03-22 16:18:35,408] multiqc [INFO ] Report : multiqc_report.html [2022-03-22 16:18:35,408] multiqc [INFO ] Data : multiqc_data [2022-03-22 16:18:35,408] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16507447/tmpuh5sdics/multiqc_data' to '/scratch/gencore/logs/html/HVNNCDRXY/merged/multiqc_data' [2022-03-22 16:18:35,526] multiqc [INFO ] MultiQC complete