[2023-03-01 23:46:07,708] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-03-01 23:46:07,708] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-03-01 23:46:07,708] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-03-01 23:46:07,710] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-03-01 23:46:07,711] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-03-01 23:46:07,711] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7NT7BGXN/merged [2023-03-01 23:46:09,500] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-03-01 23:46:09,500] multiqc [INFO ] This is MultiQC v1.9 [2023-03-01 23:46:09,500] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7NT7BGXN/merged [2023-03-01 23:46:09,500] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7NT7BGXN/merged [2023-03-01 23:46:09,500] multiqc [INFO ] Template : default [2023-03-01 23:46:09,500] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-03-01 23:46:09,500] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7NT7BGXN/merged [2023-03-01 23:46:09,500] 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 [2023-03-01 23:46:09,501] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-30676232/tmp88m53lhv [2023-03-01 23:46:09,625] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_12410_fastqc.html [2023-03-01 23:46:09,628] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_12410_fastqc.html [2023-03-01 23:46:09,673] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_11951_fastqc.html [2023-03-01 23:46:09,675] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_11951_fastqc.html [2023-03-01 23:46:09,730] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-01 23:46:09,731] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-01 23:46:09,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_7797_fastqc.html [2023-03-01 23:46:09,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_7797_fastqc.html [2023-03-01 23:46:09,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_7797_fastqc.html [2023-03-01 23:46:09,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_7797_fastqc.html [2023-03-01 23:46:09,973] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_11648_fastqc.html [2023-03-01 23:46:09,975] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_11648_fastqc.html [2023-03-01 23:46:10,015] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_undetermined_fastqc.html [2023-03-01 23:46:10,017] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_undetermined_fastqc.html [2023-03-01 23:46:10,065] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_5184_fastqc.html [2023-03-01 23:46:10,067] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_5184_fastqc.html [2023-03-01 23:46:10,120] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_Daniel_fastqc.html [2023-03-01 23:46:10,122] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_Daniel_fastqc.html [2023-03-01 23:46:10,163] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_12410_fastqc.html [2023-03-01 23:46:10,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_12410_fastqc.html [2023-03-01 23:46:10,206] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_7458_fastqc.html [2023-03-01 23:46:10,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_7458_fastqc.html [2023-03-01 23:46:10,250] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_11648_fastqc.html [2023-03-01 23:46:10,252] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_11648_fastqc.html [2023-03-01 23:46:10,293] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_7458_fastqc.html [2023-03-01 23:46:10,295] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_7458_fastqc.html [2023-03-01 23:46:10,337] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n01_Daniel_fastqc.html [2023-03-01 23:46:10,339] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n01_Daniel_fastqc.html [2023-03-01 23:46:10,382] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_undetermined_fastqc.html [2023-03-01 23:46:10,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_undetermined_fastqc.html [2023-03-01 23:46:10,424] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_5184_fastqc.html [2023-03-01 23:46:10,426] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_5184_fastqc.html [2023-03-01 23:46:10,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7NT7BGXN_n02_11951_fastqc.html [2023-03-01 23:46:10,471] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7NT7BGXN_n02_11951_fastqc.html [2023-03-01 23:46:11,037] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-01 23:46:11,039] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-01 23:46:11,051] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2023-03-01 23:46:11,052] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-03-01 23:46:11,062] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-03-01 23:46:11,072] multiqc [DEBUG ] No samples found: conpair [2023-03-01 23:46:11,081] multiqc [DEBUG ] No samples found: peddy [2023-03-01 23:46:11,089] multiqc [DEBUG ] No samples found: somalier [2023-03-01 23:46:11,096] multiqc [DEBUG ] No samples found: methylQA [2023-03-01 23:46:11,113] multiqc [DEBUG ] No samples found: mosdepth [2023-03-01 23:46:11,121] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-03-01 23:46:11,125] multiqc [DEBUG ] No samples found: qualimap [2023-03-01 23:46:11,131] multiqc [DEBUG ] No samples found: preseq [2023-03-01 23:46:11,137] multiqc [DEBUG ] No samples found: quast [2023-03-01 23:46:11,143] multiqc [DEBUG ] No samples found: qorts [2023-03-01 23:46:11,153] multiqc [DEBUG ] No samples found: rna_seqc [2023-03-01 23:46:11,163] multiqc [DEBUG ] No samples found: rockhopper [2023-03-01 23:46:11,172] multiqc [DEBUG ] No samples found: rsem [2023-03-01 23:46:11,187] multiqc [DEBUG ] No samples found: rseqc [2023-03-01 23:46:11,193] multiqc [DEBUG ] No samples found: busco [2023-03-01 23:46:11,199] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-03-01 23:46:11,205] multiqc [DEBUG ] No samples found: disambiguate [2023-03-01 23:46:11,212] multiqc [DEBUG ] No samples found: supernova [2023-03-01 23:46:11,232] multiqc [DEBUG ] No samples found: deeptools [2023-03-01 23:46:11,241] multiqc [DEBUG ] No samples found: sargasso [2023-03-01 23:46:11,247] multiqc [DEBUG ] No samples found: verifybamid [2023-03-01 23:46:11,253] multiqc [DEBUG ] No samples found: mirtrace [2023-03-01 23:46:11,262] multiqc [DEBUG ] No samples found: happy [2023-03-01 23:46:11,271] multiqc [DEBUG ] No samples found: mirtop [2023-03-01 23:46:11,280] multiqc [DEBUG ] No samples found: homer [2023-03-01 23:46:11,288] multiqc [DEBUG ] No samples found: macs2 [2023-03-01 23:46:11,294] multiqc [DEBUG ] No samples found: theta2 [2023-03-01 23:46:11,300] multiqc [DEBUG ] No samples found: snpeff [2023-03-01 23:46:11,312] multiqc [DEBUG ] No samples found: gatk [2023-03-01 23:46:11,320] multiqc [DEBUG ] No samples found: htseq [2023-03-01 23:46:11,327] multiqc [DEBUG ] No samples found: bcftools [2023-03-01 23:46:11,336] multiqc [DEBUG ] No samples found: featureCounts [2023-03-01 23:46:11,345] multiqc [DEBUG ] No samples found: fgbio [2023-03-01 23:46:11,366] multiqc [DEBUG ] No samples found: dragen [2023-03-01 23:46:11,379] multiqc [DEBUG ] No samples found: dedup [2023-03-01 23:46:11,385] multiqc [DEBUG ] No samples found: damageprofiler [2023-03-01 23:46:11,416] multiqc [DEBUG ] No samples found: biobambam2 [2023-03-01 23:46:11,424] multiqc [DEBUG ] No samples found: mtnucratio [2023-03-01 23:46:11,426] multiqc [DEBUG ] No samples found: picard [2023-03-01 23:46:11,433] multiqc [DEBUG ] No samples found: prokka [2023-03-01 23:46:11,438] multiqc [DEBUG ] No samples found: samblaster [2023-03-01 23:46:11,452] multiqc [DEBUG ] No samples found: samtools [2023-03-01 23:46:11,464] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-03-01 23:46:11,473] multiqc [DEBUG ] No samples found: bamtools [2023-03-01 23:46:11,481] multiqc [DEBUG ] No samples found: jellyfish [2023-03-01 23:46:11,492] multiqc [DEBUG ] No samples found: vcftools [2023-03-01 23:46:11,500] multiqc [DEBUG ] No samples found: longranger [2023-03-01 23:46:11,507] multiqc [DEBUG ] No samples found: stacks [2023-03-01 23:46:11,514] multiqc [DEBUG ] No samples found: varscan2 [2023-03-01 23:46:11,532] multiqc [DEBUG ] No samples found: bbmap [2023-03-01 23:46:11,538] multiqc [DEBUG ] No samples found: bismark [2023-03-01 23:46:11,545] multiqc [DEBUG ] No samples found: biscuit [2023-03-01 23:46:11,552] multiqc [DEBUG ] No samples found: hicexplorer [2023-03-01 23:46:11,564] multiqc [DEBUG ] No samples found: hicup [2023-03-01 23:46:11,573] multiqc [DEBUG ] No samples found: hicpro [2023-03-01 23:46:11,581] multiqc [DEBUG ] No samples found: salmon [2023-03-01 23:46:11,587] multiqc [DEBUG ] No samples found: kallisto [2023-03-01 23:46:11,593] multiqc [DEBUG ] No samples found: slamdunk [2023-03-01 23:46:11,599] multiqc [DEBUG ] No samples found: star [2023-03-01 23:46:11,605] multiqc [DEBUG ] No samples found: hisat2 [2023-03-01 23:46:11,610] multiqc [DEBUG ] No samples found: tophat [2023-03-01 23:46:11,618] multiqc [DEBUG ] No samples found: bowtie2 [2023-03-01 23:46:11,627] multiqc [DEBUG ] No samples found: bowtie1 [2023-03-01 23:46:11,637] multiqc [DEBUG ] No samples found: snpsplit [2023-03-01 23:46:11,642] multiqc [DEBUG ] No samples found: kat [2023-03-01 23:46:11,650] multiqc [DEBUG ] No samples found: leehom [2023-03-01 23:46:11,656] multiqc [DEBUG ] No samples found: adapterRemoval [2023-03-01 23:46:11,665] multiqc [DEBUG ] No samples found: clipandmerge [2023-03-01 23:46:11,671] multiqc [DEBUG ] No samples found: cutadapt [2023-03-01 23:46:11,677] multiqc [DEBUG ] No samples found: flexbar [2023-03-01 23:46:11,683] multiqc [DEBUG ] No samples found: kaiju [2023-03-01 23:46:11,689] multiqc [DEBUG ] No samples found: kraken [2023-03-01 23:46:11,698] multiqc [DEBUG ] No samples found: malt [2023-03-01 23:46:11,708] multiqc [DEBUG ] No samples found: trimmomatic [2023-03-01 23:46:11,714] multiqc [DEBUG ] No samples found: sickle [2023-03-01 23:46:11,721] multiqc [DEBUG ] No samples found: skewer [2023-03-01 23:46:11,729] multiqc [DEBUG ] No samples found: sortmerna [2023-03-01 23:46:11,737] multiqc [DEBUG ] No samples found: biobloomtools [2023-03-01 23:46:11,747] multiqc [DEBUG ] No samples found: fastq_screen [2023-03-01 23:46:11,756] multiqc [DEBUG ] No samples found: afterqc [2023-03-01 23:46:11,762] multiqc [DEBUG ] No samples found: fastp [2023-03-01 23:46:12,740] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2023-03-01 23:46:12,910] multiqc [DEBUG ] No samples found: pycoqc [2023-03-01 23:46:12,918] multiqc [DEBUG ] No samples found: minionqc [2023-03-01 23:46:12,925] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-03-01 23:46:12,931] multiqc [DEBUG ] No samples found: clusterflow [2023-03-01 23:46:12,936] multiqc [DEBUG ] No samples found: bcl2fastq [2023-03-01 23:46:12,942] multiqc [DEBUG ] No samples found: interop [2023-03-01 23:46:12,947] multiqc [DEBUG ] No samples found: ivar [2023-03-01 23:46:12,952] multiqc [DEBUG ] No samples found: flash [2023-03-01 23:46:12,961] multiqc [DEBUG ] No samples found: seqyclean [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-03-01 23:46:12,961] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-03-01 23:46:12,962] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-03-01 23:46:12,981] multiqc [INFO ] Compressing plot data [2023-03-01 23:46:13,255] multiqc [INFO ] Report : multiqc_report.html [2023-03-01 23:46:13,255] multiqc [INFO ] Data : multiqc_data [2023-03-01 23:46:13,255] multiqc [DEBUG ] Moving data file from '/state/partition1/job-30676232/tmp88m53lhv/multiqc_data' to '/scratch/gencore/logs/html/H7NT7BGXN/merged/multiqc_data' [2023-03-01 23:46:13,393] multiqc [INFO ] MultiQC complete