[2023-11-15 11:54:43,266] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-11-15 11:54:43,266] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-11-15 11:54:43,266] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-11-15 11:54:43,270] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-11-15 11:54:43,270] 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}} [2023-11-15 11:54:43,270] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-LBVRL/1 [2023-11-15 11:54:43,464] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-11-15 11:54:43,464] multiqc [INFO ] This is MultiQC v1.9 [2023-11-15 11:54:43,464] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-LBVRL/1 [2023-11-15 11:54:43,464] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-LBVRL/1 [2023-11-15 11:54:43,464] multiqc [INFO ] Template : default [2023-11-15 11:54:43,464] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-11-15 11:54:43,464] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-LBVRL/1 [2023-11-15 11:54:43,465] 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 [2023-11-15 11:54:43,465] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40165831/tmpdl4qvsum [2023-11-15 11:54:43,582] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_undetermined_fastqc.html [2023-11-15 11:54:43,585] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_undetermined_fastqc.html [2023-11-15 11:54:43,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-15 11:54:43,639] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-15 11:54:43,639] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-15 11:54:43,639] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-15 11:54:43,639] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-15 11:54:43,639] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-15 11:54:43,639] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-15 11:54:44,032] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_undetermined_fastqc.html [2023-11-15 11:54:44,034] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_undetermined_fastqc.html [2023-11-15 11:54:44,086] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_4JT_fastqc.html [2023-11-15 11:54:44,088] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_4JT_fastqc.html [2023-11-15 11:54:44,141] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_89_fastqc.html [2023-11-15 11:54:44,143] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_89_fastqc.html [2023-11-15 11:54:44,188] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_319_fastqc.html [2023-11-15 11:54:44,190] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_319_fastqc.html [2023-11-15 11:54:44,234] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_119_fastqc.html [2023-11-15 11:54:44,236] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_119_fastqc.html [2023-11-15 11:54:44,286] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_5-JT_fastqc.html [2023-11-15 11:54:44,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_5-JT_fastqc.html [2023-11-15 11:54:44,334] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_319_fastqc.html [2023-11-15 11:54:44,336] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_319_fastqc.html [2023-11-15 11:54:44,380] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_5-JT_fastqc.html [2023-11-15 11:54:44,382] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_5-JT_fastqc.html [2023-11-15 11:54:44,429] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_89_fastqc.html [2023-11-15 11:54:44,431] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_89_fastqc.html [2023-11-15 11:54:44,476] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_119_fastqc.html [2023-11-15 11:54:44,478] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n02_119_fastqc.html [2023-11-15 11:54:44,526] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_4JT_fastqc.html [2023-11-15 11:54:44,528] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBVRL_l01_n01_4JT_fastqc.html [2023-11-15 11:54:45,240] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-15 11:54:45,242] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-15 11:54:45,259] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-11-15 11:54:45,269] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-11-15 11:54:45,273] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 6 samples (table) [2023-11-15 11:54:45,289] multiqc [DEBUG ] No samples found: conpair [2023-11-15 11:54:45,307] multiqc [DEBUG ] No samples found: peddy [2023-11-15 11:54:45,316] multiqc [DEBUG ] No samples found: somalier [2023-11-15 11:54:45,321] multiqc [DEBUG ] No samples found: methylQA [2023-11-15 11:54:45,345] multiqc [DEBUG ] No samples found: mosdepth [2023-11-15 11:54:45,373] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-11-15 11:54:45,386] multiqc [DEBUG ] No samples found: qualimap [2023-11-15 11:54:45,400] multiqc [DEBUG ] No samples found: preseq [2023-11-15 11:54:45,420] multiqc [DEBUG ] No samples found: quast [2023-11-15 11:54:45,442] multiqc [DEBUG ] No samples found: qorts [2023-11-15 11:54:45,448] multiqc [DEBUG ] No samples found: rna_seqc [2023-11-15 11:54:45,468] multiqc [DEBUG ] No samples found: rockhopper [2023-11-15 11:54:45,482] multiqc [DEBUG ] No samples found: rsem [2023-11-15 11:54:45,528] multiqc [DEBUG ] No samples found: rseqc [2023-11-15 11:54:45,552] multiqc [DEBUG ] No samples found: busco [2023-11-15 11:54:45,564] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-11-15 11:54:45,576] multiqc [DEBUG ] No samples found: disambiguate [2023-11-15 11:54:45,582] multiqc [DEBUG ] No samples found: supernova [2023-11-15 11:54:45,635] multiqc [DEBUG ] No samples found: deeptools [2023-11-15 11:54:45,656] multiqc [DEBUG ] No samples found: sargasso [2023-11-15 11:54:45,661] multiqc [DEBUG ] No samples found: verifybamid [2023-11-15 11:54:45,672] multiqc [DEBUG ] No samples found: mirtrace [2023-11-15 11:54:45,689] multiqc [DEBUG ] No samples found: happy [2023-11-15 11:54:45,711] multiqc [DEBUG ] No samples found: mirtop [2023-11-15 11:54:45,758] multiqc [DEBUG ] No samples found: homer [2023-11-15 11:54:45,786] multiqc [DEBUG ] No samples found: macs2 [2023-11-15 11:54:45,807] multiqc [DEBUG ] No samples found: theta2 [2023-11-15 11:54:45,833] multiqc [DEBUG ] No samples found: snpeff [2023-11-15 11:54:45,871] multiqc [DEBUG ] No samples found: gatk [2023-11-15 11:54:45,893] multiqc [DEBUG ] No samples found: htseq [2023-11-15 11:54:45,925] multiqc [DEBUG ] No samples found: bcftools [2023-11-15 11:54:45,959] multiqc [DEBUG ] No samples found: featureCounts [2023-11-15 11:54:45,988] multiqc [DEBUG ] No samples found: fgbio [2023-11-15 11:54:46,087] multiqc [DEBUG ] No samples found: dragen [2023-11-15 11:54:46,100] multiqc [DEBUG ] No samples found: dedup [2023-11-15 11:54:46,108] multiqc [DEBUG ] No samples found: damageprofiler [2023-11-15 11:54:46,271] multiqc [DEBUG ] No samples found: biobambam2 [2023-11-15 11:54:46,288] multiqc [DEBUG ] No samples found: mtnucratio [2023-11-15 11:54:46,290] multiqc [DEBUG ] No samples found: picard [2023-11-15 11:54:46,305] multiqc [DEBUG ] No samples found: prokka [2023-11-15 11:54:46,311] multiqc [DEBUG ] No samples found: samblaster [2023-11-15 11:54:46,362] multiqc [DEBUG ] No samples found: samtools [2023-11-15 11:54:46,383] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-11-15 11:54:46,413] multiqc [DEBUG ] No samples found: bamtools [2023-11-15 11:54:46,438] multiqc [DEBUG ] No samples found: jellyfish [2023-11-15 11:54:46,499] multiqc [DEBUG ] No samples found: vcftools [2023-11-15 11:54:46,505] multiqc [DEBUG ] No samples found: longranger [2023-11-15 11:54:46,510] multiqc [DEBUG ] No samples found: stacks [2023-11-15 11:54:46,514] multiqc [DEBUG ] No samples found: varscan2 [2023-11-15 11:54:46,529] multiqc [DEBUG ] No samples found: bbmap [2023-11-15 11:54:46,535] multiqc [DEBUG ] No samples found: bismark [2023-11-15 11:54:46,551] multiqc [DEBUG ] No samples found: biscuit [2023-11-15 11:54:46,572] multiqc [DEBUG ] No samples found: hicexplorer [2023-11-15 11:54:46,584] multiqc [DEBUG ] No samples found: hicup [2023-11-15 11:54:46,614] multiqc [DEBUG ] No samples found: hicpro [2023-11-15 11:54:46,619] multiqc [DEBUG ] No samples found: salmon [2023-11-15 11:54:46,627] multiqc [DEBUG ] No samples found: kallisto [2023-11-15 11:54:46,637] multiqc [DEBUG ] No samples found: slamdunk [2023-11-15 11:54:46,649] multiqc [DEBUG ] No samples found: star [2023-11-15 11:54:46,654] multiqc [DEBUG ] No samples found: hisat2 [2023-11-15 11:54:46,665] multiqc [DEBUG ] No samples found: tophat [2023-11-15 11:54:46,687] multiqc [DEBUG ] No samples found: bowtie2 [2023-11-15 11:54:46,709] multiqc [DEBUG ] No samples found: bowtie1 [2023-11-15 11:54:46,725] multiqc [DEBUG ] No samples found: snpsplit [2023-11-15 11:54:46,746] multiqc [DEBUG ] No samples found: kat [2023-11-15 11:54:46,751] multiqc [DEBUG ] No samples found: leehom [2023-11-15 11:54:46,776] multiqc [DEBUG ] No samples found: adapterRemoval [2023-11-15 11:54:46,798] multiqc [DEBUG ] No samples found: clipandmerge [2023-11-15 11:54:46,810] multiqc [DEBUG ] No samples found: cutadapt [2023-11-15 11:54:46,831] multiqc [DEBUG ] No samples found: flexbar [2023-11-15 11:54:46,837] multiqc [DEBUG ] No samples found: kaiju [2023-11-15 11:54:46,842] multiqc [DEBUG ] No samples found: kraken [2023-11-15 11:54:46,858] multiqc [DEBUG ] No samples found: malt [2023-11-15 11:54:46,874] multiqc [DEBUG ] No samples found: trimmomatic [2023-11-15 11:54:46,890] multiqc [DEBUG ] No samples found: sickle [2023-11-15 11:54:46,902] multiqc [DEBUG ] No samples found: skewer [2023-11-15 11:54:46,919] multiqc [DEBUG ] No samples found: sortmerna [2023-11-15 11:54:46,942] multiqc [DEBUG ] No samples found: biobloomtools [2023-11-15 11:54:46,975] multiqc [DEBUG ] No samples found: fastq_screen [2023-11-15 11:54:46,990] multiqc [DEBUG ] No samples found: afterqc [2023-11-15 11:54:47,011] multiqc [DEBUG ] No samples found: fastp [2023-11-15 11:54:47,101] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2023-11-15 11:54:47,219] multiqc [DEBUG ] No samples found: pycoqc [2023-11-15 11:54:47,253] multiqc [DEBUG ] No samples found: minionqc [2023-11-15 11:54:47,270] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-11-15 11:54:47,292] multiqc [DEBUG ] No samples found: clusterflow [2023-11-15 11:54:47,314] multiqc [DEBUG ] No samples found: bcl2fastq [2023-11-15 11:54:47,336] multiqc [DEBUG ] No samples found: interop [2023-11-15 11:54:47,347] multiqc [DEBUG ] No samples found: ivar [2023-11-15 11:54:47,369] multiqc [DEBUG ] No samples found: flash [2023-11-15 11:54:47,390] multiqc [DEBUG ] No samples found: seqyclean [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-11-15 11:54:47,390] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-11-15 11:54:47,391] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-11-15 11:54:47,406] multiqc [INFO ] Compressing plot data [2023-11-15 11:54:47,617] multiqc [INFO ] Report : multiqc_report.html [2023-11-15 11:54:47,617] multiqc [INFO ] Data : multiqc_data [2023-11-15 11:54:47,617] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40165831/tmpdl4qvsum/multiqc_data' to '/scratch/gencore/logs/html/000000000-LBVRL/1/multiqc_data' [2023-11-15 11:54:47,828] multiqc [INFO ] MultiQC complete