[2023-02-04 02:38:44,028] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-02-04 02:38:44,028] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-02-04 02:38:44,028] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-02-04 02:38:44,031] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-02-04 02:38:44,031] 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}} [2023-02-04 02:38:44,031] 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-KMC2R/1 [2023-02-04 02:38:44,655] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-02-04 02:38:44,656] multiqc [INFO ] This is MultiQC v1.9 [2023-02-04 02:38:44,656] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KMC2R/1 [2023-02-04 02:38:44,656] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KMC2R/1 [2023-02-04 02:38:44,656] multiqc [INFO ] Template : default [2023-02-04 02:38:44,656] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-02-04 02:38:44,656] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KMC2R/1 [2023-02-04 02:38:44,656] 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 [2023-02-04 02:38:44,656] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-29826182/tmpqosz14ea [2023-02-04 02:38:44,786] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.3_fastqc.html [2023-02-04 02:38:44,788] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.3_fastqc.html [2023-02-04 02:38:44,841] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.1_fastqc.html [2023-02-04 02:38:44,843] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.1_fastqc.html [2023-02-04 02:38:44,885] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.4_fastqc.html [2023-02-04 02:38:44,887] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.4_fastqc.html [2023-02-04 02:38:44,929] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.2_fastqc.html [2023-02-04 02:38:44,930] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KMC2R_l01.2_fastqc.html [2023-02-04 02:38:45,478] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-04 02:38:45,480] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-04 02:38:45,485] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-02-04 02:38:45,486] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-02-04 02:38:45,493] multiqc [DEBUG ] No samples found: conpair [2023-02-04 02:38:45,498] multiqc [DEBUG ] No samples found: peddy [2023-02-04 02:38:45,504] multiqc [DEBUG ] No samples found: somalier [2023-02-04 02:38:45,509] multiqc [DEBUG ] No samples found: methylQA [2023-02-04 02:38:45,521] multiqc [DEBUG ] No samples found: mosdepth [2023-02-04 02:38:45,527] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-02-04 02:38:45,531] multiqc [DEBUG ] No samples found: qualimap [2023-02-04 02:38:45,539] multiqc [DEBUG ] No samples found: preseq [2023-02-04 02:38:45,546] multiqc [DEBUG ] No samples found: quast [2023-02-04 02:38:45,555] multiqc [DEBUG ] No samples found: qorts [2023-02-04 02:38:45,570] multiqc [DEBUG ] No samples found: rna_seqc [2023-02-04 02:38:45,577] multiqc [DEBUG ] No samples found: rockhopper [2023-02-04 02:38:45,582] multiqc [DEBUG ] No samples found: rsem [2023-02-04 02:38:45,602] multiqc [DEBUG ] No samples found: rseqc [2023-02-04 02:38:45,607] multiqc [DEBUG ] No samples found: busco [2023-02-04 02:38:45,615] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-02-04 02:38:45,623] multiqc [DEBUG ] No samples found: disambiguate [2023-02-04 02:38:45,630] multiqc [DEBUG ] No samples found: supernova [2023-02-04 02:38:45,662] multiqc [DEBUG ] No samples found: deeptools [2023-02-04 02:38:45,668] multiqc [DEBUG ] No samples found: sargasso [2023-02-04 02:38:45,675] multiqc [DEBUG ] No samples found: verifybamid [2023-02-04 02:38:45,683] multiqc [DEBUG ] No samples found: mirtrace [2023-02-04 02:38:45,690] multiqc [DEBUG ] No samples found: happy [2023-02-04 02:38:45,699] multiqc [DEBUG ] No samples found: mirtop [2023-02-04 02:38:45,710] multiqc [DEBUG ] No samples found: homer [2023-02-04 02:38:45,716] multiqc [DEBUG ] No samples found: macs2 [2023-02-04 02:38:45,722] multiqc [DEBUG ] No samples found: theta2 [2023-02-04 02:38:45,728] multiqc [DEBUG ] No samples found: snpeff [2023-02-04 02:38:45,741] multiqc [DEBUG ] No samples found: gatk [2023-02-04 02:38:45,751] multiqc [DEBUG ] No samples found: htseq [2023-02-04 02:38:45,766] multiqc [DEBUG ] No samples found: bcftools [2023-02-04 02:38:45,773] multiqc [DEBUG ] No samples found: featureCounts [2023-02-04 02:38:45,788] multiqc [DEBUG ] No samples found: fgbio [2023-02-04 02:38:45,818] multiqc [DEBUG ] No samples found: dragen [2023-02-04 02:38:45,823] multiqc [DEBUG ] No samples found: dedup [2023-02-04 02:38:45,830] multiqc [DEBUG ] No samples found: damageprofiler [2023-02-04 02:38:45,869] multiqc [DEBUG ] No samples found: biobambam2 [2023-02-04 02:38:45,875] multiqc [DEBUG ] No samples found: mtnucratio [2023-02-04 02:38:45,878] multiqc [DEBUG ] No samples found: picard [2023-02-04 02:38:45,884] multiqc [DEBUG ] No samples found: prokka [2023-02-04 02:38:45,890] multiqc [DEBUG ] No samples found: samblaster [2023-02-04 02:38:45,905] multiqc [DEBUG ] No samples found: samtools [2023-02-04 02:38:45,915] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-02-04 02:38:45,921] multiqc [DEBUG ] No samples found: bamtools [2023-02-04 02:38:45,927] multiqc [DEBUG ] No samples found: jellyfish [2023-02-04 02:38:45,940] multiqc [DEBUG ] No samples found: vcftools [2023-02-04 02:38:45,947] multiqc [DEBUG ] No samples found: longranger [2023-02-04 02:38:45,953] multiqc [DEBUG ] No samples found: stacks [2023-02-04 02:38:45,959] multiqc [DEBUG ] No samples found: varscan2 [2023-02-04 02:38:45,984] multiqc [DEBUG ] No samples found: bbmap [2023-02-04 02:38:45,989] multiqc [DEBUG ] No samples found: bismark [2023-02-04 02:38:46,001] multiqc [DEBUG ] No samples found: biscuit [2023-02-04 02:38:46,007] multiqc [DEBUG ] No samples found: hicexplorer [2023-02-04 02:38:46,013] multiqc [DEBUG ] No samples found: hicup [2023-02-04 02:38:46,020] multiqc [DEBUG ] No samples found: hicpro [2023-02-04 02:38:46,025] multiqc [DEBUG ] No samples found: salmon [2023-02-04 02:38:46,030] multiqc [DEBUG ] No samples found: kallisto [2023-02-04 02:38:46,037] multiqc [DEBUG ] No samples found: slamdunk [2023-02-04 02:38:46,044] multiqc [DEBUG ] No samples found: star [2023-02-04 02:38:46,049] multiqc [DEBUG ] No samples found: hisat2 [2023-02-04 02:38:46,058] multiqc [DEBUG ] No samples found: tophat [2023-02-04 02:38:46,063] multiqc [DEBUG ] No samples found: bowtie2 [2023-02-04 02:38:46,073] multiqc [DEBUG ] No samples found: bowtie1 [2023-02-04 02:38:46,079] multiqc [DEBUG ] No samples found: snpsplit [2023-02-04 02:38:46,087] multiqc [DEBUG ] No samples found: kat [2023-02-04 02:38:46,094] multiqc [DEBUG ] No samples found: leehom [2023-02-04 02:38:46,099] multiqc [DEBUG ] No samples found: adapterRemoval [2023-02-04 02:38:46,104] multiqc [DEBUG ] No samples found: clipandmerge [2023-02-04 02:38:46,109] multiqc [DEBUG ] No samples found: cutadapt [2023-02-04 02:38:46,114] multiqc [DEBUG ] No samples found: flexbar [2023-02-04 02:38:46,121] multiqc [DEBUG ] No samples found: kaiju [2023-02-04 02:38:46,128] multiqc [DEBUG ] No samples found: kraken [2023-02-04 02:38:46,138] multiqc [DEBUG ] No samples found: malt [2023-02-04 02:38:46,144] multiqc [DEBUG ] No samples found: trimmomatic [2023-02-04 02:38:46,149] multiqc [DEBUG ] No samples found: sickle [2023-02-04 02:38:46,155] multiqc [DEBUG ] No samples found: skewer [2023-02-04 02:38:46,160] multiqc [DEBUG ] No samples found: sortmerna [2023-02-04 02:38:46,165] multiqc [DEBUG ] No samples found: biobloomtools [2023-02-04 02:38:46,171] multiqc [DEBUG ] No samples found: fastq_screen [2023-02-04 02:38:46,177] multiqc [DEBUG ] No samples found: afterqc [2023-02-04 02:38:46,186] multiqc [DEBUG ] No samples found: fastp [2023-02-04 02:38:46,215] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-02-04 02:38:46,264] multiqc [DEBUG ] No samples found: pycoqc [2023-02-04 02:38:46,272] multiqc [DEBUG ] No samples found: minionqc [2023-02-04 02:38:46,277] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-02-04 02:38:46,282] multiqc [DEBUG ] No samples found: clusterflow [2023-02-04 02:38:46,290] multiqc [DEBUG ] No samples found: bcl2fastq [2023-02-04 02:38:46,297] multiqc [DEBUG ] No samples found: interop [2023-02-04 02:38:46,302] multiqc [DEBUG ] No samples found: ivar [2023-02-04 02:38:46,307] multiqc [DEBUG ] No samples found: flash [2023-02-04 02:38:46,315] multiqc [DEBUG ] No samples found: seqyclean [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-02-04 02:38:46,315] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-02-04 02:38:46,321] multiqc [INFO ] Compressing plot data [2023-02-04 02:38:46,391] multiqc [INFO ] Report : multiqc_report.html [2023-02-04 02:38:46,391] multiqc [INFO ] Data : multiqc_data [2023-02-04 02:38:46,392] multiqc [DEBUG ] Moving data file from '/state/partition1/job-29826182/tmpqosz14ea/multiqc_data' to '/scratch/gencore/logs/html/000000000-KMC2R/1/multiqc_data' [2023-02-04 02:38:46,547] multiqc [INFO ] MultiQC complete