[2023-04-28 12:22:10,382] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-04-28 12:22:10,382] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-04-28 12:22:10,382] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-04-28 12:22:10,385] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-04-28 12:22:10,385] 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}} [2023-04-28 12:22:10,385] 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-KY33L/1 [2023-04-28 12:22:10,553] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-04-28 12:22:10,553] multiqc [INFO ] This is MultiQC v1.9 [2023-04-28 12:22:10,553] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KY33L/1 [2023-04-28 12:22:10,553] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KY33L/1 [2023-04-28 12:22:10,553] multiqc [INFO ] Template : default [2023-04-28 12:22:10,553] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-04-28 12:22:10,553] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KY33L/1 [2023-04-28 12:22:10,554] 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 [2023-04-28 12:22:10,554] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-32873423/tmp5cugmxwp [2023-04-28 12:22:10,829] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KY33L_l01.2_fastqc.html [2023-04-28 12:22:10,831] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KY33L_l01.2_fastqc.html [2023-04-28 12:22:10,851] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KY33L_l01.3_fastqc.html [2023-04-28 12:22:10,853] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KY33L_l01.3_fastqc.html [2023-04-28 12:22:10,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KY33L_l01.1_fastqc.html [2023-04-28 12:22:10,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KY33L_l01.1_fastqc.html [2023-04-28 12:22:11,604] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-28 12:22:11,618] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-28 12:22:11,622] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-04-28 12:22:11,624] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-04-28 12:22:11,628] multiqc [DEBUG ] No samples found: conpair [2023-04-28 12:22:11,634] multiqc [DEBUG ] No samples found: peddy [2023-04-28 12:22:11,639] multiqc [DEBUG ] No samples found: somalier [2023-04-28 12:22:11,643] multiqc [DEBUG ] No samples found: methylQA [2023-04-28 12:22:11,652] multiqc [DEBUG ] No samples found: mosdepth [2023-04-28 12:22:11,656] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-04-28 12:22:11,660] multiqc [DEBUG ] No samples found: qualimap [2023-04-28 12:22:11,665] multiqc [DEBUG ] No samples found: preseq [2023-04-28 12:22:11,670] multiqc [DEBUG ] No samples found: quast [2023-04-28 12:22:11,675] multiqc [DEBUG ] No samples found: qorts [2023-04-28 12:22:11,680] multiqc [DEBUG ] No samples found: rna_seqc [2023-04-28 12:22:11,685] multiqc [DEBUG ] No samples found: rockhopper [2023-04-28 12:22:11,689] multiqc [DEBUG ] No samples found: rsem [2023-04-28 12:22:11,700] multiqc [DEBUG ] No samples found: rseqc [2023-04-28 12:22:11,704] multiqc [DEBUG ] No samples found: busco [2023-04-28 12:22:11,709] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-04-28 12:22:11,714] multiqc [DEBUG ] No samples found: disambiguate [2023-04-28 12:22:11,719] multiqc [DEBUG ] No samples found: supernova [2023-04-28 12:22:11,732] multiqc [DEBUG ] No samples found: deeptools [2023-04-28 12:22:11,737] multiqc [DEBUG ] No samples found: sargasso [2023-04-28 12:22:11,742] multiqc [DEBUG ] No samples found: verifybamid [2023-04-28 12:22:11,747] multiqc [DEBUG ] No samples found: mirtrace [2023-04-28 12:22:11,752] multiqc [DEBUG ] No samples found: happy [2023-04-28 12:22:11,757] multiqc [DEBUG ] No samples found: mirtop [2023-04-28 12:22:11,763] multiqc [DEBUG ] No samples found: homer [2023-04-28 12:22:11,768] multiqc [DEBUG ] No samples found: macs2 [2023-04-28 12:22:11,773] multiqc [DEBUG ] No samples found: theta2 [2023-04-28 12:22:11,778] multiqc [DEBUG ] No samples found: snpeff [2023-04-28 12:22:11,784] multiqc [DEBUG ] No samples found: gatk [2023-04-28 12:22:11,789] multiqc [DEBUG ] No samples found: htseq [2023-04-28 12:22:11,795] multiqc [DEBUG ] No samples found: bcftools [2023-04-28 12:22:11,843] multiqc [DEBUG ] No samples found: featureCounts [2023-04-28 12:22:11,849] multiqc [DEBUG ] No samples found: fgbio [2023-04-28 12:22:11,862] multiqc [DEBUG ] No samples found: dragen [2023-04-28 12:22:11,866] multiqc [DEBUG ] No samples found: dedup [2023-04-28 12:22:11,871] multiqc [DEBUG ] No samples found: damageprofiler [2023-04-28 12:22:12,197] multiqc [DEBUG ] No samples found: biobambam2 [2023-04-28 12:22:12,202] multiqc [DEBUG ] No samples found: mtnucratio [2023-04-28 12:22:12,205] multiqc [DEBUG ] No samples found: picard [2023-04-28 12:22:12,209] multiqc [DEBUG ] No samples found: prokka [2023-04-28 12:22:12,214] multiqc [DEBUG ] No samples found: samblaster [2023-04-28 12:22:12,331] multiqc [DEBUG ] No samples found: samtools [2023-04-28 12:22:12,336] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-04-28 12:22:12,341] multiqc [DEBUG ] No samples found: bamtools [2023-04-28 12:22:12,346] multiqc [DEBUG ] No samples found: jellyfish [2023-04-28 12:22:12,354] multiqc [DEBUG ] No samples found: vcftools [2023-04-28 12:22:12,359] multiqc [DEBUG ] No samples found: longranger [2023-04-28 12:22:12,365] multiqc [DEBUG ] No samples found: stacks [2023-04-28 12:22:12,370] multiqc [DEBUG ] No samples found: varscan2 [2023-04-28 12:22:12,382] multiqc [DEBUG ] No samples found: bbmap [2023-04-28 12:22:12,387] multiqc [DEBUG ] No samples found: bismark [2023-04-28 12:22:12,392] multiqc [DEBUG ] No samples found: biscuit [2023-04-28 12:22:12,397] multiqc [DEBUG ] No samples found: hicexplorer [2023-04-28 12:22:12,401] multiqc [DEBUG ] No samples found: hicup [2023-04-28 12:22:12,406] multiqc [DEBUG ] No samples found: hicpro [2023-04-28 12:22:12,411] multiqc [DEBUG ] No samples found: salmon [2023-04-28 12:22:12,415] multiqc [DEBUG ] No samples found: kallisto [2023-04-28 12:22:12,420] multiqc [DEBUG ] No samples found: slamdunk [2023-04-28 12:22:12,458] multiqc [DEBUG ] No samples found: star [2023-04-28 12:22:12,462] multiqc [DEBUG ] No samples found: hisat2 [2023-04-28 12:22:12,467] multiqc [DEBUG ] No samples found: tophat [2023-04-28 12:22:12,471] multiqc [DEBUG ] No samples found: bowtie2 [2023-04-28 12:22:12,476] multiqc [DEBUG ] No samples found: bowtie1 [2023-04-28 12:22:12,481] multiqc [DEBUG ] No samples found: snpsplit [2023-04-28 12:22:12,485] multiqc [DEBUG ] No samples found: kat [2023-04-28 12:22:12,489] multiqc [DEBUG ] No samples found: leehom [2023-04-28 12:22:12,494] multiqc [DEBUG ] No samples found: adapterRemoval [2023-04-28 12:22:12,499] multiqc [DEBUG ] No samples found: clipandmerge [2023-04-28 12:22:12,503] multiqc [DEBUG ] No samples found: cutadapt [2023-04-28 12:22:12,507] multiqc [DEBUG ] No samples found: flexbar [2023-04-28 12:22:12,512] multiqc [DEBUG ] No samples found: kaiju [2023-04-28 12:22:12,517] multiqc [DEBUG ] No samples found: kraken [2023-04-28 12:22:12,522] multiqc [DEBUG ] No samples found: malt [2023-04-28 12:22:12,526] multiqc [DEBUG ] No samples found: trimmomatic [2023-04-28 12:22:12,531] multiqc [DEBUG ] No samples found: sickle [2023-04-28 12:22:12,535] multiqc [DEBUG ] No samples found: skewer [2023-04-28 12:22:12,540] multiqc [DEBUG ] No samples found: sortmerna [2023-04-28 12:22:12,544] multiqc [DEBUG ] No samples found: biobloomtools [2023-04-28 12:22:12,549] multiqc [DEBUG ] No samples found: fastq_screen [2023-04-28 12:22:12,554] multiqc [DEBUG ] No samples found: afterqc [2023-04-28 12:22:12,559] multiqc [DEBUG ] No samples found: fastp [2023-04-28 12:22:12,566] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2023-04-28 12:22:12,567] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KY33L_l01.1' [2023-04-28 12:22:12,567] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KY33L_l01.3' [2023-04-28 12:22:12,567] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KY33L_l01.2' [2023-04-28 12:22:12,573] multiqc.modules.fastqc.fastqc [DEBUG ] sequence_quality not found in FastQC reports [2023-04-28 12:22:12,573] multiqc.modules.fastqc.fastqc [DEBUG ] per_seq_quality not found in FastQC reports [2023-04-28 12:22:12,587] multiqc.modules.fastqc.fastqc [DEBUG ] adapter_content not found in FastQC reports [2023-04-28 12:22:12,596] multiqc [DEBUG ] No samples found: pycoqc [2023-04-28 12:22:12,601] multiqc [DEBUG ] No samples found: minionqc [2023-04-28 12:22:12,605] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-04-28 12:22:12,610] multiqc [DEBUG ] No samples found: clusterflow [2023-04-28 12:22:12,615] multiqc [DEBUG ] No samples found: bcl2fastq [2023-04-28 12:22:12,620] multiqc [DEBUG ] No samples found: interop [2023-04-28 12:22:12,624] multiqc [DEBUG ] No samples found: ivar [2023-04-28 12:22:12,628] multiqc [DEBUG ] No samples found: flash [2023-04-28 12:22:12,633] multiqc [DEBUG ] No samples found: seqyclean [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-04-28 12:22:12,633] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-04-28 12:22:12,638] multiqc [INFO ] Compressing plot data [2023-04-28 12:22:12,657] multiqc [INFO ] Report : multiqc_report.html [2023-04-28 12:22:12,658] multiqc [INFO ] Data : multiqc_data [2023-04-28 12:22:12,658] multiqc [DEBUG ] Moving data file from '/state/partition1/job-32873423/tmp5cugmxwp/multiqc_data' to '/scratch/gencore/logs/html/000000000-KY33L/1/multiqc_data' [2023-04-28 12:22:13,177] multiqc [INFO ] MultiQC complete