[2023-02-07 08:29:28,081] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-02-07 08:29:28,081] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-02-07 08:29:28,082] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-02-07 08:29:28,084] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-02-07 08:29:28,084] 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}} [2023-02-07 08:29:28,085] 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-GF7FM/1 [2023-02-07 08:29:28,852] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-02-07 08:29:28,852] multiqc [INFO ] This is MultiQC v1.9 [2023-02-07 08:29:28,857] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-GF7FM/1 [2023-02-07 08:29:28,857] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-GF7FM/1 [2023-02-07 08:29:28,857] multiqc [INFO ] Template : default [2023-02-07 08:29:28,857] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-02-07 08:29:28,857] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-GF7FM/1 [2023-02-07 08:29:28,858] 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 [2023-02-07 08:29:28,858] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-29929229/tmpvlngwj1o [2023-02-07 08:29:28,977] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n01_undetermined_fastqc.html [2023-02-07 08:29:28,980] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n01_undetermined_fastqc.html [2023-02-07 08:29:29,011] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n02_BS_doli_002_fastqc.html [2023-02-07 08:29:29,012] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n02_BS_doli_002_fastqc.html [2023-02-07 08:29:29,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n01_BS_doli_002_fastqc.html [2023-02-07 08:29:29,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n01_BS_doli_002_fastqc.html [2023-02-07 08:29:29,092] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n02_undetermined_fastqc.html [2023-02-07 08:29:29,093] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GF7FM_l01_n02_undetermined_fastqc.html [2023-02-07 08:29:29,830] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-07 08:29:29,832] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-07 08:29:29,838] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-02-07 08:29:29,840] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 2 samples (table) [2023-02-07 08:29:29,842] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-02-07 08:29:29,847] multiqc [DEBUG ] No samples found: conpair [2023-02-07 08:29:29,853] multiqc [DEBUG ] No samples found: peddy [2023-02-07 08:29:29,858] multiqc [DEBUG ] No samples found: somalier [2023-02-07 08:29:29,864] multiqc [DEBUG ] No samples found: methylQA [2023-02-07 08:29:29,874] multiqc [DEBUG ] No samples found: mosdepth [2023-02-07 08:29:29,879] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-02-07 08:29:29,883] multiqc [DEBUG ] No samples found: qualimap [2023-02-07 08:29:29,890] multiqc [DEBUG ] No samples found: preseq [2023-02-07 08:29:29,896] multiqc [DEBUG ] No samples found: quast [2023-02-07 08:29:29,902] multiqc [DEBUG ] No samples found: qorts [2023-02-07 08:29:29,908] multiqc [DEBUG ] No samples found: rna_seqc [2023-02-07 08:29:29,913] multiqc [DEBUG ] No samples found: rockhopper [2023-02-07 08:29:29,919] multiqc [DEBUG ] No samples found: rsem [2023-02-07 08:29:29,931] multiqc [DEBUG ] No samples found: rseqc [2023-02-07 08:29:29,936] multiqc [DEBUG ] No samples found: busco [2023-02-07 08:29:29,941] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-02-07 08:29:29,945] multiqc [DEBUG ] No samples found: disambiguate [2023-02-07 08:29:29,951] multiqc [DEBUG ] No samples found: supernova [2023-02-07 08:29:29,965] multiqc [DEBUG ] No samples found: deeptools [2023-02-07 08:29:29,970] multiqc [DEBUG ] No samples found: sargasso [2023-02-07 08:29:29,975] multiqc [DEBUG ] No samples found: verifybamid [2023-02-07 08:29:29,980] multiqc [DEBUG ] No samples found: mirtrace [2023-02-07 08:29:29,986] multiqc [DEBUG ] No samples found: happy [2023-02-07 08:29:29,991] multiqc [DEBUG ] No samples found: mirtop [2023-02-07 08:29:29,998] multiqc [DEBUG ] No samples found: homer [2023-02-07 08:29:30,003] multiqc [DEBUG ] No samples found: macs2 [2023-02-07 08:29:30,007] multiqc [DEBUG ] No samples found: theta2 [2023-02-07 08:29:30,013] multiqc [DEBUG ] No samples found: snpeff [2023-02-07 08:29:30,021] multiqc [DEBUG ] No samples found: gatk [2023-02-07 08:29:30,027] multiqc [DEBUG ] No samples found: htseq [2023-02-07 08:29:30,034] multiqc [DEBUG ] No samples found: bcftools [2023-02-07 08:29:30,040] multiqc [DEBUG ] No samples found: featureCounts [2023-02-07 08:29:30,047] multiqc [DEBUG ] No samples found: fgbio [2023-02-07 08:29:30,063] multiqc [DEBUG ] No samples found: dragen [2023-02-07 08:29:30,069] multiqc [DEBUG ] No samples found: dedup [2023-02-07 08:29:30,074] multiqc [DEBUG ] No samples found: damageprofiler [2023-02-07 08:29:30,101] multiqc [DEBUG ] No samples found: biobambam2 [2023-02-07 08:29:30,108] multiqc [DEBUG ] No samples found: mtnucratio [2023-02-07 08:29:30,110] multiqc [DEBUG ] No samples found: picard [2023-02-07 08:29:30,115] multiqc [DEBUG ] No samples found: prokka [2023-02-07 08:29:30,120] multiqc [DEBUG ] No samples found: samblaster [2023-02-07 08:29:30,129] multiqc [DEBUG ] No samples found: samtools [2023-02-07 08:29:30,134] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-02-07 08:29:30,139] multiqc [DEBUG ] No samples found: bamtools [2023-02-07 08:29:30,144] multiqc [DEBUG ] No samples found: jellyfish [2023-02-07 08:29:30,151] multiqc [DEBUG ] No samples found: vcftools [2023-02-07 08:29:30,157] multiqc [DEBUG ] No samples found: longranger [2023-02-07 08:29:30,162] multiqc [DEBUG ] No samples found: stacks [2023-02-07 08:29:30,167] multiqc [DEBUG ] No samples found: varscan2 [2023-02-07 08:29:30,183] multiqc [DEBUG ] No samples found: bbmap [2023-02-07 08:29:30,188] multiqc [DEBUG ] No samples found: bismark [2023-02-07 08:29:30,194] multiqc [DEBUG ] No samples found: biscuit [2023-02-07 08:29:30,200] multiqc [DEBUG ] No samples found: hicexplorer [2023-02-07 08:29:30,205] multiqc [DEBUG ] No samples found: hicup [2023-02-07 08:29:30,210] multiqc [DEBUG ] No samples found: hicpro [2023-02-07 08:29:30,215] multiqc [DEBUG ] No samples found: salmon [2023-02-07 08:29:30,220] multiqc [DEBUG ] No samples found: kallisto [2023-02-07 08:29:30,225] multiqc [DEBUG ] No samples found: slamdunk [2023-02-07 08:29:30,230] multiqc [DEBUG ] No samples found: star [2023-02-07 08:29:30,235] multiqc [DEBUG ] No samples found: hisat2 [2023-02-07 08:29:30,240] multiqc [DEBUG ] No samples found: tophat [2023-02-07 08:29:30,246] multiqc [DEBUG ] No samples found: bowtie2 [2023-02-07 08:29:30,252] multiqc [DEBUG ] No samples found: bowtie1 [2023-02-07 08:29:30,257] multiqc [DEBUG ] No samples found: snpsplit [2023-02-07 08:29:30,262] multiqc [DEBUG ] No samples found: kat [2023-02-07 08:29:30,266] multiqc [DEBUG ] No samples found: leehom [2023-02-07 08:29:30,272] multiqc [DEBUG ] No samples found: adapterRemoval [2023-02-07 08:29:30,277] multiqc [DEBUG ] No samples found: clipandmerge [2023-02-07 08:29:30,282] multiqc [DEBUG ] No samples found: cutadapt [2023-02-07 08:29:30,287] multiqc [DEBUG ] No samples found: flexbar [2023-02-07 08:29:30,292] multiqc [DEBUG ] No samples found: kaiju [2023-02-07 08:29:30,298] multiqc [DEBUG ] No samples found: kraken [2023-02-07 08:29:30,303] multiqc [DEBUG ] No samples found: malt [2023-02-07 08:29:30,308] multiqc [DEBUG ] No samples found: trimmomatic [2023-02-07 08:29:30,314] multiqc [DEBUG ] No samples found: sickle [2023-02-07 08:29:30,319] multiqc [DEBUG ] No samples found: skewer [2023-02-07 08:29:30,325] multiqc [DEBUG ] No samples found: sortmerna [2023-02-07 08:29:30,329] multiqc [DEBUG ] No samples found: biobloomtools [2023-02-07 08:29:30,335] multiqc [DEBUG ] No samples found: fastq_screen [2023-02-07 08:29:30,340] multiqc [DEBUG ] No samples found: afterqc [2023-02-07 08:29:30,345] multiqc [DEBUG ] No samples found: fastp [2023-02-07 08:29:30,360] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-02-07 08:29:30,360] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-GF7FM_l01_n01_undetermined' [2023-02-07 08:29:30,360] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-GF7FM_l01_n02_undetermined' [2023-02-07 08:29:30,407] multiqc [DEBUG ] No samples found: pycoqc [2023-02-07 08:29:30,413] multiqc [DEBUG ] No samples found: minionqc [2023-02-07 08:29:30,418] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-02-07 08:29:30,424] multiqc [DEBUG ] No samples found: clusterflow [2023-02-07 08:29:30,429] multiqc [DEBUG ] No samples found: bcl2fastq [2023-02-07 08:29:30,436] multiqc [DEBUG ] No samples found: interop [2023-02-07 08:29:30,446] multiqc [DEBUG ] No samples found: ivar [2023-02-07 08:29:30,453] multiqc [DEBUG ] No samples found: flash [2023-02-07 08:29:30,459] multiqc [DEBUG ] No samples found: seqyclean [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-02-07 08:29:30,459] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-02-07 08:29:30,460] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-02-07 08:29:30,465] multiqc [INFO ] Compressing plot data [2023-02-07 08:29:30,521] multiqc [INFO ] Report : multiqc_report.html [2023-02-07 08:29:30,521] multiqc [INFO ] Data : multiqc_data [2023-02-07 08:29:30,521] multiqc [DEBUG ] Moving data file from '/state/partition1/job-29929229/tmpvlngwj1o/multiqc_data' to '/scratch/gencore/logs/html/000000000-GF7FM/1/multiqc_data' [2023-02-07 08:29:30,677] multiqc [INFO ] MultiQC complete