[2023-02-24 01:09:20,042] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-02-24 01:09:20,043] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-02-24 01:09:20,043] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-02-24 01:09:20,045] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-02-24 01:09:20,045] 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}} [2023-02-24 01:09:20,045] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5JMGDSX5/merged [2023-02-24 01:09:20,846] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-02-24 01:09:20,846] multiqc [INFO ] This is MultiQC v1.9 [2023-02-24 01:09:20,846] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5JMGDSX5/merged [2023-02-24 01:09:20,846] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5JMGDSX5/merged [2023-02-24 01:09:20,846] multiqc [INFO ] Template : default [2023-02-24 01:09:20,846] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-02-24 01:09:20,846] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5JMGDSX5/merged [2023-02-24 01:09:20,846] 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 [2023-02-24 01:09:20,846] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-30450725/tmp31a_xm3_ [2023-02-24 01:09:20,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5JMGDSX5_n01_f3HRB0245_fastqc.html [2023-02-24 01:09:20,978] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H5JMGDSX5_n02_f3HRB0245_fastqc.html [2023-02-24 01:09:24,020] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5JMGDSX5_n01_f3HRB0212_fastqc.html [2023-02-24 01:09:24,021] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5JMGDSX5_n01_f3HRB0212_fastqc.html [2023-02-24 01:09:24,088] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5JMGDSX5_n02_f3HRB0323_fastqc.html [2023-02-24 01:09:24,090] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5JMGDSX5_n02_f3HRB0323_fastqc.html [2023-02-24 01:09:24,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5JMGDSX5_n02_f3HRB0322_fastqc.html [2023-02-24 01:09:24,153] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5JMGDSX5_n02_f3HRB0322_fastqc.html [2023-02-24 01:09:24,214] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5JMGDSX5_n02_f3HRB0083_fastqc.html [2023-02-24 01:09:24,216] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5JMGDSX5_n02_f3HRB0083_fastqc.html [2023-02-24 01:09:24,275] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5JMGDSX5_n01_f3HRB0244_fastqc.html [2023-02-24 01:09:24,277] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5JMGDSX5_n01_f3HRB0244_fastqc.html [2023-02-24 01:09:24,825] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-24 01:09:24,826] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-24 01:09:24,848] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 27 samples (table) [2023-02-24 01:09:24,857] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-02-24 01:09:24,859] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-02-24 01:09:24,864] multiqc [DEBUG ] No samples found: conpair [2023-02-24 01:09:24,871] multiqc [DEBUG ] No samples found: peddy [2023-02-24 01:09:24,877] multiqc [DEBUG ] No samples found: somalier [2023-02-24 01:09:24,882] multiqc [DEBUG ] No samples found: methylQA [2023-02-24 01:09:24,891] multiqc [DEBUG ] No samples found: mosdepth [2023-02-24 01:09:24,896] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-02-24 01:09:24,901] multiqc [DEBUG ] No samples found: qualimap [2023-02-24 01:09:24,906] multiqc [DEBUG ] No samples found: preseq [2023-02-24 01:09:24,911] multiqc [DEBUG ] No samples found: quast [2023-02-24 01:09:24,916] multiqc [DEBUG ] No samples found: qorts [2023-02-24 01:09:24,921] multiqc [DEBUG ] No samples found: rna_seqc [2023-02-24 01:09:24,926] multiqc [DEBUG ] No samples found: rockhopper [2023-02-24 01:09:24,930] multiqc [DEBUG ] No samples found: rsem [2023-02-24 01:09:24,942] multiqc [DEBUG ] No samples found: rseqc [2023-02-24 01:09:24,946] multiqc [DEBUG ] No samples found: busco [2023-02-24 01:09:24,951] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-02-24 01:09:24,957] multiqc [DEBUG ] No samples found: disambiguate [2023-02-24 01:09:24,962] multiqc [DEBUG ] No samples found: supernova [2023-02-24 01:09:24,974] multiqc [DEBUG ] No samples found: deeptools [2023-02-24 01:09:24,979] multiqc [DEBUG ] No samples found: sargasso [2023-02-24 01:09:24,984] multiqc [DEBUG ] No samples found: verifybamid [2023-02-24 01:09:24,989] multiqc [DEBUG ] No samples found: mirtrace [2023-02-24 01:09:24,994] multiqc [DEBUG ] No samples found: happy [2023-02-24 01:09:24,999] multiqc [DEBUG ] No samples found: mirtop [2023-02-24 01:09:25,005] multiqc [DEBUG ] No samples found: homer [2023-02-24 01:09:25,010] multiqc [DEBUG ] No samples found: macs2 [2023-02-24 01:09:25,014] multiqc [DEBUG ] No samples found: theta2 [2023-02-24 01:09:25,019] multiqc [DEBUG ] No samples found: snpeff [2023-02-24 01:09:25,026] multiqc [DEBUG ] No samples found: gatk [2023-02-24 01:09:25,030] multiqc [DEBUG ] No samples found: htseq [2023-02-24 01:09:25,036] multiqc [DEBUG ] No samples found: bcftools [2023-02-24 01:09:25,040] multiqc [DEBUG ] No samples found: featureCounts [2023-02-24 01:09:25,046] multiqc [DEBUG ] No samples found: fgbio [2023-02-24 01:09:25,059] multiqc [DEBUG ] No samples found: dragen [2023-02-24 01:09:25,064] multiqc [DEBUG ] No samples found: dedup [2023-02-24 01:09:25,069] multiqc [DEBUG ] No samples found: damageprofiler [2023-02-24 01:09:25,092] multiqc [DEBUG ] No samples found: biobambam2 [2023-02-24 01:09:25,097] multiqc [DEBUG ] No samples found: mtnucratio [2023-02-24 01:09:25,099] multiqc [DEBUG ] No samples found: picard [2023-02-24 01:09:25,104] multiqc [DEBUG ] No samples found: prokka [2023-02-24 01:09:25,108] multiqc [DEBUG ] No samples found: samblaster [2023-02-24 01:09:25,118] multiqc [DEBUG ] No samples found: samtools [2023-02-24 01:09:25,122] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-02-24 01:09:25,127] multiqc [DEBUG ] No samples found: bamtools [2023-02-24 01:09:25,132] multiqc [DEBUG ] No samples found: jellyfish [2023-02-24 01:09:25,141] multiqc [DEBUG ] No samples found: vcftools [2023-02-24 01:09:25,147] multiqc [DEBUG ] No samples found: longranger [2023-02-24 01:09:25,152] multiqc [DEBUG ] No samples found: stacks [2023-02-24 01:09:25,157] multiqc [DEBUG ] No samples found: varscan2 [2023-02-24 01:09:25,171] multiqc [DEBUG ] No samples found: bbmap [2023-02-24 01:09:25,176] multiqc [DEBUG ] No samples found: bismark [2023-02-24 01:09:25,181] multiqc [DEBUG ] No samples found: biscuit [2023-02-24 01:09:25,186] multiqc [DEBUG ] No samples found: hicexplorer [2023-02-24 01:09:25,191] multiqc [DEBUG ] No samples found: hicup [2023-02-24 01:09:25,195] multiqc [DEBUG ] No samples found: hicpro [2023-02-24 01:09:25,200] multiqc [DEBUG ] No samples found: salmon [2023-02-24 01:09:25,205] multiqc [DEBUG ] No samples found: kallisto [2023-02-24 01:09:25,210] multiqc [DEBUG ] No samples found: slamdunk [2023-02-24 01:09:25,215] multiqc [DEBUG ] No samples found: star [2023-02-24 01:09:25,219] multiqc [DEBUG ] No samples found: hisat2 [2023-02-24 01:09:25,224] multiqc [DEBUG ] No samples found: tophat [2023-02-24 01:09:25,230] multiqc [DEBUG ] No samples found: bowtie2 [2023-02-24 01:09:25,236] multiqc [DEBUG ] No samples found: bowtie1 [2023-02-24 01:09:25,241] multiqc [DEBUG ] No samples found: snpsplit [2023-02-24 01:09:25,246] multiqc [DEBUG ] No samples found: kat [2023-02-24 01:09:25,250] multiqc [DEBUG ] No samples found: leehom [2023-02-24 01:09:25,255] multiqc [DEBUG ] No samples found: adapterRemoval [2023-02-24 01:09:25,259] multiqc [DEBUG ] No samples found: clipandmerge [2023-02-24 01:09:25,265] multiqc [DEBUG ] No samples found: cutadapt [2023-02-24 01:09:25,269] multiqc [DEBUG ] No samples found: flexbar [2023-02-24 01:09:25,273] multiqc [DEBUG ] No samples found: kaiju [2023-02-24 01:09:25,278] multiqc [DEBUG ] No samples found: kraken [2023-02-24 01:09:25,283] multiqc [DEBUG ] No samples found: malt [2023-02-24 01:09:25,289] multiqc [DEBUG ] No samples found: trimmomatic [2023-02-24 01:09:25,293] multiqc [DEBUG ] No samples found: sickle [2023-02-24 01:09:25,299] multiqc [DEBUG ] No samples found: skewer [2023-02-24 01:09:25,304] multiqc [DEBUG ] No samples found: sortmerna [2023-02-24 01:09:25,308] multiqc [DEBUG ] No samples found: biobloomtools [2023-02-24 01:09:25,314] multiqc [DEBUG ] No samples found: fastq_screen [2023-02-24 01:09:25,318] multiqc [DEBUG ] No samples found: afterqc [2023-02-24 01:09:25,324] multiqc [DEBUG ] No samples found: fastp [2023-02-24 01:09:34,142] multiqc.modules.fastqc.fastqc [INFO ] Found 54 reports [2023-02-24 01:09:34,523] multiqc [DEBUG ] No samples found: pycoqc [2023-02-24 01:09:34,528] multiqc [DEBUG ] No samples found: minionqc [2023-02-24 01:09:34,534] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-02-24 01:09:34,539] multiqc [DEBUG ] No samples found: clusterflow [2023-02-24 01:09:34,544] multiqc [DEBUG ] No samples found: bcl2fastq [2023-02-24 01:09:34,549] multiqc [DEBUG ] No samples found: interop [2023-02-24 01:09:34,553] multiqc [DEBUG ] No samples found: ivar [2023-02-24 01:09:34,558] multiqc [DEBUG ] No samples found: flash [2023-02-24 01:09:34,564] multiqc [DEBUG ] No samples found: seqyclean [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-02-24 01:09:34,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-02-24 01:09:34,565] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-02-24 01:09:34,565] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-02-24 01:09:34,565] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-02-24 01:09:34,627] multiqc [INFO ] Compressing plot data [2023-02-24 01:09:35,509] multiqc [INFO ] Report : multiqc_report.html [2023-02-24 01:09:35,509] multiqc [INFO ] Data : multiqc_data [2023-02-24 01:09:35,509] multiqc [DEBUG ] Moving data file from '/state/partition1/job-30450725/tmp31a_xm3_/multiqc_data' to '/scratch/gencore/logs/html/H5JMGDSX5/merged/multiqc_data' [2023-02-24 01:09:35,638] multiqc [INFO ] MultiQC complete