[2023-05-17 06:31:59,521] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-17 06:31:59,522] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-17 06:31:59,522] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-17 06:31:59,524] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-17 06:31:59,524] 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}} [2023-05-17 06:31:59,524] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5NY3DRX3/merged [2023-05-17 06:31:59,718] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-17 06:31:59,719] multiqc [INFO ] This is MultiQC v1.9 [2023-05-17 06:31:59,719] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5NY3DRX3/merged [2023-05-17 06:31:59,719] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5NY3DRX3/merged [2023-05-17 06:31:59,719] multiqc [INFO ] Template : default [2023-05-17 06:31:59,719] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-17 06:31:59,719] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5NY3DRX3/merged [2023-05-17 06:31:59,719] 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 [2023-05-17 06:31:59,719] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33491254/tmpnlu4jvoh [2023-05-17 06:31:59,839] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NY3DRX3_2_fastqc.html [2023-05-17 06:31:59,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NY3DRX3_2_fastqc.html [2023-05-17 06:31:59,902] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NY3DRX3_3_fastqc.html [2023-05-17 06:31:59,904] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NY3DRX3_3_fastqc.html [2023-05-17 06:31:59,947] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NY3DRX3_4_fastqc.html [2023-05-17 06:31:59,949] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NY3DRX3_4_fastqc.html [2023-05-17 06:32:00,010] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NY3DRX3_1_fastqc.html [2023-05-17 06:32:00,012] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NY3DRX3_1_fastqc.html [2023-05-17 06:32:00,514] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-17 06:32:00,515] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-17 06:32:00,518] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-05-17 06:32:00,520] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-17 06:32:00,523] multiqc [DEBUG ] No samples found: conpair [2023-05-17 06:32:00,527] multiqc [DEBUG ] No samples found: peddy [2023-05-17 06:32:00,532] multiqc [DEBUG ] No samples found: somalier [2023-05-17 06:32:00,534] multiqc [DEBUG ] No samples found: methylQA [2023-05-17 06:32:00,538] multiqc [DEBUG ] No samples found: mosdepth [2023-05-17 06:32:00,541] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-17 06:32:00,544] multiqc [DEBUG ] No samples found: qualimap [2023-05-17 06:32:00,546] multiqc [DEBUG ] No samples found: preseq [2023-05-17 06:32:00,549] multiqc [DEBUG ] No samples found: quast [2023-05-17 06:32:00,553] multiqc [DEBUG ] No samples found: qorts [2023-05-17 06:32:00,555] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-17 06:32:00,558] multiqc [DEBUG ] No samples found: rockhopper [2023-05-17 06:32:00,561] multiqc [DEBUG ] No samples found: rsem [2023-05-17 06:32:00,565] multiqc [DEBUG ] No samples found: rseqc [2023-05-17 06:32:00,568] multiqc [DEBUG ] No samples found: busco [2023-05-17 06:32:00,571] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-17 06:32:00,573] multiqc [DEBUG ] No samples found: disambiguate [2023-05-17 06:32:00,576] multiqc [DEBUG ] No samples found: supernova [2023-05-17 06:32:00,581] multiqc [DEBUG ] No samples found: deeptools [2023-05-17 06:32:00,584] multiqc [DEBUG ] No samples found: sargasso [2023-05-17 06:32:00,586] multiqc [DEBUG ] No samples found: verifybamid [2023-05-17 06:32:00,589] multiqc [DEBUG ] No samples found: mirtrace [2023-05-17 06:32:00,594] multiqc [DEBUG ] No samples found: happy [2023-05-17 06:32:00,597] multiqc [DEBUG ] No samples found: mirtop [2023-05-17 06:32:00,600] multiqc [DEBUG ] No samples found: homer [2023-05-17 06:32:00,603] multiqc [DEBUG ] No samples found: macs2 [2023-05-17 06:32:00,606] multiqc [DEBUG ] No samples found: theta2 [2023-05-17 06:32:00,609] multiqc [DEBUG ] No samples found: snpeff [2023-05-17 06:32:00,612] multiqc [DEBUG ] No samples found: gatk [2023-05-17 06:32:00,615] multiqc [DEBUG ] No samples found: htseq [2023-05-17 06:32:00,618] multiqc [DEBUG ] No samples found: bcftools [2023-05-17 06:32:00,621] multiqc [DEBUG ] No samples found: featureCounts [2023-05-17 06:32:00,625] multiqc [DEBUG ] No samples found: fgbio [2023-05-17 06:32:00,632] multiqc [DEBUG ] No samples found: dragen [2023-05-17 06:32:00,634] multiqc [DEBUG ] No samples found: dedup [2023-05-17 06:32:00,637] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-17 06:32:00,650] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-17 06:32:00,653] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-17 06:32:00,655] multiqc [DEBUG ] No samples found: picard [2023-05-17 06:32:00,658] multiqc [DEBUG ] No samples found: prokka [2023-05-17 06:32:00,661] multiqc [DEBUG ] No samples found: samblaster [2023-05-17 06:32:00,666] multiqc [DEBUG ] No samples found: samtools [2023-05-17 06:32:00,669] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-17 06:32:00,671] multiqc [DEBUG ] No samples found: bamtools [2023-05-17 06:32:00,674] multiqc [DEBUG ] No samples found: jellyfish [2023-05-17 06:32:00,679] multiqc [DEBUG ] No samples found: vcftools [2023-05-17 06:32:00,682] multiqc [DEBUG ] No samples found: longranger [2023-05-17 06:32:00,685] multiqc [DEBUG ] No samples found: stacks [2023-05-17 06:32:00,690] multiqc [DEBUG ] No samples found: varscan2 [2023-05-17 06:32:00,695] multiqc [DEBUG ] No samples found: bbmap [2023-05-17 06:32:00,698] multiqc [DEBUG ] No samples found: bismark [2023-05-17 06:32:00,700] multiqc [DEBUG ] No samples found: biscuit [2023-05-17 06:32:00,703] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-17 06:32:00,706] multiqc [DEBUG ] No samples found: hicup [2023-05-17 06:32:00,709] multiqc [DEBUG ] No samples found: hicpro [2023-05-17 06:32:00,712] multiqc [DEBUG ] No samples found: salmon [2023-05-17 06:32:00,715] multiqc [DEBUG ] No samples found: kallisto [2023-05-17 06:32:00,718] multiqc [DEBUG ] No samples found: slamdunk [2023-05-17 06:32:00,721] multiqc [DEBUG ] No samples found: star [2023-05-17 06:32:00,724] multiqc [DEBUG ] No samples found: hisat2 [2023-05-17 06:32:00,727] multiqc [DEBUG ] No samples found: tophat [2023-05-17 06:32:00,730] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-17 06:32:00,733] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-17 06:32:00,736] multiqc [DEBUG ] No samples found: snpsplit [2023-05-17 06:32:00,739] multiqc [DEBUG ] No samples found: kat [2023-05-17 06:32:00,742] multiqc [DEBUG ] No samples found: leehom [2023-05-17 06:32:00,745] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-17 06:32:00,747] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-17 06:32:00,750] multiqc [DEBUG ] No samples found: cutadapt [2023-05-17 06:32:00,753] multiqc [DEBUG ] No samples found: flexbar [2023-05-17 06:32:00,756] multiqc [DEBUG ] No samples found: kaiju [2023-05-17 06:32:00,759] multiqc [DEBUG ] No samples found: kraken [2023-05-17 06:32:00,763] multiqc [DEBUG ] No samples found: malt [2023-05-17 06:32:00,765] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-17 06:32:00,768] multiqc [DEBUG ] No samples found: sickle [2023-05-17 06:32:00,771] multiqc [DEBUG ] No samples found: skewer [2023-05-17 06:32:00,774] multiqc [DEBUG ] No samples found: sortmerna [2023-05-17 06:32:00,776] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-17 06:32:00,780] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-17 06:32:00,783] multiqc [DEBUG ] No samples found: afterqc [2023-05-17 06:32:00,786] multiqc [DEBUG ] No samples found: fastp [2023-05-17 06:32:00,913] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-05-17 06:32:00,952] multiqc [DEBUG ] No samples found: pycoqc [2023-05-17 06:32:00,955] multiqc [DEBUG ] No samples found: minionqc [2023-05-17 06:32:00,957] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-17 06:32:00,961] multiqc [DEBUG ] No samples found: clusterflow [2023-05-17 06:32:00,964] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-17 06:32:00,967] multiqc [DEBUG ] No samples found: interop [2023-05-17 06:32:00,970] multiqc [DEBUG ] No samples found: ivar [2023-05-17 06:32:00,973] multiqc [DEBUG ] No samples found: flash [2023-05-17 06:32:00,976] multiqc [DEBUG ] No samples found: seqyclean [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-17 06:32:00,976] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-17 06:32:00,977] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-17 06:32:00,977] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-17 06:32:00,982] multiqc [INFO ] Compressing plot data [2023-05-17 06:32:01,048] multiqc [INFO ] Report : multiqc_report.html [2023-05-17 06:32:01,048] multiqc [INFO ] Data : multiqc_data [2023-05-17 06:32:01,048] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33491254/tmpnlu4jvoh/multiqc_data' to '/scratch/gencore/logs/html/H5NY3DRX3/merged/multiqc_data' [2023-05-17 06:32:01,153] multiqc [INFO ] MultiQC complete