[2023-09-12 00:01:01,653] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-09-12 00:01:01,653] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-09-12 00:01:01,653] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-09-12 00:01:01,656] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-09-12 00:01:01,656] 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}} [2023-09-12 00:01:01,656] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWNHNBGXT/merged [2023-09-12 00:01:01,829] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-09-12 00:01:01,829] multiqc [INFO ] This is MultiQC v1.9 [2023-09-12 00:01:01,829] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWNHNBGXT/merged [2023-09-12 00:01:01,829] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWNHNBGXT/merged [2023-09-12 00:01:01,829] multiqc [INFO ] Template : default [2023-09-12 00:01:01,829] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-09-12 00:01:01,829] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWNHNBGXT/merged [2023-09-12 00:01:01,829] 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 [2023-09-12 00:01:01,829] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-37587822/tmp86fwlhsr [2023-09-12 00:01:01,947] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-09-12 00:01:01,949] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-09-12 00:01:02,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWNHNBGXT_n01_3688_1_fastqc.html [2023-09-12 00:01:02,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWNHNBGXT_n01_3688_1_fastqc.html [2023-09-12 00:01:02,105] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWNHNBGXT_n01_67192_2_fastqc.html [2023-09-12 00:01:02,107] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWNHNBGXT_n01_67192_2_fastqc.html [2023-09-12 00:01:02,155] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWNHNBGXT_n01_3688_3_fastqc.html [2023-09-12 00:01:02,157] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWNHNBGXT_n01_3688_3_fastqc.html [2023-09-12 00:01:02,205] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWNHNBGXT_n01_3688_2_fastqc.html [2023-09-12 00:01:02,207] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWNHNBGXT_n01_3688_2_fastqc.html [2023-09-12 00:01:02,256] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWNHNBGXT_n01_67192_3_fastqc.html [2023-09-12 00:01:02,258] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWNHNBGXT_n01_67192_3_fastqc.html [2023-09-12 00:01:02,306] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWNHNBGXT_n01_undetermined_fastqc.html [2023-09-12 00:01:02,307] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWNHNBGXT_n01_undetermined_fastqc.html [2023-09-12 00:01:02,615] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-12 00:01:02,617] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-12 00:01:02,626] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2023-09-12 00:01:02,636] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-09-12 00:01:02,637] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-09-12 00:01:02,641] multiqc [DEBUG ] No samples found: conpair [2023-09-12 00:01:02,645] multiqc [DEBUG ] No samples found: peddy [2023-09-12 00:01:02,650] multiqc [DEBUG ] No samples found: somalier [2023-09-12 00:01:02,654] multiqc [DEBUG ] No samples found: methylQA [2023-09-12 00:01:02,661] multiqc [DEBUG ] No samples found: mosdepth [2023-09-12 00:01:02,664] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-09-12 00:01:02,667] multiqc [DEBUG ] No samples found: qualimap [2023-09-12 00:01:02,672] multiqc [DEBUG ] No samples found: preseq [2023-09-12 00:01:02,676] multiqc [DEBUG ] No samples found: quast [2023-09-12 00:01:02,680] multiqc [DEBUG ] No samples found: qorts [2023-09-12 00:01:02,684] multiqc [DEBUG ] No samples found: rna_seqc [2023-09-12 00:01:02,688] multiqc [DEBUG ] No samples found: rockhopper [2023-09-12 00:01:02,692] multiqc [DEBUG ] No samples found: rsem [2023-09-12 00:01:02,701] multiqc [DEBUG ] No samples found: rseqc [2023-09-12 00:01:02,705] multiqc [DEBUG ] No samples found: busco [2023-09-12 00:01:02,709] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-09-12 00:01:02,712] multiqc [DEBUG ] No samples found: disambiguate [2023-09-12 00:01:02,717] multiqc [DEBUG ] No samples found: supernova [2023-09-12 00:01:02,727] multiqc [DEBUG ] No samples found: deeptools [2023-09-12 00:01:02,731] multiqc [DEBUG ] No samples found: sargasso [2023-09-12 00:01:02,735] multiqc [DEBUG ] No samples found: verifybamid [2023-09-12 00:01:02,740] multiqc [DEBUG ] No samples found: mirtrace [2023-09-12 00:01:02,744] multiqc [DEBUG ] No samples found: happy [2023-09-12 00:01:02,748] multiqc [DEBUG ] No samples found: mirtop [2023-09-12 00:01:02,753] multiqc [DEBUG ] No samples found: homer [2023-09-12 00:01:02,757] multiqc [DEBUG ] No samples found: macs2 [2023-09-12 00:01:02,761] multiqc [DEBUG ] No samples found: theta2 [2023-09-12 00:01:02,765] multiqc [DEBUG ] No samples found: snpeff [2023-09-12 00:01:02,770] multiqc [DEBUG ] No samples found: gatk [2023-09-12 00:01:02,774] multiqc [DEBUG ] No samples found: htseq [2023-09-12 00:01:02,779] multiqc [DEBUG ] No samples found: bcftools [2023-09-12 00:01:02,783] multiqc [DEBUG ] No samples found: featureCounts [2023-09-12 00:01:02,788] multiqc [DEBUG ] No samples found: fgbio [2023-09-12 00:01:02,798] multiqc [DEBUG ] No samples found: dragen [2023-09-12 00:01:02,802] multiqc [DEBUG ] No samples found: dedup [2023-09-12 00:01:02,807] multiqc [DEBUG ] No samples found: damageprofiler [2023-09-12 00:01:02,824] multiqc [DEBUG ] No samples found: biobambam2 [2023-09-12 00:01:02,828] multiqc [DEBUG ] No samples found: mtnucratio [2023-09-12 00:01:02,831] multiqc [DEBUG ] No samples found: picard [2023-09-12 00:01:02,835] multiqc [DEBUG ] No samples found: prokka [2023-09-12 00:01:02,838] multiqc [DEBUG ] No samples found: samblaster [2023-09-12 00:01:02,846] multiqc [DEBUG ] No samples found: samtools [2023-09-12 00:01:02,850] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-09-12 00:01:02,854] multiqc [DEBUG ] No samples found: bamtools [2023-09-12 00:01:02,858] multiqc [DEBUG ] No samples found: jellyfish [2023-09-12 00:01:02,864] multiqc [DEBUG ] No samples found: vcftools [2023-09-12 00:01:02,868] multiqc [DEBUG ] No samples found: longranger [2023-09-12 00:01:02,872] multiqc [DEBUG ] No samples found: stacks [2023-09-12 00:01:02,876] multiqc [DEBUG ] No samples found: varscan2 [2023-09-12 00:01:02,888] multiqc [DEBUG ] No samples found: bbmap [2023-09-12 00:01:02,892] multiqc [DEBUG ] No samples found: bismark [2023-09-12 00:01:02,896] multiqc [DEBUG ] No samples found: biscuit [2023-09-12 00:01:02,900] multiqc [DEBUG ] No samples found: hicexplorer [2023-09-12 00:01:02,904] multiqc [DEBUG ] No samples found: hicup [2023-09-12 00:01:02,908] multiqc [DEBUG ] No samples found: hicpro [2023-09-12 00:01:02,912] multiqc [DEBUG ] No samples found: salmon [2023-09-12 00:01:02,916] multiqc [DEBUG ] No samples found: kallisto [2023-09-12 00:01:02,920] multiqc [DEBUG ] No samples found: slamdunk [2023-09-12 00:01:02,924] multiqc [DEBUG ] No samples found: star [2023-09-12 00:01:02,928] multiqc [DEBUG ] No samples found: hisat2 [2023-09-12 00:01:02,932] multiqc [DEBUG ] No samples found: tophat [2023-09-12 00:01:02,936] multiqc [DEBUG ] No samples found: bowtie2 [2023-09-12 00:01:02,940] multiqc [DEBUG ] No samples found: bowtie1 [2023-09-12 00:01:02,944] multiqc [DEBUG ] No samples found: snpsplit [2023-09-12 00:01:02,948] multiqc [DEBUG ] No samples found: kat [2023-09-12 00:01:02,952] multiqc [DEBUG ] No samples found: leehom [2023-09-12 00:01:02,956] multiqc [DEBUG ] No samples found: adapterRemoval [2023-09-12 00:01:02,960] multiqc [DEBUG ] No samples found: clipandmerge [2023-09-12 00:01:02,964] multiqc [DEBUG ] No samples found: cutadapt [2023-09-12 00:01:02,968] multiqc [DEBUG ] No samples found: flexbar [2023-09-12 00:01:02,972] multiqc [DEBUG ] No samples found: kaiju [2023-09-12 00:01:02,976] multiqc [DEBUG ] No samples found: kraken [2023-09-12 00:01:02,980] multiqc [DEBUG ] No samples found: malt [2023-09-12 00:01:02,984] multiqc [DEBUG ] No samples found: trimmomatic [2023-09-12 00:01:02,988] multiqc [DEBUG ] No samples found: sickle [2023-09-12 00:01:02,992] multiqc [DEBUG ] No samples found: skewer [2023-09-12 00:01:02,996] multiqc [DEBUG ] No samples found: sortmerna [2023-09-12 00:01:02,999] multiqc [DEBUG ] No samples found: biobloomtools [2023-09-12 00:01:03,003] multiqc [DEBUG ] No samples found: fastq_screen [2023-09-12 00:01:03,007] multiqc [DEBUG ] No samples found: afterqc [2023-09-12 00:01:03,011] multiqc [DEBUG ] No samples found: fastp [2023-09-12 00:01:03,424] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-09-12 00:01:03,500] multiqc [DEBUG ] No samples found: pycoqc [2023-09-12 00:01:03,504] multiqc [DEBUG ] No samples found: minionqc [2023-09-12 00:01:03,509] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-09-12 00:01:03,513] multiqc [DEBUG ] No samples found: clusterflow [2023-09-12 00:01:03,517] multiqc [DEBUG ] No samples found: bcl2fastq [2023-09-12 00:01:03,521] multiqc [DEBUG ] No samples found: interop [2023-09-12 00:01:03,525] multiqc [DEBUG ] No samples found: ivar [2023-09-12 00:01:03,529] multiqc [DEBUG ] No samples found: flash [2023-09-12 00:01:03,533] multiqc [DEBUG ] No samples found: seqyclean [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-09-12 00:01:03,533] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-09-12 00:01:03,534] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-09-12 00:01:03,542] multiqc [INFO ] Compressing plot data [2023-09-12 00:01:03,662] multiqc [INFO ] Report : multiqc_report.html [2023-09-12 00:01:03,662] multiqc [INFO ] Data : multiqc_data [2023-09-12 00:01:03,662] multiqc [DEBUG ] Moving data file from '/state/partition1/job-37587822/tmp86fwlhsr/multiqc_data' to '/scratch/gencore/logs/html/HWNHNBGXT/merged/multiqc_data' [2023-09-12 00:01:03,775] multiqc [INFO ] MultiQC complete