[2023-06-05 19:01:24,398] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-06-05 19:01:24,398] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2023-06-05 19:01:24,398] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-05 19:01:24,400] multiqc [DEBUG ] Loading config settings from: /home/mk5636/nf-hpcpipe/bin/mqc_config.yaml [2023-06-05 19:01:24,400] 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}} [2023-06-05 19:01:24,400] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/bin/mqc_config.yaml . [2023-06-05 19:01:24,594] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-06-05 19:01:24,594] multiqc [INFO ] This is MultiQC v1.9 [2023-06-05 19:01:24,595] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/bin/mqc_config.yaml . [2023-06-05 19:01:24,595] multiqc [DEBUG ] Working dir : /scratch/mk5636/nf-pipeline-test/work/4f/aa95baf09e360da64ce49464e8f6d1/merged [2023-06-05 19:01:24,595] multiqc [INFO ] Template : default [2023-06-05 19:01:24,595] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-06-05 19:01:24,595] multiqc [INFO ] Searching : /scratch/mk5636/nf-pipeline-test/work/4f/aa95baf09e360da64ce49464e8f6d1/merged [2023-06-05 19:01:24,595] 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 [2023-06-05 19:01:24,595] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-34259404/tmp3ek819j7 [2023-06-05 19:01:24,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN114_hs_fastqc.html [2023-06-05 19:01:24,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN114_hs_fastqc.html [2023-06-05 19:01:24,770] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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HHWYGAFX5_n01_EN154_hs_fastqc.html [2023-06-05 19:01:29,186] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n01_EN154_hs_fastqc.html [2023-06-05 19:01:29,232] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN147_hs_fastqc.html [2023-06-05 19:01:29,234] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN147_hs_fastqc.html [2023-06-05 19:01:29,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN123_hs_fastqc.html [2023-06-05 19:01:29,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN123_hs_fastqc.html [2023-06-05 19:01:29,331] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN126_hs_fastqc.html [2023-06-05 19:01:29,333] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN126_hs_fastqc.html [2023-06-05 19:01:29,688] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-05 19:01:29,688] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-05 19:01:29,718] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 49 samples (table) [2023-06-05 19:01:29,720] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-06-05 19:01:29,730] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-06-05 19:01:29,734] multiqc [DEBUG ] No samples found: conpair [2023-06-05 19:01:29,737] multiqc [DEBUG ] No samples found: peddy [2023-06-05 19:01:29,740] multiqc [DEBUG ] No samples found: somalier [2023-06-05 19:01:29,743] multiqc [DEBUG ] No samples found: methylQA [2023-06-05 19:01:29,747] multiqc [DEBUG ] No samples found: mosdepth [2023-06-05 19:01:29,750] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-05 19:01:29,753] multiqc [DEBUG ] No samples found: qualimap [2023-06-05 19:01:29,756] multiqc [DEBUG ] No samples found: preseq [2023-06-05 19:01:29,759] multiqc [DEBUG ] No samples found: quast [2023-06-05 19:01:29,762] multiqc [DEBUG ] No samples found: qorts [2023-06-05 19:01:29,765] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-05 19:01:29,768] multiqc [DEBUG ] No samples found: rockhopper [2023-06-05 19:01:29,771] multiqc [DEBUG ] No samples found: rsem [2023-06-05 19:01:29,776] multiqc [DEBUG ] No samples found: rseqc [2023-06-05 19:01:29,779] multiqc [DEBUG ] No samples found: busco [2023-06-05 19:01:29,782] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-05 19:01:29,785] multiqc [DEBUG ] No samples found: disambiguate [2023-06-05 19:01:29,788] multiqc [DEBUG ] No samples found: supernova [2023-06-05 19:01:29,793] multiqc [DEBUG ] No samples found: deeptools [2023-06-05 19:01:29,796] multiqc [DEBUG ] No samples found: sargasso [2023-06-05 19:01:29,799] multiqc [DEBUG ] No samples found: verifybamid [2023-06-05 19:01:29,802] multiqc [DEBUG ] No samples found: mirtrace [2023-06-05 19:01:29,805] multiqc [DEBUG ] No samples found: happy [2023-06-05 19:01:29,808] multiqc [DEBUG ] No samples found: mirtop [2023-06-05 19:01:29,811] multiqc [DEBUG ] No samples found: homer [2023-06-05 19:01:29,814] multiqc [DEBUG ] No samples found: macs2 [2023-06-05 19:01:29,817] multiqc [DEBUG ] No samples found: theta2 [2023-06-05 19:01:29,820] multiqc [DEBUG ] No samples found: snpeff [2023-06-05 19:01:29,824] multiqc [DEBUG ] No samples found: gatk [2023-06-05 19:01:29,827] multiqc [DEBUG ] No samples found: htseq [2023-06-05 19:01:29,830] multiqc [DEBUG ] No samples found: bcftools [2023-06-05 19:01:29,833] multiqc [DEBUG ] No samples found: featureCounts [2023-06-05 19:01:29,836] multiqc [DEBUG ] No samples found: fgbio [2023-06-05 19:01:29,842] multiqc [DEBUG ] No samples found: dragen [2023-06-05 19:01:29,845] multiqc [DEBUG ] No samples found: dedup [2023-06-05 19:01:29,848] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-05 19:01:29,856] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-05 19:01:29,859] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-05 19:01:29,861] multiqc [DEBUG ] No samples found: picard [2023-06-05 19:01:29,864] multiqc [DEBUG ] No samples found: prokka [2023-06-05 19:01:29,867] multiqc [DEBUG ] No samples found: samblaster [2023-06-05 19:01:29,871] multiqc [DEBUG ] No samples found: samtools [2023-06-05 19:01:29,874] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-05 19:01:29,877] multiqc [DEBUG ] No samples found: bamtools [2023-06-05 19:01:29,880] multiqc [DEBUG ] No samples found: jellyfish [2023-06-05 19:01:29,884] multiqc [DEBUG ] No samples found: vcftools [2023-06-05 19:01:29,887] multiqc [DEBUG ] No samples found: longranger [2023-06-05 19:01:29,890] multiqc [DEBUG ] No samples found: stacks [2023-06-05 19:01:29,893] multiqc [DEBUG ] No samples found: varscan2 [2023-06-05 19:01:29,899] multiqc [DEBUG ] No samples found: bbmap [2023-06-05 19:01:29,902] multiqc [DEBUG ] No samples found: bismark [2023-06-05 19:01:29,905] multiqc [DEBUG ] No samples found: biscuit [2023-06-05 19:01:29,908] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-05 19:01:29,911] multiqc [DEBUG ] No samples found: hicup [2023-06-05 19:01:29,914] multiqc [DEBUG ] No samples found: hicpro [2023-06-05 19:01:29,917] multiqc [DEBUG ] No samples found: salmon [2023-06-05 19:01:29,919] multiqc [DEBUG ] No samples found: kallisto [2023-06-05 19:01:29,923] multiqc [DEBUG ] No samples found: slamdunk [2023-06-05 19:01:29,925] multiqc [DEBUG ] No samples found: star [2023-06-05 19:01:29,928] multiqc [DEBUG ] No samples found: hisat2 [2023-06-05 19:01:29,931] multiqc [DEBUG ] No samples found: tophat [2023-06-05 19:01:29,934] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-05 19:01:29,937] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-05 19:01:29,940] multiqc [DEBUG ] No samples found: snpsplit [2023-06-05 19:01:29,943] multiqc [DEBUG ] No samples found: kat [2023-06-05 19:01:29,946] multiqc [DEBUG ] No samples found: leehom [2023-06-05 19:01:29,949] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-05 19:01:29,952] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-05 19:01:29,955] multiqc [DEBUG ] No samples found: cutadapt [2023-06-05 19:01:29,958] multiqc [DEBUG ] No samples found: flexbar [2023-06-05 19:01:29,960] multiqc [DEBUG ] No samples found: kaiju [2023-06-05 19:01:29,963] multiqc [DEBUG ] No samples found: kraken [2023-06-05 19:01:29,966] multiqc [DEBUG ] No samples found: malt [2023-06-05 19:01:29,969] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-05 19:01:29,972] multiqc [DEBUG ] No samples found: sickle [2023-06-05 19:01:29,975] multiqc [DEBUG ] No samples found: skewer [2023-06-05 19:01:29,978] multiqc [DEBUG ] No samples found: sortmerna [2023-06-05 19:01:29,981] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-05 19:01:29,984] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-05 19:01:29,987] multiqc [DEBUG ] No samples found: afterqc [2023-06-05 19:01:29,990] multiqc [DEBUG ] No samples found: fastp [2023-06-05 19:01:33,191] multiqc.modules.fastqc.fastqc [INFO ] Found 98 reports [2023-06-05 19:01:35,120] multiqc [DEBUG ] No samples found: pycoqc [2023-06-05 19:01:35,123] multiqc [DEBUG ] No samples found: minionqc [2023-06-05 19:01:35,126] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-06-05 19:01:35,130] multiqc [DEBUG ] No samples found: clusterflow [2023-06-05 19:01:35,133] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-05 19:01:35,136] multiqc [DEBUG ] No samples found: interop [2023-06-05 19:01:35,138] multiqc [DEBUG ] No samples found: ivar [2023-06-05 19:01:35,141] multiqc [DEBUG ] No samples found: flash [2023-06-05 19:01:35,144] multiqc [DEBUG ] No samples found: seqyclean [2023-06-05 19:01:35,144] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-06-05 19:01:35,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-06-05 19:01:35,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-06-05 19:01:35,144] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-06-05 19:01:35,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-06-05 19:01:35,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-06-05 19:01:35,144] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-06-05 19:01:35,145] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-06-05 19:01:35,259] multiqc [INFO ] Compressing plot data [2023-06-05 19:01:37,007] multiqc [INFO ] Report : multiqc_report.html [2023-06-05 19:01:37,007] multiqc [INFO ] Data : multiqc_data [2023-06-05 19:01:37,007] multiqc [DEBUG ] Moving data file from '/state/partition1/job-34259404/tmp3ek819j7/multiqc_data' to '/scratch/mk5636/nf-pipeline-test/work/4f/aa95baf09e360da64ce49464e8f6d1/merged/multiqc_data' [2023-06-05 19:01:37,111] multiqc [INFO ] MultiQC complete