[2023-07-06 23:37:45,231] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-07-06 23:37:45,231] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2023-07-06 23:37:45,231] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-07-06 23:37:45,233] multiqc [DEBUG ] Loading config settings from: /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml [2023-07-06 23:37:45,233] 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}} [2023-07-06 23:37:45,233] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml . [2023-07-06 23:37:46,615] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-07-06 23:37:46,615] multiqc [INFO ] This is MultiQC v1.9 [2023-07-06 23:37:46,615] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml . [2023-07-06 23:37:46,615] multiqc [DEBUG ] Working dir : /scratch/mk5636/nf-pipeline-test/work/6f/c02eaf7b95771e5edffc31038faf00/1 [2023-07-06 23:37:46,615] multiqc [INFO ] Template : default [2023-07-06 23:37:46,615] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-07-06 23:37:46,615] multiqc [INFO ] Searching : /scratch/mk5636/nf-pipeline-test/work/6f/c02eaf7b95771e5edffc31038faf00/1 [2023-07-06 23:37:46,615] 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 [2023-07-06 23:37:46,616] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-35184704/tmphn37zg9p [2023-07-06 23:37:46,783] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L387F_l01.2_fastqc.html [2023-07-06 23:37:46,786] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L387F_l01.2_fastqc.html [2023-07-06 23:37:46,832] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L387F_l01.3_fastqc.html [2023-07-06 23:37:46,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L387F_l01.3_fastqc.html [2023-07-06 23:37:46,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L387F_l01.1_fastqc.html [2023-07-06 23:37:46,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L387F_l01.1_fastqc.html [2023-07-06 23:37:47,759] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 23:37:47,765] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 23:37:47,769] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-07-06 23:37:47,781] multiqc [DEBUG ] No samples found: conpair [2023-07-06 23:37:47,787] multiqc [DEBUG ] No samples found: peddy [2023-07-06 23:37:47,791] multiqc [DEBUG ] No samples found: somalier [2023-07-06 23:37:47,796] multiqc [DEBUG ] No samples found: methylQA [2023-07-06 23:37:47,802] multiqc [DEBUG ] No samples found: mosdepth [2023-07-06 23:37:47,809] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-07-06 23:37:47,812] multiqc [DEBUG ] No samples found: qualimap [2023-07-06 23:37:47,816] multiqc [DEBUG ] No samples found: preseq [2023-07-06 23:37:47,820] multiqc [DEBUG ] No samples found: quast [2023-07-06 23:37:47,824] multiqc [DEBUG ] No samples found: qorts [2023-07-06 23:37:47,828] multiqc [DEBUG ] No samples found: rna_seqc [2023-07-06 23:37:47,832] multiqc [DEBUG ] No samples found: rockhopper [2023-07-06 23:37:47,836] multiqc [DEBUG ] No samples found: rsem [2023-07-06 23:37:47,850] multiqc [DEBUG ] No samples found: rseqc [2023-07-06 23:37:47,853] multiqc [DEBUG ] No samples found: busco [2023-07-06 23:37:47,872] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-07-06 23:37:47,884] multiqc [DEBUG ] No samples found: disambiguate [2023-07-06 23:37:47,893] multiqc [DEBUG ] No samples found: supernova [2023-07-06 23:37:47,906] multiqc [DEBUG ] No samples found: deeptools [2023-07-06 23:37:47,911] multiqc [DEBUG ] No samples found: sargasso [2023-07-06 23:37:47,918] multiqc [DEBUG ] No samples found: verifybamid [2023-07-06 23:37:47,922] multiqc [DEBUG ] No samples found: mirtrace [2023-07-06 23:37:47,926] multiqc [DEBUG ] No samples found: happy [2023-07-06 23:37:47,930] multiqc [DEBUG ] No samples found: mirtop [2023-07-06 23:37:47,941] multiqc [DEBUG ] No samples found: homer [2023-07-06 23:37:47,945] multiqc [DEBUG ] No samples found: macs2 [2023-07-06 23:37:47,953] multiqc [DEBUG ] No samples found: theta2 [2023-07-06 23:37:47,973] multiqc [DEBUG ] No samples found: snpeff [2023-07-06 23:37:47,979] multiqc [DEBUG ] No samples found: gatk [2023-07-06 23:37:47,986] multiqc [DEBUG ] No samples found: htseq [2023-07-06 23:37:47,991] multiqc [DEBUG ] No samples found: bcftools [2023-07-06 23:37:47,995] multiqc [DEBUG ] No samples found: featureCounts [2023-07-06 23:37:48,000] multiqc [DEBUG ] No samples found: fgbio [2023-07-06 23:37:48,011] multiqc [DEBUG ] No samples found: dragen [2023-07-06 23:37:48,015] multiqc [DEBUG ] No samples found: dedup [2023-07-06 23:37:48,019] multiqc [DEBUG ] No samples found: damageprofiler [2023-07-06 23:37:48,040] multiqc [DEBUG ] No samples found: biobambam2 [2023-07-06 23:37:48,044] multiqc [DEBUG ] No samples found: mtnucratio [2023-07-06 23:37:48,046] multiqc [DEBUG ] No samples found: picard [2023-07-06 23:37:48,050] multiqc [DEBUG ] No samples found: prokka [2023-07-06 23:37:48,054] multiqc [DEBUG ] No samples found: samblaster [2023-07-06 23:37:48,073] multiqc [DEBUG ] No samples found: samtools [2023-07-06 23:37:48,080] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-07-06 23:37:48,084] multiqc [DEBUG ] No samples found: bamtools [2023-07-06 23:37:48,088] multiqc [DEBUG ] No samples found: jellyfish [2023-07-06 23:37:48,095] multiqc [DEBUG ] No samples found: vcftools [2023-07-06 23:37:48,099] multiqc [DEBUG ] No samples found: longranger [2023-07-06 23:37:48,107] multiqc [DEBUG ] No samples found: stacks [2023-07-06 23:37:48,111] multiqc [DEBUG ] No samples found: varscan2 [2023-07-06 23:37:48,122] multiqc [DEBUG ] No samples found: bbmap [2023-07-06 23:37:48,133] multiqc [DEBUG ] No samples found: bismark [2023-07-06 23:37:48,137] multiqc [DEBUG ] No samples found: biscuit [2023-07-06 23:37:48,144] multiqc [DEBUG ] No samples found: hicexplorer [2023-07-06 23:37:48,148] multiqc [DEBUG ] No samples found: hicup [2023-07-06 23:37:48,152] multiqc [DEBUG ] No samples found: hicpro [2023-07-06 23:37:48,156] multiqc [DEBUG ] No samples found: salmon [2023-07-06 23:37:48,165] multiqc [DEBUG ] No samples found: kallisto [2023-07-06 23:37:48,181] multiqc [DEBUG ] No samples found: slamdunk [2023-07-06 23:37:48,185] multiqc [DEBUG ] No samples found: star [2023-07-06 23:37:48,190] multiqc [DEBUG ] No samples found: hisat2 [2023-07-06 23:37:48,194] multiqc [DEBUG ] No samples found: tophat [2023-07-06 23:37:48,198] multiqc [DEBUG ] No samples found: bowtie2 [2023-07-06 23:37:48,201] multiqc [DEBUG ] No samples found: bowtie1 [2023-07-06 23:37:48,205] multiqc [DEBUG ] No samples found: snpsplit [2023-07-06 23:37:48,209] multiqc [DEBUG ] No samples found: kat [2023-07-06 23:37:48,213] multiqc [DEBUG ] No samples found: leehom [2023-07-06 23:37:48,217] multiqc [DEBUG ] No samples found: adapterRemoval [2023-07-06 23:37:48,221] multiqc [DEBUG ] No samples found: clipandmerge [2023-07-06 23:37:48,225] multiqc [DEBUG ] No samples found: cutadapt [2023-07-06 23:37:48,229] multiqc [DEBUG ] No samples found: flexbar [2023-07-06 23:37:48,234] multiqc [DEBUG ] No samples found: kaiju [2023-07-06 23:37:48,238] multiqc [DEBUG ] No samples found: kraken [2023-07-06 23:37:48,242] multiqc [DEBUG ] No samples found: malt [2023-07-06 23:37:48,246] multiqc [DEBUG ] No samples found: trimmomatic [2023-07-06 23:37:48,254] multiqc [DEBUG ] No samples found: sickle [2023-07-06 23:37:48,260] multiqc [DEBUG ] No samples found: skewer [2023-07-06 23:37:48,275] multiqc [DEBUG ] No samples found: sortmerna [2023-07-06 23:37:48,288] multiqc [DEBUG ] No samples found: biobloomtools [2023-07-06 23:37:48,295] multiqc [DEBUG ] No samples found: fastq_screen [2023-07-06 23:37:48,299] multiqc [DEBUG ] No samples found: afterqc [2023-07-06 23:37:48,303] multiqc [DEBUG ] No samples found: fastp [2023-07-06 23:37:48,326] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2023-07-06 23:37:48,396] multiqc [DEBUG ] No samples found: pycoqc [2023-07-06 23:37:48,408] multiqc [DEBUG ] No samples found: minionqc [2023-07-06 23:37:48,412] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-07-06 23:37:48,416] multiqc [DEBUG ] No samples found: clusterflow [2023-07-06 23:37:48,420] multiqc [DEBUG ] No samples found: bcl2fastq [2023-07-06 23:37:48,424] multiqc [DEBUG ] No samples found: interop [2023-07-06 23:37:48,428] multiqc [DEBUG ] No samples found: ivar [2023-07-06 23:37:48,442] multiqc [DEBUG ] No samples found: flash [2023-07-06 23:37:48,446] multiqc [DEBUG ] No samples found: seqyclean [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-07-06 23:37:48,446] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-07-06 23:37:48,451] multiqc [INFO ] Compressing plot data [2023-07-06 23:37:48,514] multiqc [INFO ] Report : multiqc_report.html [2023-07-06 23:37:48,514] multiqc [INFO ] Data : multiqc_data [2023-07-06 23:37:48,514] multiqc [DEBUG ] Moving data file from '/state/partition1/job-35184704/tmphn37zg9p/multiqc_data' to '/scratch/mk5636/nf-pipeline-test/work/6f/c02eaf7b95771e5edffc31038faf00/1/multiqc_data' [2023-07-06 23:37:48,627] multiqc [INFO ] MultiQC complete