[2023-07-07 00:52:07,162] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-07-07 00:52:07,162] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2023-07-07 00:52:07,162] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-07-07 00:52:07,165] multiqc [DEBUG ] Loading config settings from: /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml [2023-07-07 00:52:07,165] 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}} [2023-07-07 00:52:07,165] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml . [2023-07-07 00:52:07,336] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-07-07 00:52:07,336] multiqc [INFO ] This is MultiQC v1.9 [2023-07-07 00:52:07,336] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml . [2023-07-07 00:52:07,336] multiqc [DEBUG ] Working dir : /scratch/mk5636/nf-pipeline-test/work/14/d3072196970dc54a5aa3453dd67e55/1 [2023-07-07 00:52:07,336] multiqc [INFO ] Template : default [2023-07-07 00:52:07,336] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-07-07 00:52:07,336] multiqc [INFO ] Searching : /scratch/mk5636/nf-pipeline-test/work/14/d3072196970dc54a5aa3453dd67e55/1 [2023-07-07 00:52:07,337] 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 [2023-07-07 00:52:07,337] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-35192341/tmp_jo6r2z5 [2023-07-07 00:52:07,427] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-07 00:52:07,429] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-07 00:52:07,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_SRF_fastqc.html [2023-07-07 00:52:07,626] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_SRF_fastqc.html [2023-07-07 00:52:07,666] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_IgG_fastqc.html [2023-07-07 00:52:07,668] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_IgG_fastqc.html [2023-07-07 00:52:07,708] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_BPTF_fastqc.html [2023-07-07 00:52:07,710] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_BPTF_fastqc.html [2023-07-07 00:52:07,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_undetermined_fastqc.html [2023-07-07 00:52:07,750] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_undetermined_fastqc.html [2023-07-07 00:52:07,790] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_H3K4me3_fastqc.html [2023-07-07 00:52:07,792] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_H3K4me3_fastqc.html [2023-07-07 00:52:07,832] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_undetermined_fastqc.html [2023-07-07 00:52:07,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_undetermined_fastqc.html [2023-07-07 00:52:07,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_H3K4me3_fastqc.html [2023-07-07 00:52:07,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_H3K4me3_fastqc.html [2023-07-07 00:52:07,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_SRF_fastqc.html [2023-07-07 00:52:07,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n02_SRF_fastqc.html [2023-07-07 00:52:07,955] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_BPTF_fastqc.html [2023-07-07 00:52:07,957] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_BPTF_fastqc.html [2023-07-07 00:52:07,996] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_IgG_fastqc.html [2023-07-07 00:52:07,998] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWDDC_l01_n01_IgG_fastqc.html [2023-07-07 00:52:08,285] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-07 00:52:08,285] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-07 00:52:08,293] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2023-07-07 00:52:08,295] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-07-07 00:52:08,304] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-07-07 00:52:08,307] multiqc [DEBUG ] No samples found: conpair [2023-07-07 00:52:08,310] multiqc [DEBUG ] No samples found: peddy [2023-07-07 00:52:08,313] multiqc [DEBUG ] No samples found: somalier [2023-07-07 00:52:08,316] multiqc [DEBUG ] No samples found: methylQA [2023-07-07 00:52:08,319] multiqc [DEBUG ] No samples found: mosdepth [2023-07-07 00:52:08,322] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-07-07 00:52:08,325] multiqc [DEBUG ] No samples found: qualimap [2023-07-07 00:52:08,327] multiqc [DEBUG ] No samples found: preseq [2023-07-07 00:52:08,330] multiqc [DEBUG ] No samples found: quast [2023-07-07 00:52:08,333] multiqc [DEBUG ] No samples found: qorts [2023-07-07 00:52:08,336] multiqc [DEBUG ] No samples found: rna_seqc [2023-07-07 00:52:08,339] multiqc [DEBUG ] No samples found: rockhopper [2023-07-07 00:52:08,341] multiqc [DEBUG ] No samples found: rsem [2023-07-07 00:52:08,346] multiqc [DEBUG ] No samples found: rseqc [2023-07-07 00:52:08,349] multiqc [DEBUG ] No samples found: busco [2023-07-07 00:52:08,352] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-07-07 00:52:08,355] multiqc [DEBUG ] No samples found: disambiguate [2023-07-07 00:52:08,358] multiqc [DEBUG ] No samples found: supernova [2023-07-07 00:52:08,362] multiqc [DEBUG ] No samples found: deeptools [2023-07-07 00:52:08,365] multiqc [DEBUG ] No samples found: sargasso [2023-07-07 00:52:08,368] multiqc [DEBUG ] No samples found: verifybamid [2023-07-07 00:52:08,371] multiqc [DEBUG ] No samples found: mirtrace [2023-07-07 00:52:08,373] multiqc [DEBUG ] No samples found: happy [2023-07-07 00:52:08,376] multiqc [DEBUG ] No samples found: mirtop [2023-07-07 00:52:08,379] multiqc [DEBUG ] No samples found: homer [2023-07-07 00:52:08,382] multiqc [DEBUG ] No samples found: macs2 [2023-07-07 00:52:08,385] multiqc [DEBUG ] No samples found: theta2 [2023-07-07 00:52:08,387] multiqc [DEBUG ] No samples found: snpeff [2023-07-07 00:52:08,391] multiqc [DEBUG ] No samples found: gatk [2023-07-07 00:52:08,394] multiqc [DEBUG ] No samples found: htseq [2023-07-07 00:52:08,397] multiqc [DEBUG ] No samples found: bcftools [2023-07-07 00:52:08,399] multiqc [DEBUG ] No samples found: featureCounts [2023-07-07 00:52:08,402] multiqc [DEBUG ] No samples found: fgbio [2023-07-07 00:52:08,407] multiqc [DEBUG ] No samples found: dragen [2023-07-07 00:52:08,410] multiqc [DEBUG ] No samples found: dedup [2023-07-07 00:52:08,413] multiqc [DEBUG ] No samples found: damageprofiler [2023-07-07 00:52:08,420] multiqc [DEBUG ] No samples found: biobambam2 [2023-07-07 00:52:08,423] multiqc [DEBUG ] No samples found: mtnucratio [2023-07-07 00:52:08,425] multiqc [DEBUG ] No samples found: picard [2023-07-07 00:52:08,428] multiqc [DEBUG ] No samples found: prokka [2023-07-07 00:52:08,431] multiqc [DEBUG ] No samples found: samblaster [2023-07-07 00:52:08,434] multiqc [DEBUG ] No samples found: samtools [2023-07-07 00:52:08,437] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-07-07 00:52:08,440] multiqc [DEBUG ] No samples found: bamtools [2023-07-07 00:52:08,443] multiqc [DEBUG ] No samples found: jellyfish [2023-07-07 00:52:08,446] multiqc [DEBUG ] No samples found: vcftools [2023-07-07 00:52:08,449] multiqc [DEBUG ] No samples found: longranger [2023-07-07 00:52:08,452] multiqc [DEBUG ] No samples found: stacks [2023-07-07 00:52:08,454] multiqc [DEBUG ] No samples found: varscan2 [2023-07-07 00:52:08,459] multiqc [DEBUG ] No samples found: bbmap [2023-07-07 00:52:08,462] multiqc [DEBUG ] No samples found: bismark [2023-07-07 00:52:08,465] multiqc [DEBUG ] No samples found: biscuit [2023-07-07 00:52:08,468] multiqc [DEBUG ] No samples found: hicexplorer [2023-07-07 00:52:08,471] multiqc [DEBUG ] No samples found: hicup [2023-07-07 00:52:08,473] multiqc [DEBUG ] No samples found: hicpro [2023-07-07 00:52:08,476] multiqc [DEBUG ] No samples found: salmon [2023-07-07 00:52:08,479] multiqc [DEBUG ] No samples found: kallisto [2023-07-07 00:52:08,481] multiqc [DEBUG ] No samples found: slamdunk [2023-07-07 00:52:08,484] multiqc [DEBUG ] No samples found: star [2023-07-07 00:52:08,487] multiqc [DEBUG ] No samples found: hisat2 [2023-07-07 00:52:08,490] multiqc [DEBUG ] No samples found: tophat [2023-07-07 00:52:08,492] multiqc [DEBUG ] No samples found: bowtie2 [2023-07-07 00:52:08,495] multiqc [DEBUG ] No samples found: bowtie1 [2023-07-07 00:52:08,498] multiqc [DEBUG ] No samples found: snpsplit [2023-07-07 00:52:08,500] multiqc [DEBUG ] No samples found: kat [2023-07-07 00:52:08,503] multiqc [DEBUG ] No samples found: leehom [2023-07-07 00:52:08,506] multiqc [DEBUG ] No samples found: adapterRemoval [2023-07-07 00:52:08,509] multiqc [DEBUG ] No samples found: clipandmerge [2023-07-07 00:52:08,511] multiqc [DEBUG ] No samples found: cutadapt [2023-07-07 00:52:08,514] multiqc [DEBUG ] No samples found: flexbar [2023-07-07 00:52:08,517] multiqc [DEBUG ] No samples found: kaiju [2023-07-07 00:52:08,519] multiqc [DEBUG ] No samples found: kraken [2023-07-07 00:52:08,522] multiqc [DEBUG ] No samples found: malt [2023-07-07 00:52:08,525] multiqc [DEBUG ] No samples found: trimmomatic [2023-07-07 00:52:08,528] multiqc [DEBUG ] No samples found: sickle [2023-07-07 00:52:08,530] multiqc [DEBUG ] No samples found: skewer [2023-07-07 00:52:08,533] multiqc [DEBUG ] No samples found: sortmerna [2023-07-07 00:52:08,536] multiqc [DEBUG ] No samples found: biobloomtools [2023-07-07 00:52:08,538] multiqc [DEBUG ] No samples found: fastq_screen [2023-07-07 00:52:08,541] multiqc [DEBUG ] No samples found: afterqc [2023-07-07 00:52:08,544] multiqc [DEBUG ] No samples found: fastp [2023-07-07 00:52:08,625] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-07-07 00:52:08,840] multiqc [DEBUG ] No samples found: pycoqc [2023-07-07 00:52:08,843] multiqc [DEBUG ] No samples found: minionqc [2023-07-07 00:52:08,845] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-07-07 00:52:08,848] multiqc [DEBUG ] No samples found: clusterflow [2023-07-07 00:52:08,851] multiqc [DEBUG ] No samples found: bcl2fastq [2023-07-07 00:52:08,854] multiqc [DEBUG ] No samples found: interop [2023-07-07 00:52:08,856] multiqc [DEBUG ] No samples found: ivar [2023-07-07 00:52:08,859] multiqc [DEBUG ] No samples found: flash [2023-07-07 00:52:08,862] multiqc [DEBUG ] No samples found: seqyclean [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-07-07 00:52:08,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-07-07 00:52:08,863] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-07-07 00:52:08,875] multiqc [INFO ] Compressing plot data [2023-07-07 00:52:09,056] multiqc [INFO ] Report : multiqc_report.html [2023-07-07 00:52:09,056] multiqc [INFO ] Data : multiqc_data [2023-07-07 00:52:09,056] multiqc [DEBUG ] Moving data file from '/state/partition1/job-35192341/tmp_jo6r2z5/multiqc_data' to '/scratch/mk5636/nf-pipeline-test/work/14/d3072196970dc54a5aa3453dd67e55/1/multiqc_data' [2023-07-07 00:52:09,149] multiqc [INFO ] MultiQC complete