[2023-07-06 17:40:03,849] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-07-06 17:40:03,849] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2023-07-06 17:40:03,849] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-07-06 17:40:03,852] multiqc [DEBUG ] Loading config settings from: /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml [2023-07-06 17:40:03,852] 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 17:40:03,852] 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 17:40:03,991] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-07-06 17:40:03,992] multiqc [INFO ] This is MultiQC v1.9 [2023-07-06 17:40:03,992] 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 17:40:03,992] multiqc [DEBUG ] Working dir : /scratch/mk5636/nf-pipeline-test/work/f1/2f19e3eac28a4d45975f87acbdda3b/3 [2023-07-06 17:40:03,992] multiqc [INFO ] Template : default [2023-07-06 17:40:03,992] 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 17:40:03,992] multiqc [INFO ] Searching : /scratch/mk5636/nf-pipeline-test/work/f1/2f19e3eac28a4d45975f87acbdda3b/3 [2023-07-06 17:40:03,992] 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 17:40:03,992] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-35180271/tmpnyisn96b [2023-07-06 17:40:04,088] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_2R_1-10_fastqc.html [2023-07-06 17:40:04,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_2R_1-10_fastqc.html [2023-07-06 17:40:04,144] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_5R_1-9_fastqc.html [2023-07-06 17:40:04,146] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_5R_1-9_fastqc.html [2023-07-06 17:40:04,195] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_4R_1-9_fastqc.html [2023-07-06 17:40:04,197] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_4R_1-9_fastqc.html [2023-07-06 17:40:04,247] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_14G_1-15_fastqc.html [2023-07-06 17:40:04,249] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_14G_1-15_fastqc.html [2023-07-06 17:40:04,300] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10R_1-15_fastqc.html [2023-07-06 17:40:04,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10R_1-15_fastqc.html [2023-07-06 17:40:04,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_4R_1-10_fastqc.html [2023-07-06 17:40:04,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_4R_1-10_fastqc.html [2023-07-06 17:40:04,404] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_11R_1-10_fastqc.html [2023-07-06 17:40:04,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_11R_1-10_fastqc.html [2023-07-06 17:40:04,457] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_12R_1-15_fastqc.html [2023-07-06 17:40:04,458] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_12R_1-15_fastqc.html [2023-07-06 17:40:04,509] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_11R_1-15_fastqc.html [2023-07-06 17:40:04,511] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_11R_1-15_fastqc.html [2023-07-06 17:40:04,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10G_1-15_fastqc.html [2023-07-06 17:40:04,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10G_1-15_fastqc.html [2023-07-06 17:40:04,612] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_3R_1-9_fastqc.html [2023-07-06 17:40:04,614] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_3R_1-9_fastqc.html [2023-07-06 17:40:04,663] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10R_1-9_fastqc.html [2023-07-06 17:40:04,665] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10R_1-9_fastqc.html [2023-07-06 17:40:05,000] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 17:40:05,001] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 17:40:05,052] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 98 samples (table) [2023-07-06 17:40:05,062] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-07-06 17:40:05,064] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-07-06 17:40:05,067] multiqc [DEBUG ] No samples found: conpair [2023-07-06 17:40:05,071] multiqc [DEBUG ] No samples found: peddy [2023-07-06 17:40:05,074] multiqc [DEBUG ] No samples found: somalier [2023-07-06 17:40:05,077] multiqc [DEBUG ] No samples found: methylQA [2023-07-06 17:40:05,081] multiqc [DEBUG ] No samples found: mosdepth [2023-07-06 17:40:05,084] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-07-06 17:40:05,087] multiqc [DEBUG ] No samples found: qualimap [2023-07-06 17:40:05,089] multiqc [DEBUG ] No samples found: preseq [2023-07-06 17:40:05,092] multiqc [DEBUG ] No samples found: quast [2023-07-06 17:40:05,095] multiqc [DEBUG ] No samples found: qorts [2023-07-06 17:40:05,098] multiqc [DEBUG ] No samples found: rna_seqc [2023-07-06 17:40:05,101] multiqc [DEBUG ] No samples found: rockhopper [2023-07-06 17:40:05,105] multiqc [DEBUG ] No samples found: rsem [2023-07-06 17:40:05,110] multiqc [DEBUG ] No samples found: rseqc [2023-07-06 17:40:05,113] multiqc [DEBUG ] No samples found: busco [2023-07-06 17:40:05,116] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-07-06 17:40:05,119] multiqc [DEBUG ] No samples found: disambiguate [2023-07-06 17:40:05,122] multiqc [DEBUG ] No samples found: supernova [2023-07-06 17:40:05,127] multiqc [DEBUG ] No samples found: deeptools [2023-07-06 17:40:05,130] multiqc [DEBUG ] No samples found: sargasso [2023-07-06 17:40:05,133] multiqc [DEBUG ] No samples found: verifybamid [2023-07-06 17:40:05,136] multiqc [DEBUG ] No samples found: mirtrace [2023-07-06 17:40:05,139] multiqc [DEBUG ] No samples found: happy [2023-07-06 17:40:05,142] multiqc [DEBUG ] No samples found: mirtop [2023-07-06 17:40:05,145] multiqc [DEBUG ] No samples found: homer [2023-07-06 17:40:05,148] multiqc [DEBUG ] No samples found: macs2 [2023-07-06 17:40:05,151] multiqc [DEBUG ] No samples found: theta2 [2023-07-06 17:40:05,154] multiqc [DEBUG ] No samples found: snpeff [2023-07-06 17:40:05,158] multiqc [DEBUG ] No samples found: gatk [2023-07-06 17:40:05,161] multiqc [DEBUG ] No samples found: htseq [2023-07-06 17:40:05,164] multiqc [DEBUG ] No samples found: bcftools [2023-07-06 17:40:05,167] multiqc [DEBUG ] No samples found: featureCounts [2023-07-06 17:40:05,173] multiqc [DEBUG ] No samples found: fgbio [2023-07-06 17:40:05,180] multiqc [DEBUG ] No samples found: dragen [2023-07-06 17:40:05,183] multiqc [DEBUG ] No samples found: dedup [2023-07-06 17:40:05,186] multiqc [DEBUG ] No samples found: damageprofiler [2023-07-06 17:40:05,195] multiqc [DEBUG ] No samples found: biobambam2 [2023-07-06 17:40:05,198] multiqc [DEBUG ] No samples found: mtnucratio [2023-07-06 17:40:05,200] multiqc [DEBUG ] No samples found: picard [2023-07-06 17:40:05,203] multiqc [DEBUG ] No samples found: prokka [2023-07-06 17:40:05,206] multiqc [DEBUG ] No samples found: samblaster [2023-07-06 17:40:05,210] multiqc [DEBUG ] No samples found: samtools [2023-07-06 17:40:05,213] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-07-06 17:40:05,216] multiqc [DEBUG ] No samples found: bamtools [2023-07-06 17:40:05,219] multiqc [DEBUG ] No samples found: jellyfish [2023-07-06 17:40:05,223] multiqc [DEBUG ] No samples found: vcftools [2023-07-06 17:40:05,226] multiqc [DEBUG ] No samples found: longranger [2023-07-06 17:40:05,229] multiqc [DEBUG ] No samples found: stacks [2023-07-06 17:40:05,232] multiqc [DEBUG ] No samples found: varscan2 [2023-07-06 17:40:05,237] multiqc [DEBUG ] No samples found: bbmap [2023-07-06 17:40:05,240] multiqc [DEBUG ] No samples found: bismark [2023-07-06 17:40:05,243] multiqc [DEBUG ] No samples found: biscuit [2023-07-06 17:40:05,246] multiqc [DEBUG ] No samples found: hicexplorer [2023-07-06 17:40:05,249] multiqc [DEBUG ] No samples found: hicup [2023-07-06 17:40:05,252] multiqc [DEBUG ] No samples found: hicpro [2023-07-06 17:40:05,255] multiqc [DEBUG ] No samples found: salmon [2023-07-06 17:40:05,258] multiqc [DEBUG ] No samples found: kallisto [2023-07-06 17:40:05,261] multiqc [DEBUG ] No samples found: slamdunk [2023-07-06 17:40:05,264] multiqc [DEBUG ] No samples found: star [2023-07-06 17:40:05,267] multiqc [DEBUG ] No samples found: hisat2 [2023-07-06 17:40:05,270] multiqc [DEBUG ] No samples found: tophat [2023-07-06 17:40:05,273] multiqc [DEBUG ] No samples found: bowtie2 [2023-07-06 17:40:05,276] multiqc [DEBUG ] No samples found: bowtie1 [2023-07-06 17:40:05,279] multiqc [DEBUG ] No samples found: snpsplit [2023-07-06 17:40:05,281] multiqc [DEBUG ] No samples found: kat [2023-07-06 17:40:05,284] multiqc [DEBUG ] No samples found: leehom [2023-07-06 17:40:05,287] multiqc [DEBUG ] No samples found: adapterRemoval [2023-07-06 17:40:05,290] multiqc [DEBUG ] No samples found: clipandmerge [2023-07-06 17:40:05,293] multiqc [DEBUG ] No samples found: cutadapt [2023-07-06 17:40:05,296] multiqc [DEBUG ] No samples found: flexbar [2023-07-06 17:40:05,299] multiqc [DEBUG ] No samples found: kaiju [2023-07-06 17:40:05,302] multiqc [DEBUG ] No samples found: kraken [2023-07-06 17:40:05,304] multiqc [DEBUG ] No samples found: malt [2023-07-06 17:40:05,307] multiqc [DEBUG ] No samples found: trimmomatic [2023-07-06 17:40:05,310] multiqc [DEBUG ] No samples found: sickle [2023-07-06 17:40:05,313] multiqc [DEBUG ] No samples found: skewer [2023-07-06 17:40:05,316] multiqc [DEBUG ] No samples found: sortmerna [2023-07-06 17:40:05,319] multiqc [DEBUG ] No samples found: biobloomtools [2023-07-06 17:40:05,322] multiqc [DEBUG ] No samples found: fastq_screen [2023-07-06 17:40:05,325] multiqc [DEBUG ] No samples found: afterqc [2023-07-06 17:40:05,328] multiqc [DEBUG ] No samples found: fastp [2023-07-06 17:40:07,615] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2023-07-06 17:40:07,786] multiqc [DEBUG ] No samples found: pycoqc [2023-07-06 17:40:07,789] multiqc [DEBUG ] No samples found: minionqc [2023-07-06 17:40:07,792] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-07-06 17:40:07,795] multiqc [DEBUG ] No samples found: clusterflow [2023-07-06 17:40:07,798] multiqc [DEBUG ] No samples found: bcl2fastq [2023-07-06 17:40:07,801] multiqc [DEBUG ] No samples found: interop [2023-07-06 17:40:07,803] multiqc [DEBUG ] No samples found: ivar [2023-07-06 17:40:07,807] multiqc [DEBUG ] No samples found: flash [2023-07-06 17:40:07,810] multiqc [DEBUG ] No samples found: seqyclean [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:40:07,810] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-07-06 17:40:07,811] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-07-06 17:40:07,826] multiqc [INFO ] Compressing plot data [2023-07-06 17:40:08,055] multiqc [INFO ] Report : multiqc_report.html [2023-07-06 17:40:08,055] multiqc [INFO ] Data : multiqc_data [2023-07-06 17:40:08,055] multiqc [DEBUG ] Moving data file from '/state/partition1/job-35180271/tmpnyisn96b/multiqc_data' to '/scratch/mk5636/nf-pipeline-test/work/f1/2f19e3eac28a4d45975f87acbdda3b/3/multiqc_data' [2023-07-06 17:40:08,210] multiqc [INFO ] MultiQC complete