[2023-07-06 19:13:29,979] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-07-06 19:13:29,979] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2023-07-06 19:13:29,980] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-07-06 19:13:29,982] multiqc [DEBUG ] Loading config settings from: /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml [2023-07-06 19:13:29,982] 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 19:13:29,982] 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 19:13:30,128] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-07-06 19:13:30,128] multiqc [INFO ] This is MultiQC v1.9 [2023-07-06 19:13:30,128] 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 19:13:30,128] multiqc [DEBUG ] Working dir : /scratch/mk5636/nf-pipeline-test/work/32/8b9d6526cafe28af56c20162db09b3/2 [2023-07-06 19:13:30,128] multiqc [INFO ] Template : default [2023-07-06 19:13:30,128] 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 19:13:30,128] multiqc [INFO ] Searching : /scratch/mk5636/nf-pipeline-test/work/32/8b9d6526cafe28af56c20162db09b3/2 [2023-07-06 19:13:30,129] 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 19:13:30,129] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-35180271/tmp_xfbd94x [2023-07-06 19:13:30,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_2R_1-12_fastqc.html [2023-07-06 19:13:30,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_2R_1-12_fastqc.html [2023-07-06 19:13:30,275] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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H52YHDSX7_l02_n01_12G_1-14_fastqc.html [2023-07-06 19:13:39,205] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_12G_1-14_fastqc.html [2023-07-06 19:13:39,252] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_3R_1-15_fastqc.html [2023-07-06 19:13:39,254] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_3R_1-15_fastqc.html [2023-07-06 19:13:39,300] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_10R_1-12_fastqc.html [2023-07-06 19:13:39,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_10R_1-12_fastqc.html [2023-07-06 19:13:39,349] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H52YHDSX7_l02_n01_15G_1-18_fastqc.html [2023-07-06 19:13:39,494] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_15G_1-18_fastqc.html [2023-07-06 19:13:39,541] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_undetermined_fastqc.html [2023-07-06 19:13:39,542] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_undetermined_fastqc.html [2023-07-06 19:13:39,586] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_3G_1-18_fastqc.html [2023-07-06 19:13:39,588] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_3G_1-18_fastqc.html [2023-07-06 19:13:39,632] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-8_fastqc.html [2023-07-06 19:13:39,634] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-8_fastqc.html [2023-07-06 19:13:39,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-14_fastqc.html [2023-07-06 19:13:39,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-14_fastqc.html [2023-07-06 19:13:39,725] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_14G_1-8_fastqc.html [2023-07-06 19:13:39,727] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_14G_1-8_fastqc.html [2023-07-06 19:13:40,058] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 19:13:40,058] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 19:13:40,074] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-07-06 19:13:40,119] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 98 samples (table) [2023-07-06 19:13:40,121] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-07-06 19:13:40,124] multiqc [DEBUG ] No samples found: conpair [2023-07-06 19:13:40,127] multiqc [DEBUG ] No samples found: peddy [2023-07-06 19:13:40,130] multiqc [DEBUG ] No samples found: somalier [2023-07-06 19:13:40,133] multiqc [DEBUG ] No samples found: methylQA [2023-07-06 19:13:40,136] multiqc [DEBUG ] No samples found: mosdepth [2023-07-06 19:13:40,139] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-07-06 19:13:40,142] multiqc [DEBUG ] No samples found: qualimap [2023-07-06 19:13:40,145] multiqc [DEBUG ] No samples found: preseq [2023-07-06 19:13:40,147] multiqc [DEBUG ] No samples found: quast [2023-07-06 19:13:40,150] multiqc [DEBUG ] No samples found: qorts [2023-07-06 19:13:40,153] multiqc [DEBUG ] No samples found: rna_seqc [2023-07-06 19:13:40,156] multiqc [DEBUG ] No samples found: rockhopper [2023-07-06 19:13:40,159] multiqc [DEBUG ] No samples found: rsem [2023-07-06 19:13:40,163] multiqc [DEBUG ] No samples found: rseqc [2023-07-06 19:13:40,166] multiqc [DEBUG ] No samples found: busco [2023-07-06 19:13:40,169] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-07-06 19:13:40,172] multiqc [DEBUG ] No samples found: disambiguate [2023-07-06 19:13:40,175] multiqc [DEBUG ] No samples found: supernova [2023-07-06 19:13:40,180] multiqc [DEBUG ] No samples found: deeptools [2023-07-06 19:13:40,183] multiqc [DEBUG ] No samples found: sargasso [2023-07-06 19:13:40,185] multiqc [DEBUG ] No samples found: verifybamid [2023-07-06 19:13:40,188] multiqc [DEBUG ] No samples found: mirtrace [2023-07-06 19:13:40,191] multiqc [DEBUG ] No samples found: happy [2023-07-06 19:13:40,194] multiqc [DEBUG ] No samples found: mirtop [2023-07-06 19:13:40,197] multiqc [DEBUG ] No samples found: homer [2023-07-06 19:13:40,200] multiqc [DEBUG ] No samples found: macs2 [2023-07-06 19:13:40,203] multiqc [DEBUG ] No samples found: theta2 [2023-07-06 19:13:40,206] multiqc [DEBUG ] No samples found: snpeff [2023-07-06 19:13:40,209] multiqc [DEBUG ] No samples found: gatk [2023-07-06 19:13:40,212] multiqc [DEBUG ] No samples found: htseq [2023-07-06 19:13:40,215] multiqc [DEBUG ] No samples found: bcftools [2023-07-06 19:13:40,217] multiqc [DEBUG ] No samples found: featureCounts [2023-07-06 19:13:40,221] multiqc [DEBUG ] No samples found: fgbio [2023-07-06 19:13:40,226] multiqc [DEBUG ] No samples found: dragen [2023-07-06 19:13:40,229] multiqc [DEBUG ] No samples found: dedup [2023-07-06 19:13:40,232] multiqc [DEBUG ] No samples found: damageprofiler [2023-07-06 19:13:40,240] multiqc [DEBUG ] No samples found: biobambam2 [2023-07-06 19:13:40,243] multiqc [DEBUG ] No samples found: mtnucratio [2023-07-06 19:13:40,245] multiqc [DEBUG ] No samples found: picard [2023-07-06 19:13:40,248] multiqc [DEBUG ] No samples found: prokka [2023-07-06 19:13:40,250] multiqc [DEBUG ] No samples found: samblaster [2023-07-06 19:13:40,254] multiqc [DEBUG ] No samples found: samtools [2023-07-06 19:13:40,257] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-07-06 19:13:40,260] multiqc [DEBUG ] No samples found: bamtools [2023-07-06 19:13:40,263] multiqc [DEBUG ] No samples found: jellyfish [2023-07-06 19:13:40,266] multiqc [DEBUG ] No samples found: vcftools [2023-07-06 19:13:40,269] multiqc [DEBUG ] No samples found: longranger [2023-07-06 19:13:40,272] multiqc [DEBUG ] No samples found: stacks [2023-07-06 19:13:40,275] multiqc [DEBUG ] No samples found: varscan2 [2023-07-06 19:13:40,280] multiqc [DEBUG ] No samples found: bbmap [2023-07-06 19:13:40,283] multiqc [DEBUG ] No samples found: bismark [2023-07-06 19:13:40,286] multiqc [DEBUG ] No samples found: biscuit [2023-07-06 19:13:40,289] multiqc [DEBUG ] No samples found: hicexplorer [2023-07-06 19:13:40,292] multiqc [DEBUG ] No samples found: hicup [2023-07-06 19:13:40,294] multiqc [DEBUG ] No samples found: hicpro [2023-07-06 19:13:40,297] multiqc [DEBUG ] No samples found: salmon [2023-07-06 19:13:40,300] multiqc [DEBUG ] No samples found: kallisto [2023-07-06 19:13:40,303] multiqc [DEBUG ] No samples found: slamdunk [2023-07-06 19:13:40,306] multiqc [DEBUG ] No samples found: star [2023-07-06 19:13:40,309] multiqc [DEBUG ] No samples found: hisat2 [2023-07-06 19:13:40,311] multiqc [DEBUG ] No samples found: tophat [2023-07-06 19:13:40,314] multiqc [DEBUG ] No samples found: bowtie2 [2023-07-06 19:13:40,317] multiqc [DEBUG ] No samples found: bowtie1 [2023-07-06 19:13:40,320] multiqc [DEBUG ] No samples found: snpsplit [2023-07-06 19:13:40,322] multiqc [DEBUG ] No samples found: kat [2023-07-06 19:13:40,325] multiqc [DEBUG ] No samples found: leehom [2023-07-06 19:13:40,328] multiqc [DEBUG ] No samples found: adapterRemoval [2023-07-06 19:13:40,331] multiqc [DEBUG ] No samples found: clipandmerge [2023-07-06 19:13:40,333] multiqc [DEBUG ] No samples found: cutadapt [2023-07-06 19:13:40,336] multiqc [DEBUG ] No samples found: flexbar [2023-07-06 19:13:40,339] multiqc [DEBUG ] No samples found: kaiju [2023-07-06 19:13:40,342] multiqc [DEBUG ] No samples found: kraken [2023-07-06 19:13:40,345] multiqc [DEBUG ] No samples found: malt [2023-07-06 19:13:40,347] multiqc [DEBUG ] No samples found: trimmomatic [2023-07-06 19:13:40,350] multiqc [DEBUG ] No samples found: sickle [2023-07-06 19:13:40,353] multiqc [DEBUG ] No samples found: skewer [2023-07-06 19:13:40,356] multiqc [DEBUG ] No samples found: sortmerna [2023-07-06 19:13:40,358] multiqc [DEBUG ] No samples found: biobloomtools [2023-07-06 19:13:40,361] multiqc [DEBUG ] No samples found: fastq_screen [2023-07-06 19:13:40,364] multiqc [DEBUG ] No samples found: afterqc [2023-07-06 19:13:40,367] multiqc [DEBUG ] No samples found: fastp [2023-07-06 19:14:17,077] multiqc.modules.fastqc.fastqc [INFO ] Found 196 reports [2023-07-06 19:14:40,000] multiqc [DEBUG ] No samples found: pycoqc [2023-07-06 19:14:40,003] multiqc [DEBUG ] No samples found: minionqc [2023-07-06 19:14:40,006] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-07-06 19:14:40,009] multiqc [DEBUG ] No samples found: clusterflow [2023-07-06 19:14:40,012] multiqc [DEBUG ] No samples found: bcl2fastq [2023-07-06 19:14:40,015] multiqc [DEBUG ] No samples found: interop [2023-07-06 19:14:40,018] multiqc [DEBUG ] No samples found: ivar [2023-07-06 19:14:40,021] multiqc [DEBUG ] No samples found: flash [2023-07-06 19:14:40,024] multiqc [DEBUG ] No samples found: seqyclean [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-07-06 19:14:40,024] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-07-06 19:14:40,025] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-07-06 19:14:40,025] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-07-06 19:14:40,025] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-07-06 19:14:40,025] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-07-06 19:14:40,025] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-07-06 19:14:40,025] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-07-06 19:14:40,248] multiqc [INFO ] Compressing plot data [2023-07-06 19:14:40,319] multiqc [INFO ] Report : multiqc_report.html [2023-07-06 19:14:40,319] multiqc [INFO ] Data : multiqc_data [2023-07-06 19:14:40,319] multiqc [DEBUG ] Moving data file from '/state/partition1/job-35180271/tmp_xfbd94x/multiqc_data' to '/scratch/mk5636/nf-pipeline-test/work/32/8b9d6526cafe28af56c20162db09b3/2/multiqc_data' [2023-07-06 19:14:40,429] multiqc [INFO ] MultiQC complete