[2024-08-16 17:18:04,035] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-16 17:18:04,035] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-16 17:18:04,035] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-16 17:18:04,038] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-16 17:18:04,038] 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}} [2024-08-16 17:18:04,038] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-16 17:18:04,082] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-16 17:18:04,082] multiqc [INFO ] This is MultiQC v1.9 [2024-08-16 17:18:04,082] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-16 17:18:04,082] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/be/5c0da2fb316fea4fcb11ef5937b0c9/merged [2024-08-16 17:18:04,082] multiqc [INFO ] Template : default [2024-08-16 17:18:04,082] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-16 17:18:04,082] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/be/5c0da2fb316fea4fcb11ef5937b0c9/merged [2024-08-16 17:18:04,083] 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 [2024-08-16 17:18:04,083] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49990304/tmpo7uc64g5 [2024-08-16 17:18:04,203] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_12894_Spikein_Input_13Aug24_fastqc.html [2024-08-16 17:18:04,206] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_12894_Spikein_Input_13Aug24_fastqc.html [2024-08-16 17:18:04,255] multiqc [DEBUG ] File ignored by hicexplorer because it 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[2024-08-16 17:18:05,778] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_11281_ChIP_3hr_13Aug24_fastqc.html [2024-08-16 17:18:05,780] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_11281_ChIP_3hr_13Aug24_fastqc.html [2024-08-16 17:18:05,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_11364_ChIP_3hr_13Aug24_fastqc.html [2024-08-16 17:18:05,827] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_11364_ChIP_3hr_13Aug24_fastqc.html [2024-08-16 17:18:05,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n01_2861_Spikein_ChIP_Rep1_13Aug24_fastqc.html [2024-08-16 17:18:05,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n01_2861_Spikein_ChIP_Rep2_13Aug24_fastqc.html [2024-08-16 17:18:06,062] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_7797_ChIP_6hr_13Aug24_fastqc.html [2024-08-16 17:18:06,064] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_7797_ChIP_6hr_13Aug24_fastqc.html [2024-08-16 17:18:06,109] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n01_11281_Input_6hr_13Aug24_fastqc.html [2024-08-16 17:18:06,111] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n01_11281_Input_6hr_13Aug24_fastqc.html [2024-08-16 17:18:06,160] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_12894_Spikein_ChIP_13Aug24_fastqc.html [2024-08-16 17:18:06,162] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_12894_Spikein_ChIP_13Aug24_fastqc.html [2024-08-16 17:18:06,206] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n01_3084_Spikein_Input_13Aug24_fastqc.html [2024-08-16 17:18:06,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n01_3084_Spikein_Input_13Aug24_fastqc.html [2024-08-16 17:18:06,254] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n01_11281_ChIP_6hr_13Aug24_fastqc.html [2024-08-16 17:18:06,256] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n01_11281_ChIP_6hr_13Aug24_fastqc.html [2024-08-16 17:18:06,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_7797_Input_3hr_13Aug24_fastqc.html [2024-08-16 17:18:06,304] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_7797_Input_3hr_13Aug24_fastqc.html [2024-08-16 17:18:06,349] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_7797_ChIP_3hr_13Aug24_fastqc.html [2024-08-16 17:18:06,351] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_7797_ChIP_3hr_13Aug24_fastqc.html [2024-08-16 17:18:06,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_2861_Spikein_Input_Rep2_13Aug24_fastqc.html [2024-08-16 17:18:06,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_2861_Spikein_Input_Rep2_13Aug24_fastqc.html [2024-08-16 17:18:06,441] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3CLFAFX7_n02_3084_Spikein_ChIP_13Aug24_fastqc.html [2024-08-16 17:18:06,443] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3CLFAFX7_n02_3084_Spikein_ChIP_13Aug24_fastqc.html [2024-08-16 17:18:07,024] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-16 17:18:07,027] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-16 17:18:07,046] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2024-08-16 17:18:07,056] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-16 17:18:07,057] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-16 17:18:07,064] multiqc [DEBUG ] No samples found: conpair [2024-08-16 17:18:07,070] multiqc [DEBUG ] No samples found: peddy [2024-08-16 17:18:07,077] multiqc [DEBUG ] No samples found: somalier [2024-08-16 17:18:07,084] multiqc [DEBUG ] No samples found: methylQA [2024-08-16 17:18:07,095] multiqc [DEBUG ] No samples found: mosdepth [2024-08-16 17:18:07,101] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-16 17:18:07,105] multiqc [DEBUG ] No samples found: qualimap [2024-08-16 17:18:07,112] multiqc [DEBUG ] No samples found: preseq [2024-08-16 17:18:07,118] multiqc [DEBUG ] No samples found: quast [2024-08-16 17:18:07,125] multiqc [DEBUG ] No samples found: qorts [2024-08-16 17:18:07,131] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-16 17:18:07,138] multiqc [DEBUG ] No samples found: rockhopper [2024-08-16 17:18:07,144] multiqc [DEBUG ] No samples found: rsem [2024-08-16 17:18:07,160] multiqc [DEBUG ] No samples found: rseqc [2024-08-16 17:18:07,166] multiqc [DEBUG ] No samples found: busco [2024-08-16 17:18:07,172] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-16 17:18:07,179] multiqc [DEBUG ] No samples found: disambiguate [2024-08-16 17:18:07,186] multiqc [DEBUG ] No samples found: supernova [2024-08-16 17:18:07,205] multiqc [DEBUG ] No samples found: deeptools [2024-08-16 17:18:07,211] multiqc [DEBUG ] No samples found: sargasso [2024-08-16 17:18:07,218] multiqc [DEBUG ] No samples found: verifybamid [2024-08-16 17:18:07,224] multiqc [DEBUG ] No samples found: mirtrace [2024-08-16 17:18:07,230] multiqc [DEBUG ] No samples found: happy [2024-08-16 17:18:07,237] multiqc [DEBUG ] No samples found: mirtop [2024-08-16 17:18:07,245] multiqc [DEBUG ] No samples found: homer [2024-08-16 17:18:07,252] multiqc [DEBUG ] No samples found: macs2 [2024-08-16 17:18:07,258] multiqc [DEBUG ] No samples found: theta2 [2024-08-16 17:18:07,265] multiqc [DEBUG ] No samples found: snpeff [2024-08-16 17:18:07,274] multiqc [DEBUG ] No samples found: gatk [2024-08-16 17:18:07,280] multiqc [DEBUG ] No samples found: htseq [2024-08-16 17:18:07,287] multiqc [DEBUG ] No samples found: bcftools [2024-08-16 17:18:07,293] multiqc [DEBUG ] No samples found: featureCounts [2024-08-16 17:18:07,302] multiqc [DEBUG ] No samples found: fgbio [2024-08-16 17:18:07,320] multiqc [DEBUG ] No samples found: dragen [2024-08-16 17:18:07,326] multiqc [DEBUG ] No samples found: dedup [2024-08-16 17:18:07,332] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-16 17:18:07,366] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-16 17:18:07,372] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-16 17:18:07,374] multiqc [DEBUG ] No samples found: picard [2024-08-16 17:18:07,381] multiqc [DEBUG ] No samples found: prokka [2024-08-16 17:18:07,386] multiqc [DEBUG ] No samples found: samblaster [2024-08-16 17:18:07,397] multiqc [DEBUG ] No samples found: samtools [2024-08-16 17:18:07,403] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-16 17:18:07,410] multiqc [DEBUG ] No samples found: bamtools [2024-08-16 17:18:07,416] multiqc [DEBUG ] No samples found: jellyfish [2024-08-16 17:18:07,426] multiqc [DEBUG ] No samples found: vcftools [2024-08-16 17:18:07,433] multiqc [DEBUG ] No samples found: longranger [2024-08-16 17:18:07,439] multiqc [DEBUG ] No samples found: stacks [2024-08-16 17:18:07,445] multiqc [DEBUG ] No samples found: varscan2 [2024-08-16 17:18:07,465] multiqc [DEBUG ] No samples found: bbmap [2024-08-16 17:18:07,471] multiqc [DEBUG ] No samples found: bismark [2024-08-16 17:18:07,478] multiqc [DEBUG ] No samples found: biscuit [2024-08-16 17:18:07,484] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-16 17:18:07,491] multiqc [DEBUG ] No samples found: hicup [2024-08-16 17:18:07,497] multiqc [DEBUG ] No samples found: hicpro [2024-08-16 17:18:07,504] multiqc [DEBUG ] No samples found: salmon [2024-08-16 17:18:07,510] multiqc [DEBUG ] No samples found: kallisto [2024-08-16 17:18:07,516] multiqc [DEBUG ] No samples found: slamdunk [2024-08-16 17:18:07,522] multiqc [DEBUG ] No samples found: star [2024-08-16 17:18:07,528] multiqc [DEBUG ] No samples found: hisat2 [2024-08-16 17:18:07,534] multiqc [DEBUG ] No samples found: tophat [2024-08-16 17:18:07,540] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-16 17:18:07,546] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-16 17:18:07,552] multiqc [DEBUG ] No samples found: snpsplit [2024-08-16 17:18:07,558] multiqc [DEBUG ] No samples found: kat [2024-08-16 17:18:07,563] multiqc [DEBUG ] No samples found: leehom [2024-08-16 17:18:07,570] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-16 17:18:07,577] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-16 17:18:07,583] multiqc [DEBUG ] No samples found: cutadapt [2024-08-16 17:18:07,588] multiqc [DEBUG ] No samples found: flexbar [2024-08-16 17:18:07,594] multiqc [DEBUG ] No samples found: kaiju [2024-08-16 17:18:07,600] multiqc [DEBUG ] No samples found: kraken [2024-08-16 17:18:07,606] multiqc [DEBUG ] No samples found: malt [2024-08-16 17:18:07,612] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-16 17:18:07,618] multiqc [DEBUG ] No samples found: sickle [2024-08-16 17:18:07,623] multiqc [DEBUG ] No samples found: skewer [2024-08-16 17:18:07,629] multiqc [DEBUG ] No samples found: sortmerna [2024-08-16 17:18:07,634] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-16 17:18:07,640] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-16 17:18:07,646] multiqc [DEBUG ] No samples found: afterqc [2024-08-16 17:18:07,652] multiqc [DEBUG ] No samples found: fastp [2024-08-16 17:18:08,736] multiqc.modules.fastqc.fastqc [INFO ] Found 46 reports [2024-08-16 17:18:09,132] multiqc [DEBUG ] No samples found: pycoqc [2024-08-16 17:18:09,138] multiqc [DEBUG ] No samples found: minionqc [2024-08-16 17:18:09,144] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-16 17:18:09,150] multiqc [DEBUG ] No samples found: clusterflow [2024-08-16 17:18:09,156] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-16 17:18:09,162] multiqc [DEBUG ] No samples found: interop [2024-08-16 17:18:09,168] multiqc [DEBUG ] No samples found: ivar [2024-08-16 17:18:09,173] multiqc [DEBUG ] No samples found: flash [2024-08-16 17:18:09,179] multiqc [DEBUG ] No samples found: seqyclean [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-16 17:18:09,179] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-16 17:18:09,180] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-16 17:18:09,180] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-16 17:18:09,180] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-16 17:18:09,235] multiqc [INFO ] Compressing plot data [2024-08-16 17:18:10,040] multiqc [INFO ] Report : multiqc_report.html [2024-08-16 17:18:10,040] multiqc [INFO ] Data : multiqc_data [2024-08-16 17:18:10,040] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49990304/tmpo7uc64g5/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/be/5c0da2fb316fea4fcb11ef5937b0c9/merged/multiqc_data' [2024-08-16 17:18:10,189] multiqc [INFO ] MultiQC complete