[2024-05-14 15:53:19,306] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-05-14 15:53:19,306] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-05-14 15:53:19,306] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-05-14 15:53:19,308] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-05-14 15:53:19,309] 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}} [2024-05-14 15:53:19,309] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-14 15:53:19,409] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-05-14 15:53:19,410] multiqc [INFO ] This is MultiQC v1.9 [2024-05-14 15:53:19,410] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-14 15:53:19,410] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/4a/59a516ba480c5140afc685e71f3106/1 [2024-05-14 15:53:19,410] multiqc [INFO ] Template : default [2024-05-14 15:53:19,410] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-05-14 15:53:19,410] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/4a/59a516ba480c5140afc685e71f3106/1 [2024-05-14 15:53:19,410] 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 [2024-05-14 15:53:19,410] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-46482234/tmp10_2gkuy [2024-05-14 15:53:19,547] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_41_fastqc.html [2024-05-14 15:53:19,556] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_41_fastqc.html [2024-05-14 15:53:19,625] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_42_fastqc.html [2024-05-14 15:53:19,632] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_42_fastqc.html [2024-05-14 15:53:19,695] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_43_fastqc.html [2024-05-14 15:53:19,701] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_43_fastqc.html [2024-05-14 15:53:19,765] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_44_fastqc.html [2024-05-14 15:53:19,772] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_BS_CR_44_fastqc.html [2024-05-14 15:53:19,835] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_undetermined_fastqc.html [2024-05-14 15:53:19,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n01_undetermined_fastqc.html [2024-05-14 15:53:19,907] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_41_fastqc.html [2024-05-14 15:53:19,915] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_41_fastqc.html [2024-05-14 15:53:19,976] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_42_fastqc.html [2024-05-14 15:53:19,983] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_42_fastqc.html [2024-05-14 15:53:20,045] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_43_fastqc.html [2024-05-14 15:53:20,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_43_fastqc.html [2024-05-14 15:53:20,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_44_fastqc.html [2024-05-14 15:53:20,123] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_BS_CR_44_fastqc.html [2024-05-14 15:53:20,187] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_undetermined_fastqc.html [2024-05-14 15:53:20,193] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHRNB_l01_n02_undetermined_fastqc.html [2024-05-14 15:53:20,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:20,268] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:20,268] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:20,268] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:20,268] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:20,269] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:20,269] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:20,298] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-14 15:53:22,028] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-14 15:53:22,030] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-14 15:53:22,042] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2024-05-14 15:53:22,043] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-05-14 15:53:22,053] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-05-14 15:53:22,061] multiqc [DEBUG ] No samples found: conpair [2024-05-14 15:53:22,069] multiqc [DEBUG ] No samples found: peddy [2024-05-14 15:53:22,077] multiqc [DEBUG ] No samples found: somalier [2024-05-14 15:53:22,085] multiqc [DEBUG ] No samples found: methylQA [2024-05-14 15:53:22,100] multiqc [DEBUG ] No samples found: mosdepth [2024-05-14 15:53:22,107] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-05-14 15:53:22,112] multiqc [DEBUG ] No samples found: qualimap [2024-05-14 15:53:22,121] multiqc [DEBUG ] No samples found: preseq [2024-05-14 15:53:22,128] multiqc [DEBUG ] No samples found: quast [2024-05-14 15:53:22,137] multiqc [DEBUG ] No samples found: qorts [2024-05-14 15:53:22,146] multiqc [DEBUG ] No samples found: rna_seqc [2024-05-14 15:53:22,154] multiqc [DEBUG ] No samples found: rockhopper [2024-05-14 15:53:22,160] multiqc [DEBUG ] No samples found: rsem [2024-05-14 15:53:22,180] multiqc [DEBUG ] No samples found: rseqc [2024-05-14 15:53:22,186] multiqc [DEBUG ] No samples found: busco [2024-05-14 15:53:22,193] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-05-14 15:53:22,201] multiqc [DEBUG ] No samples found: disambiguate [2024-05-14 15:53:22,208] multiqc [DEBUG ] No samples found: supernova [2024-05-14 15:53:22,234] multiqc [DEBUG ] No samples found: deeptools [2024-05-14 15:53:22,242] multiqc [DEBUG ] No samples found: sargasso [2024-05-14 15:53:22,251] multiqc [DEBUG ] No samples found: verifybamid [2024-05-14 15:53:22,258] multiqc [DEBUG ] No samples found: mirtrace [2024-05-14 15:53:22,265] multiqc [DEBUG ] No samples found: happy [2024-05-14 15:53:22,272] multiqc [DEBUG ] No samples found: mirtop [2024-05-14 15:53:22,285] multiqc [DEBUG ] No samples found: homer [2024-05-14 15:53:22,293] multiqc [DEBUG ] No samples found: macs2 [2024-05-14 15:53:22,300] multiqc [DEBUG ] No samples found: theta2 [2024-05-14 15:53:22,306] multiqc [DEBUG ] No samples found: snpeff [2024-05-14 15:53:22,318] multiqc [DEBUG ] No samples found: gatk [2024-05-14 15:53:22,325] multiqc [DEBUG ] No samples found: htseq [2024-05-14 15:53:22,336] multiqc [DEBUG ] No samples found: bcftools [2024-05-14 15:53:22,341] multiqc [DEBUG ] No samples found: featureCounts [2024-05-14 15:53:22,354] multiqc [DEBUG ] No samples found: fgbio [2024-05-14 15:53:22,378] multiqc [DEBUG ] No samples found: dragen [2024-05-14 15:53:22,384] multiqc [DEBUG ] No samples found: dedup [2024-05-14 15:53:22,392] multiqc [DEBUG ] No samples found: damageprofiler [2024-05-14 15:53:22,436] multiqc [DEBUG ] No samples found: biobambam2 [2024-05-14 15:53:22,444] multiqc [DEBUG ] No samples found: mtnucratio [2024-05-14 15:53:22,447] multiqc [DEBUG ] No samples found: picard [2024-05-14 15:53:22,454] multiqc [DEBUG ] No samples found: prokka [2024-05-14 15:53:22,460] multiqc [DEBUG ] No samples found: samblaster [2024-05-14 15:53:22,473] multiqc [DEBUG ] No samples found: samtools [2024-05-14 15:53:22,479] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-05-14 15:53:22,488] multiqc [DEBUG ] No samples found: bamtools [2024-05-14 15:53:22,493] multiqc [DEBUG ] No samples found: jellyfish [2024-05-14 15:53:22,508] multiqc [DEBUG ] No samples found: vcftools [2024-05-14 15:53:22,516] multiqc [DEBUG ] No samples found: longranger [2024-05-14 15:53:22,524] multiqc [DEBUG ] No samples found: stacks [2024-05-14 15:53:22,532] multiqc [DEBUG ] No samples found: varscan2 [2024-05-14 15:53:22,559] multiqc [DEBUG ] No samples found: bbmap [2024-05-14 15:53:22,567] multiqc [DEBUG ] No samples found: bismark [2024-05-14 15:53:22,575] multiqc [DEBUG ] No samples found: biscuit [2024-05-14 15:53:22,581] multiqc [DEBUG ] No samples found: hicexplorer [2024-05-14 15:53:22,587] multiqc [DEBUG ] No samples found: hicup [2024-05-14 15:53:22,596] multiqc [DEBUG ] No samples found: hicpro [2024-05-14 15:53:22,604] multiqc [DEBUG ] No samples found: salmon [2024-05-14 15:53:22,610] multiqc [DEBUG ] No samples found: kallisto [2024-05-14 15:53:22,617] multiqc [DEBUG ] No samples found: slamdunk [2024-05-14 15:53:22,623] multiqc [DEBUG ] No samples found: star [2024-05-14 15:53:22,629] multiqc [DEBUG ] No samples found: hisat2 [2024-05-14 15:53:22,635] multiqc [DEBUG ] No samples found: tophat [2024-05-14 15:53:22,643] multiqc [DEBUG ] No samples found: bowtie2 [2024-05-14 15:53:22,651] multiqc [DEBUG ] No samples found: bowtie1 [2024-05-14 15:53:22,660] multiqc [DEBUG ] No samples found: snpsplit [2024-05-14 15:53:22,666] multiqc [DEBUG ] No samples found: kat [2024-05-14 15:53:22,674] multiqc [DEBUG ] No samples found: leehom [2024-05-14 15:53:22,682] multiqc [DEBUG ] No samples found: adapterRemoval [2024-05-14 15:53:22,689] multiqc [DEBUG ] No samples found: clipandmerge [2024-05-14 15:53:22,695] multiqc [DEBUG ] No samples found: cutadapt [2024-05-14 15:53:22,703] multiqc [DEBUG ] No samples found: flexbar [2024-05-14 15:53:22,712] multiqc [DEBUG ] No samples found: kaiju [2024-05-14 15:53:22,718] multiqc [DEBUG ] No samples found: kraken [2024-05-14 15:53:22,725] multiqc [DEBUG ] No samples found: malt [2024-05-14 15:53:22,732] multiqc [DEBUG ] No samples found: trimmomatic [2024-05-14 15:53:22,739] multiqc [DEBUG ] No samples found: sickle [2024-05-14 15:53:22,746] multiqc [DEBUG ] No samples found: skewer [2024-05-14 15:53:22,753] multiqc [DEBUG ] No samples found: sortmerna [2024-05-14 15:53:22,760] multiqc [DEBUG ] No samples found: biobloomtools [2024-05-14 15:53:22,768] multiqc [DEBUG ] No samples found: fastq_screen [2024-05-14 15:53:22,776] multiqc [DEBUG ] No samples found: afterqc [2024-05-14 15:53:22,782] multiqc [DEBUG ] No samples found: fastp [2024-05-14 15:53:22,891] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2024-05-14 15:53:23,007] multiqc [DEBUG ] No samples found: pycoqc [2024-05-14 15:53:23,013] multiqc [DEBUG ] No samples found: minionqc [2024-05-14 15:53:23,020] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-05-14 15:53:23,028] multiqc [DEBUG ] No samples found: clusterflow [2024-05-14 15:53:23,036] multiqc [DEBUG ] No samples found: bcl2fastq [2024-05-14 15:53:23,044] multiqc [DEBUG ] No samples found: interop [2024-05-14 15:53:23,051] multiqc [DEBUG ] No samples found: ivar [2024-05-14 15:53:23,058] multiqc [DEBUG ] No samples found: flash [2024-05-14 15:53:23,067] multiqc [DEBUG ] No samples found: seqyclean [2024-05-14 15:53:23,067] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-05-14 15:53:23,067] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-05-14 15:53:23,067] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-05-14 15:53:23,068] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-05-14 15:53:23,081] multiqc [INFO ] Compressing plot data [2024-05-14 15:53:23,262] multiqc [INFO ] Report : multiqc_report.html [2024-05-14 15:53:23,262] multiqc [INFO ] Data : multiqc_data [2024-05-14 15:53:23,262] multiqc [DEBUG ] Moving data file from '/state/partition1/job-46482234/tmp10_2gkuy/multiqc_data' to '/vast/gencore/GENEFLOW/work/4a/59a516ba480c5140afc685e71f3106/1/multiqc_data' [2024-05-14 15:53:23,442] multiqc [INFO ] MultiQC complete