[2024-02-09 14:45:23,102] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-09 14:45:23,102] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-09 14:45:23,103] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-09 14:45:23,105] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-09 14:45:23,105] 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}} [2024-02-09 14:45:23,105] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-09 14:45:24,319] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-02-09 14:45:24,319] multiqc [INFO ] This is MultiQC v1.9 [2024-02-09 14:45:24,319] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-09 14:45:24,319] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/a6/1ea84a0673e9e27f240d6947ed82ef/1 [2024-02-09 14:45:24,319] multiqc [INFO ] Template : default [2024-02-09 14:45:24,319] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-09 14:45:24,319] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/a6/1ea84a0673e9e27f240d6947ed82ef/1 [2024-02-09 14:45:24,320] 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 [2024-02-09 14:45:24,320] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42762830/tmpcfut29ol [2024-02-09 14:45:24,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n01_K562_4sU_200_01h_1_fastqc.html [2024-02-09 14:45:24,475] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n01_K562_4sU_200_01h_1_fastqc.html [2024-02-09 14:45:24,547] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search 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14:45:28,159] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_K562_6sG_1000_24h_1_fastqc.html [2024-02-09 14:45:28,167] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_K562_6sG_1000_24h_1_fastqc.html [2024-02-09 14:45:28,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_K562_6sG_200_24h_1_fastqc.html [2024-02-09 14:45:28,246] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_K562_6sG_200_24h_1_fastqc.html [2024-02-09 14:45:28,316] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_RS_4sU_1000_15h_2_fastqc.html [2024-02-09 14:45:28,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_RS_4sU_1000_15h_2_fastqc.html [2024-02-09 14:45:28,390] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_RS_4sU_1000_24h_2_fastqc.html [2024-02-09 14:45:28,398] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_RS_4sU_1000_24h_2_fastqc.html [2024-02-09 14:45:28,465] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_undetermined_fastqc.html [2024-02-09 14:45:28,472] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFJ94_l01_n02_undetermined_fastqc.html [2024-02-09 14:45:28,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-09 14:45:28,540] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-09 14:45:28,540] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-09 14:45:28,540] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-09 14:45:28,540] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-09 14:45:28,540] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-09 14:45:28,540] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-09 14:45:29,443] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-09 14:45:29,445] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-09 14:45:29,468] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-02-09 14:45:29,469] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-09 14:45:29,480] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-09 14:45:29,486] multiqc [DEBUG ] No samples found: conpair [2024-02-09 14:45:29,494] multiqc [DEBUG ] No samples found: peddy [2024-02-09 14:45:29,501] multiqc [DEBUG ] No samples found: somalier [2024-02-09 14:45:29,508] multiqc [DEBUG ] No samples found: methylQA [2024-02-09 14:45:29,520] multiqc [DEBUG ] No samples found: mosdepth [2024-02-09 14:45:29,527] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-09 14:45:29,531] multiqc [DEBUG ] No samples found: qualimap [2024-02-09 14:45:29,538] multiqc [DEBUG ] No samples found: preseq [2024-02-09 14:45:29,544] multiqc [DEBUG ] No samples found: quast [2024-02-09 14:45:29,551] multiqc [DEBUG ] No samples found: qorts [2024-02-09 14:45:29,558] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-09 14:45:29,565] multiqc [DEBUG ] No samples found: rockhopper [2024-02-09 14:45:29,571] multiqc [DEBUG ] No samples found: rsem [2024-02-09 14:45:29,590] multiqc [DEBUG ] No samples found: rseqc [2024-02-09 14:45:29,596] multiqc [DEBUG ] No samples found: busco [2024-02-09 14:45:29,602] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-09 14:45:29,608] multiqc [DEBUG ] No samples found: disambiguate [2024-02-09 14:45:29,615] multiqc [DEBUG ] No samples found: supernova [2024-02-09 14:45:29,639] multiqc [DEBUG ] No samples found: deeptools [2024-02-09 14:45:29,645] multiqc [DEBUG ] No samples found: sargasso [2024-02-09 14:45:29,651] multiqc [DEBUG ] No samples found: verifybamid [2024-02-09 14:45:29,657] multiqc [DEBUG ] No samples found: mirtrace [2024-02-09 14:45:29,663] multiqc [DEBUG ] No samples found: happy [2024-02-09 14:45:29,670] multiqc [DEBUG ] No samples found: mirtop [2024-02-09 14:45:29,679] multiqc [DEBUG ] No samples found: homer [2024-02-09 14:45:29,685] multiqc [DEBUG ] No samples found: macs2 [2024-02-09 14:45:29,691] multiqc [DEBUG ] No samples found: theta2 [2024-02-09 14:45:29,697] multiqc [DEBUG ] No samples found: snpeff [2024-02-09 14:45:29,706] multiqc [DEBUG ] No samples found: gatk [2024-02-09 14:45:29,712] multiqc [DEBUG ] No samples found: htseq [2024-02-09 14:45:29,719] multiqc [DEBUG ] No samples found: bcftools [2024-02-09 14:45:29,724] multiqc [DEBUG ] No samples found: featureCounts [2024-02-09 14:45:29,732] multiqc [DEBUG ] No samples found: fgbio [2024-02-09 14:45:29,756] multiqc [DEBUG ] No samples found: dragen [2024-02-09 14:45:29,762] multiqc [DEBUG ] No samples found: dedup [2024-02-09 14:45:29,769] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-09 14:45:29,806] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-09 14:45:29,813] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-09 14:45:29,815] multiqc [DEBUG ] No samples found: picard [2024-02-09 14:45:29,821] multiqc [DEBUG ] No samples found: prokka [2024-02-09 14:45:29,826] multiqc [DEBUG ] No samples found: samblaster [2024-02-09 14:45:29,845] multiqc [DEBUG ] No samples found: samtools [2024-02-09 14:45:29,854] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-09 14:45:29,862] multiqc [DEBUG ] No samples found: bamtools [2024-02-09 14:45:29,871] multiqc [DEBUG ] No samples found: jellyfish [2024-02-09 14:45:29,885] multiqc [DEBUG ] No samples found: vcftools [2024-02-09 14:45:29,898] multiqc [DEBUG ] No samples found: longranger [2024-02-09 14:45:29,905] multiqc [DEBUG ] No samples found: stacks [2024-02-09 14:45:29,915] multiqc [DEBUG ] No samples found: varscan2 [2024-02-09 14:45:29,949] multiqc [DEBUG ] No samples found: bbmap [2024-02-09 14:45:29,955] multiqc [DEBUG ] No samples found: bismark [2024-02-09 14:45:29,961] multiqc [DEBUG ] No samples found: biscuit [2024-02-09 14:45:29,967] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-09 14:45:29,974] multiqc [DEBUG ] No samples found: hicup [2024-02-09 14:45:29,980] multiqc [DEBUG ] No samples found: hicpro [2024-02-09 14:45:29,986] multiqc [DEBUG ] No samples found: salmon [2024-02-09 14:45:29,992] multiqc [DEBUG ] No samples found: kallisto [2024-02-09 14:45:29,999] multiqc [DEBUG ] No samples found: slamdunk [2024-02-09 14:45:30,005] multiqc [DEBUG ] No samples found: star [2024-02-09 14:45:30,012] multiqc [DEBUG ] No samples found: hisat2 [2024-02-09 14:45:30,018] multiqc [DEBUG ] No samples found: tophat [2024-02-09 14:45:30,024] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-09 14:45:30,030] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-09 14:45:30,037] multiqc [DEBUG ] No samples found: snpsplit [2024-02-09 14:45:30,042] multiqc [DEBUG ] No samples found: kat [2024-02-09 14:45:30,048] multiqc [DEBUG ] No samples found: leehom [2024-02-09 14:45:30,055] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-09 14:45:30,061] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-09 14:45:30,068] multiqc [DEBUG ] No samples found: cutadapt [2024-02-09 14:45:30,073] multiqc [DEBUG ] No samples found: flexbar [2024-02-09 14:45:30,079] multiqc [DEBUG ] No samples found: kaiju [2024-02-09 14:45:30,085] multiqc [DEBUG ] No samples found: kraken [2024-02-09 14:45:30,091] multiqc [DEBUG ] No samples found: malt [2024-02-09 14:45:30,098] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-09 14:45:30,104] multiqc [DEBUG ] No samples found: sickle [2024-02-09 14:45:30,110] multiqc [DEBUG ] No samples found: skewer [2024-02-09 14:45:30,116] multiqc [DEBUG ] No samples found: sortmerna [2024-02-09 14:45:30,122] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-09 14:45:30,129] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-09 14:45:30,134] multiqc [DEBUG ] No samples found: afterqc [2024-02-09 14:45:30,140] multiqc [DEBUG ] No samples found: fastp [2024-02-09 14:45:30,680] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2024-02-09 14:45:31,848] multiqc [DEBUG ] No samples found: pycoqc [2024-02-09 14:45:31,854] multiqc [DEBUG ] No samples found: minionqc [2024-02-09 14:45:31,861] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-09 14:45:31,867] multiqc [DEBUG ] No samples found: clusterflow [2024-02-09 14:45:31,874] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-09 14:45:31,881] multiqc [DEBUG ] No samples found: interop [2024-02-09 14:45:31,887] multiqc [DEBUG ] No samples found: ivar [2024-02-09 14:45:31,893] multiqc [DEBUG ] No samples found: flash [2024-02-09 14:45:31,899] multiqc [DEBUG ] No samples found: seqyclean [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-09 14:45:31,900] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-09 14:45:31,901] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-09 14:45:31,960] multiqc [INFO ] Compressing plot data [2024-02-09 14:45:32,773] multiqc [INFO ] Report : multiqc_report.html [2024-02-09 14:45:32,773] multiqc [INFO ] Data : multiqc_data [2024-02-09 14:45:32,773] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42762830/tmpcfut29ol/multiqc_data' to '/vast/gencore/GENEFLOW/work/a6/1ea84a0673e9e27f240d6947ed82ef/1/multiqc_data' [2024-02-09 14:45:32,989] multiqc [INFO ] MultiQC complete