[2024-06-30 09:23:11,350] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-30 09:23:11,350] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-30 09:23:11,351] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-30 09:23:11,353] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-30 09:23:11,353] 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}} [2024-06-30 09:23:11,353] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-30 09:23:11,389] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-30 09:23:11,389] multiqc [INFO ] This is MultiQC v1.9 [2024-06-30 09:23:11,389] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-30 09:23:11,389] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/94/3ebf968e24a9f1a716cb2ef100cafd/merged [2024-06-30 09:23:11,389] multiqc [INFO ] Template : default [2024-06-30 09:23:11,389] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-30 09:23:11,389] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/94/3ebf968e24a9f1a716cb2ef100cafd/merged [2024-06-30 09:23:11,390] 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 [2024-06-30 09:23:11,390] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-48078027/tmp8gbtgv8g [2024-06-30 09:23:11,515] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AA86_S2_fastqc.html [2024-06-30 09:23:11,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AA86_S2_fastqc.html [2024-06-30 09:23:11,590] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AA87_S2_fastqc.html [2024-06-30 09:23:11,598] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AA87_S2_fastqc.html [2024-06-30 09:23:11,666] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AA88_S2_fastqc.html [2024-06-30 09:23:11,674] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AA88_S2_fastqc.html [2024-06-30 09:23:11,739] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AS02_S2_fastqc.html [2024-06-30 09:23:11,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AS02_S2_fastqc.html [2024-06-30 09:23:11,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AS03_S2_fastqc.html [2024-06-30 09:23:11,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n01_NYUEB_HiC_AS03_S2_fastqc.html [2024-06-30 09:23:11,879] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n01_undetermined_fastqc.html [2024-06-30 09:23:11,886] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n01_undetermined_fastqc.html [2024-06-30 09:23:11,949] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AA86_S2_fastqc.html [2024-06-30 09:23:11,956] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AA86_S2_fastqc.html [2024-06-30 09:23:12,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AA87_S2_fastqc.html [2024-06-30 09:23:12,025] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AA87_S2_fastqc.html [2024-06-30 09:23:12,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AA88_S2_fastqc.html [2024-06-30 09:23:12,097] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AA88_S2_fastqc.html [2024-06-30 09:23:12,159] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AS02_S2_fastqc.html [2024-06-30 09:23:12,166] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AS02_S2_fastqc.html [2024-06-30 09:23:12,230] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AS03_S2_fastqc.html [2024-06-30 09:23:12,236] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n02_NYUEB_HiC_AS03_S2_fastqc.html [2024-06-30 09:23:12,306] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW7G5DMXY_n02_undetermined_fastqc.html [2024-06-30 09:23:12,313] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW7G5DMXY_n02_undetermined_fastqc.html [2024-06-30 09:23:12,821] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-30 09:23:12,823] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-30 09:23:12,834] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2024-06-30 09:23:12,836] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-30 09:23:12,846] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-30 09:23:12,850] multiqc [DEBUG ] No samples found: conpair [2024-06-30 09:23:12,855] multiqc [DEBUG ] No samples found: peddy [2024-06-30 09:23:12,860] multiqc [DEBUG ] No samples found: somalier [2024-06-30 09:23:12,864] multiqc [DEBUG ] No samples found: methylQA [2024-06-30 09:23:12,873] multiqc [DEBUG ] No samples found: mosdepth [2024-06-30 09:23:12,877] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-30 09:23:12,881] multiqc [DEBUG ] No samples found: qualimap [2024-06-30 09:23:12,885] multiqc [DEBUG ] No samples found: preseq [2024-06-30 09:23:12,890] multiqc [DEBUG ] No samples found: quast [2024-06-30 09:23:12,895] multiqc [DEBUG ] No samples found: qorts [2024-06-30 09:23:12,900] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-30 09:23:12,904] multiqc [DEBUG ] No samples found: rockhopper [2024-06-30 09:23:12,909] multiqc [DEBUG ] No samples found: rsem [2024-06-30 09:23:12,922] multiqc [DEBUG ] No samples found: rseqc [2024-06-30 09:23:12,927] multiqc [DEBUG ] No samples found: busco [2024-06-30 09:23:12,931] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-30 09:23:12,935] multiqc [DEBUG ] No samples found: disambiguate [2024-06-30 09:23:12,940] multiqc [DEBUG ] No samples found: supernova [2024-06-30 09:23:12,954] multiqc [DEBUG ] No samples found: deeptools [2024-06-30 09:23:12,959] multiqc [DEBUG ] No samples found: sargasso [2024-06-30 09:23:12,964] multiqc [DEBUG ] No samples found: verifybamid [2024-06-30 09:23:12,973] multiqc [DEBUG ] No samples found: mirtrace [2024-06-30 09:23:12,978] multiqc [DEBUG ] No samples found: happy [2024-06-30 09:23:12,982] multiqc [DEBUG ] No samples found: mirtop [2024-06-30 09:23:12,988] multiqc [DEBUG ] No samples found: homer [2024-06-30 09:23:12,993] multiqc [DEBUG ] No samples found: macs2 [2024-06-30 09:23:12,997] multiqc [DEBUG ] No samples found: theta2 [2024-06-30 09:23:13,002] multiqc [DEBUG ] No samples found: snpeff [2024-06-30 09:23:13,008] multiqc [DEBUG ] No samples found: gatk [2024-06-30 09:23:13,013] multiqc [DEBUG ] No samples found: htseq [2024-06-30 09:23:13,019] multiqc [DEBUG ] No samples found: bcftools [2024-06-30 09:23:13,023] multiqc [DEBUG ] No samples found: featureCounts [2024-06-30 09:23:13,030] multiqc [DEBUG ] No samples found: fgbio [2024-06-30 09:23:13,044] multiqc [DEBUG ] No samples found: dragen [2024-06-30 09:23:13,048] multiqc [DEBUG ] No samples found: dedup [2024-06-30 09:23:13,052] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-30 09:23:13,080] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-30 09:23:13,085] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-30 09:23:13,087] multiqc [DEBUG ] No samples found: picard [2024-06-30 09:23:13,091] multiqc [DEBUG ] No samples found: prokka [2024-06-30 09:23:13,096] multiqc [DEBUG ] No samples found: samblaster [2024-06-30 09:23:13,104] multiqc [DEBUG ] No samples found: samtools [2024-06-30 09:23:13,108] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-30 09:23:13,114] multiqc [DEBUG ] No samples found: bamtools [2024-06-30 09:23:13,118] multiqc [DEBUG ] No samples found: jellyfish [2024-06-30 09:23:13,126] multiqc [DEBUG ] No samples found: vcftools [2024-06-30 09:23:13,131] multiqc [DEBUG ] No samples found: longranger [2024-06-30 09:23:13,136] multiqc [DEBUG ] No samples found: stacks [2024-06-30 09:23:13,140] multiqc [DEBUG ] No samples found: varscan2 [2024-06-30 09:23:13,159] multiqc [DEBUG ] No samples found: bbmap [2024-06-30 09:23:13,164] multiqc [DEBUG ] No samples found: bismark [2024-06-30 09:23:13,169] multiqc [DEBUG ] No samples found: biscuit [2024-06-30 09:23:13,174] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-30 09:23:13,179] multiqc [DEBUG ] No samples found: hicup [2024-06-30 09:23:13,183] multiqc [DEBUG ] No samples found: hicpro [2024-06-30 09:23:13,188] multiqc [DEBUG ] No samples found: salmon [2024-06-30 09:23:13,192] multiqc [DEBUG ] No samples found: kallisto [2024-06-30 09:23:13,197] multiqc [DEBUG ] No samples found: slamdunk [2024-06-30 09:23:13,202] multiqc [DEBUG ] No samples found: star [2024-06-30 09:23:13,206] multiqc [DEBUG ] No samples found: hisat2 [2024-06-30 09:23:13,211] multiqc [DEBUG ] No samples found: tophat [2024-06-30 09:23:13,215] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-30 09:23:13,220] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-30 09:23:13,224] multiqc [DEBUG ] No samples found: snpsplit [2024-06-30 09:23:13,228] multiqc [DEBUG ] No samples found: kat [2024-06-30 09:23:13,232] multiqc [DEBUG ] No samples found: leehom [2024-06-30 09:23:13,237] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-30 09:23:13,241] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-30 09:23:13,246] multiqc [DEBUG ] No samples found: cutadapt [2024-06-30 09:23:13,250] multiqc [DEBUG ] No samples found: flexbar [2024-06-30 09:23:13,255] multiqc [DEBUG ] No samples found: kaiju [2024-06-30 09:23:13,259] multiqc [DEBUG ] No samples found: kraken [2024-06-30 09:23:13,263] multiqc [DEBUG ] No samples found: malt [2024-06-30 09:23:13,268] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-30 09:23:13,273] multiqc [DEBUG ] No samples found: sickle [2024-06-30 09:23:13,277] multiqc [DEBUG ] No samples found: skewer [2024-06-30 09:23:13,281] multiqc [DEBUG ] No samples found: sortmerna [2024-06-30 09:23:13,285] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-30 09:23:13,289] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-30 09:23:13,294] multiqc [DEBUG ] No samples found: afterqc [2024-06-30 09:23:13,299] multiqc [DEBUG ] No samples found: fastp [2024-06-30 09:23:14,501] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2024-06-30 09:23:14,647] multiqc [DEBUG ] No samples found: pycoqc [2024-06-30 09:23:14,652] multiqc [DEBUG ] No samples found: minionqc [2024-06-30 09:23:14,656] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-30 09:23:14,661] multiqc [DEBUG ] No samples found: clusterflow [2024-06-30 09:23:14,666] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-30 09:23:14,670] multiqc [DEBUG ] No samples found: interop [2024-06-30 09:23:14,674] multiqc [DEBUG ] No samples found: ivar [2024-06-30 09:23:14,678] multiqc [DEBUG ] No samples found: flash [2024-06-30 09:23:14,683] multiqc [DEBUG ] No samples found: seqyclean [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 09:23:14,683] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-30 09:23:14,684] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-30 09:23:14,699] multiqc [INFO ] Compressing plot data [2024-06-30 09:23:14,920] multiqc [INFO ] Report : multiqc_report.html [2024-06-30 09:23:14,920] multiqc [INFO ] Data : multiqc_data [2024-06-30 09:23:14,920] multiqc [DEBUG ] Moving data file from '/state/partition1/job-48078027/tmp8gbtgv8g/multiqc_data' to '/vast/gencore/GENEFLOW/work/94/3ebf968e24a9f1a716cb2ef100cafd/merged/multiqc_data' [2024-06-30 09:23:15,080] multiqc [INFO ] MultiQC complete