[2024-07-10 05:23:27,699] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-07-10 05:23:27,699] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-07-10 05:23:27,699] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-07-10 05:23:27,702] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-07-10 05:23:27,702] 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}} [2024-07-10 05:23:27,702] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-10 05:23:27,737] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-07-10 05:23:27,737] multiqc [INFO ] This is MultiQC v1.9 [2024-07-10 05:23:27,737] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-10 05:23:27,737] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/82/2a448785c8f141a6a060976612eaff/merged [2024-07-10 05:23:27,737] multiqc [INFO ] Template : default [2024-07-10 05:23:27,737] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-07-10 05:23:27,737] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/82/2a448785c8f141a6a060976612eaff/merged [2024-07-10 05:23:27,737] 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 [2024-07-10 05:23:27,738] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-48331731/tmpm_vl1b8j [2024-07-10 05:23:27,859] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_NT_10_fastqc.html [2024-07-10 05:23:27,867] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_NT_10_fastqc.html [2024-07-10 05:23:27,935] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_NT_50_fastqc.html [2024-07-10 05:23:27,941] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_NT_50_fastqc.html [2024-07-10 05:23:28,008] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g1_10_fastqc.html [2024-07-10 05:23:28,014] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g1_10_fastqc.html [2024-07-10 05:23:28,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g1_50_fastqc.html [2024-07-10 05:23:28,086] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g1_50_fastqc.html [2024-07-10 05:23:28,149] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g2_10_fastqc.html [2024-07-10 05:23:28,155] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g2_10_fastqc.html [2024-07-10 05:23:28,223] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g2_50_fastqc.html [2024-07-10 05:23:28,229] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n01_HT29_g2_50_fastqc.html [2024-07-10 05:23:28,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n01_undetermined_fastqc.html [2024-07-10 05:23:28,310] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n01_undetermined_fastqc.html [2024-07-10 05:23:28,377] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_NT_10_fastqc.html [2024-07-10 05:23:28,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_NT_10_fastqc.html [2024-07-10 05:23:28,451] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_NT_50_fastqc.html [2024-07-10 05:23:28,458] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_NT_50_fastqc.html [2024-07-10 05:23:28,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g1_10_fastqc.html [2024-07-10 05:23:28,531] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g1_10_fastqc.html [2024-07-10 05:23:28,597] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g1_50_fastqc.html [2024-07-10 05:23:28,603] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g1_50_fastqc.html [2024-07-10 05:23:28,667] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g2_10_fastqc.html [2024-07-10 05:23:28,674] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g2_10_fastqc.html [2024-07-10 05:23:28,738] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g2_50_fastqc.html [2024-07-10 05:23:28,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n02_HT29_g2_50_fastqc.html [2024-07-10 05:23:28,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV77LBGXV_n02_undetermined_fastqc.html [2024-07-10 05:23:28,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV77LBGXV_n02_undetermined_fastqc.html [2024-07-10 05:23:29,164] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-10 05:23:29,166] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-10 05:23:29,178] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2024-07-10 05:23:29,180] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-07-10 05:23:29,190] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-07-10 05:23:29,194] multiqc [DEBUG ] No samples found: conpair [2024-07-10 05:23:29,199] multiqc [DEBUG ] No samples found: peddy [2024-07-10 05:23:29,204] multiqc [DEBUG ] No samples found: somalier [2024-07-10 05:23:29,209] multiqc [DEBUG ] No samples found: methylQA [2024-07-10 05:23:29,217] multiqc [DEBUG ] No samples found: mosdepth [2024-07-10 05:23:29,221] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-07-10 05:23:29,225] multiqc [DEBUG ] No samples found: qualimap [2024-07-10 05:23:29,229] multiqc [DEBUG ] No samples found: preseq [2024-07-10 05:23:29,234] multiqc [DEBUG ] No samples found: quast [2024-07-10 05:23:29,239] multiqc [DEBUG ] No samples found: qorts [2024-07-10 05:23:29,243] multiqc [DEBUG ] No samples found: rna_seqc [2024-07-10 05:23:29,248] multiqc [DEBUG ] No samples found: rockhopper [2024-07-10 05:23:29,253] multiqc [DEBUG ] No samples found: rsem [2024-07-10 05:23:29,267] multiqc [DEBUG ] No samples found: rseqc [2024-07-10 05:23:29,271] multiqc [DEBUG ] No samples found: busco [2024-07-10 05:23:29,276] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-07-10 05:23:29,280] multiqc [DEBUG ] No samples found: disambiguate [2024-07-10 05:23:29,284] multiqc [DEBUG ] No samples found: supernova [2024-07-10 05:23:29,297] multiqc [DEBUG ] No samples found: deeptools [2024-07-10 05:23:29,302] multiqc [DEBUG ] No samples found: sargasso [2024-07-10 05:23:29,307] multiqc [DEBUG ] No samples found: verifybamid [2024-07-10 05:23:29,315] multiqc [DEBUG ] No samples found: mirtrace [2024-07-10 05:23:29,319] multiqc [DEBUG ] No samples found: happy [2024-07-10 05:23:29,324] multiqc [DEBUG ] No samples found: mirtop [2024-07-10 05:23:29,333] multiqc [DEBUG ] No samples found: homer [2024-07-10 05:23:29,340] multiqc [DEBUG ] No samples found: macs2 [2024-07-10 05:23:29,344] multiqc [DEBUG ] No samples found: theta2 [2024-07-10 05:23:29,349] multiqc [DEBUG ] No samples found: snpeff [2024-07-10 05:23:29,356] multiqc [DEBUG ] No samples found: gatk [2024-07-10 05:23:29,361] multiqc [DEBUG ] No samples found: htseq [2024-07-10 05:23:29,367] multiqc [DEBUG ] No samples found: bcftools [2024-07-10 05:23:29,371] multiqc [DEBUG ] No samples found: featureCounts [2024-07-10 05:23:29,378] multiqc [DEBUG ] No samples found: fgbio [2024-07-10 05:23:29,391] multiqc [DEBUG ] No samples found: dragen [2024-07-10 05:23:29,396] multiqc [DEBUG ] No samples found: dedup [2024-07-10 05:23:29,401] multiqc [DEBUG ] No samples found: damageprofiler [2024-07-10 05:23:29,427] multiqc [DEBUG ] No samples found: biobambam2 [2024-07-10 05:23:29,432] multiqc [DEBUG ] No samples found: mtnucratio [2024-07-10 05:23:29,434] multiqc [DEBUG ] No samples found: picard [2024-07-10 05:23:29,438] multiqc [DEBUG ] No samples found: prokka [2024-07-10 05:23:29,443] multiqc [DEBUG ] No samples found: samblaster [2024-07-10 05:23:29,451] multiqc [DEBUG ] No samples found: samtools [2024-07-10 05:23:29,455] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-07-10 05:23:29,460] multiqc [DEBUG ] No samples found: bamtools [2024-07-10 05:23:29,464] multiqc [DEBUG ] No samples found: jellyfish [2024-07-10 05:23:29,472] multiqc [DEBUG ] No samples found: vcftools [2024-07-10 05:23:29,476] multiqc [DEBUG ] No samples found: longranger [2024-07-10 05:23:29,481] multiqc [DEBUG ] No samples found: stacks [2024-07-10 05:23:29,486] multiqc [DEBUG ] No samples found: varscan2 [2024-07-10 05:23:29,500] multiqc [DEBUG ] No samples found: bbmap [2024-07-10 05:23:29,505] multiqc [DEBUG ] No samples found: bismark [2024-07-10 05:23:29,510] multiqc [DEBUG ] No samples found: biscuit [2024-07-10 05:23:29,515] multiqc [DEBUG ] No samples found: hicexplorer [2024-07-10 05:23:29,520] multiqc [DEBUG ] No samples found: hicup [2024-07-10 05:23:29,525] multiqc [DEBUG ] No samples found: hicpro [2024-07-10 05:23:29,529] multiqc [DEBUG ] No samples found: salmon [2024-07-10 05:23:29,534] multiqc [DEBUG ] No samples found: kallisto [2024-07-10 05:23:29,538] multiqc [DEBUG ] No samples found: slamdunk [2024-07-10 05:23:29,546] multiqc [DEBUG ] No samples found: star [2024-07-10 05:23:29,551] multiqc [DEBUG ] No samples found: hisat2 [2024-07-10 05:23:29,555] multiqc [DEBUG ] No samples found: tophat [2024-07-10 05:23:29,560] multiqc [DEBUG ] No samples found: bowtie2 [2024-07-10 05:23:29,565] multiqc [DEBUG ] No samples found: bowtie1 [2024-07-10 05:23:29,570] multiqc [DEBUG ] No samples found: snpsplit [2024-07-10 05:23:29,574] multiqc [DEBUG ] No samples found: kat [2024-07-10 05:23:29,578] multiqc [DEBUG ] No samples found: leehom [2024-07-10 05:23:29,583] multiqc [DEBUG ] No samples found: adapterRemoval [2024-07-10 05:23:29,587] multiqc [DEBUG ] No samples found: clipandmerge [2024-07-10 05:23:29,592] multiqc [DEBUG ] No samples found: cutadapt [2024-07-10 05:23:29,596] multiqc [DEBUG ] No samples found: flexbar [2024-07-10 05:23:29,601] multiqc [DEBUG ] No samples found: kaiju [2024-07-10 05:23:29,605] multiqc [DEBUG ] No samples found: kraken [2024-07-10 05:23:29,610] multiqc [DEBUG ] No samples found: malt [2024-07-10 05:23:29,615] multiqc [DEBUG ] No samples found: trimmomatic [2024-07-10 05:23:29,619] multiqc [DEBUG ] No samples found: sickle [2024-07-10 05:23:29,624] multiqc [DEBUG ] No samples found: skewer [2024-07-10 05:23:29,628] multiqc [DEBUG ] No samples found: sortmerna [2024-07-10 05:23:29,632] multiqc [DEBUG ] No samples found: biobloomtools [2024-07-10 05:23:29,637] multiqc [DEBUG ] No samples found: fastq_screen [2024-07-10 05:23:29,642] multiqc [DEBUG ] No samples found: afterqc [2024-07-10 05:23:29,646] multiqc [DEBUG ] No samples found: fastp [2024-07-10 05:23:30,368] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2024-07-10 05:23:30,453] multiqc [DEBUG ] No samples found: pycoqc [2024-07-10 05:23:30,458] multiqc [DEBUG ] No samples found: minionqc [2024-07-10 05:23:30,462] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-07-10 05:23:30,467] multiqc [DEBUG ] No samples found: clusterflow [2024-07-10 05:23:30,472] multiqc [DEBUG ] No samples found: bcl2fastq [2024-07-10 05:23:30,477] multiqc [DEBUG ] No samples found: interop [2024-07-10 05:23:30,481] multiqc [DEBUG ] No samples found: ivar [2024-07-10 05:23:30,487] multiqc [DEBUG ] No samples found: flash [2024-07-10 05:23:30,495] multiqc [DEBUG ] No samples found: seqyclean [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-07-10 05:23:30,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-07-10 05:23:30,496] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-07-10 05:23:30,496] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-07-10 05:23:30,496] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-07-10 05:23:30,496] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-07-10 05:23:30,496] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-07-10 05:23:30,513] multiqc [INFO ] Compressing plot data [2024-07-10 05:23:30,740] multiqc [INFO ] Report : multiqc_report.html [2024-07-10 05:23:30,740] multiqc [INFO ] Data : multiqc_data [2024-07-10 05:23:30,740] multiqc [DEBUG ] Moving data file from '/state/partition1/job-48331731/tmpm_vl1b8j/multiqc_data' to '/vast/gencore/GENEFLOW/work/82/2a448785c8f141a6a060976612eaff/merged/multiqc_data' [2024-07-10 05:23:30,950] multiqc [INFO ] MultiQC complete