[2023-10-17 10:16:59,041] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-10-17 10:16:59,042] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-10-17 10:16:59,042] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-10-17 10:16:59,045] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-10-17 10:16:59,045] 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}} [2023-10-17 10:16:59,045] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-17 10:17:00,212] multiqc [WARNING] MultiQC Version v1.16 now available! [2023-10-17 10:17:00,212] multiqc [INFO ] This is MultiQC v1.9 [2023-10-17 10:17:00,212] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-17 10:17:00,212] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/dc/dd772c2f757a86511c425ed8969a0a/merged [2023-10-17 10:17:00,212] multiqc [INFO ] Template : default [2023-10-17 10:17:00,212] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-10-17 10:17:00,212] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/dc/dd772c2f757a86511c425ed8969a0a/merged [2023-10-17 10:17:00,213] 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 [2023-10-17 10:17:00,213] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-38952089/tmpbruj8pi5 [2023-10-17 10:17:00,339] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K1_fastqc.html [2023-10-17 10:17:00,352] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K1_fastqc.html [2023-10-17 10:17:00,430] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K2_fastqc.html [2023-10-17 10:17:00,438] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K2_fastqc.html [2023-10-17 10:17:00,509] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N1_fastqc.html [2023-10-17 10:17:00,517] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N1_fastqc.html [2023-10-17 10:17:00,591] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N2_fastqc.html [2023-10-17 10:17:00,599] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N2_fastqc.html [2023-10-17 10:17:00,679] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_undetermined_fastqc.html [2023-10-17 10:17:00,698] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_undetermined_fastqc.html [2023-10-17 10:17:00,770] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K1_fastqc.html [2023-10-17 10:17:00,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K1_fastqc.html [2023-10-17 10:17:00,852] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K2_fastqc.html [2023-10-17 10:17:00,861] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K2_fastqc.html [2023-10-17 10:17:00,937] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N1_fastqc.html [2023-10-17 10:17:00,944] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N1_fastqc.html [2023-10-17 10:17:01,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N2_fastqc.html [2023-10-17 10:17:01,047] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N2_fastqc.html [2023-10-17 10:17:01,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_undetermined_fastqc.html [2023-10-17 10:17:01,143] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_undetermined_fastqc.html [2023-10-17 10:17:01,572] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 10:17:01,573] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 10:17:01,583] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2023-10-17 10:17:01,584] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-10-17 10:17:01,594] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-10-17 10:17:01,598] multiqc [DEBUG ] No samples found: conpair [2023-10-17 10:17:01,603] multiqc [DEBUG ] No samples found: peddy [2023-10-17 10:17:01,607] multiqc [DEBUG ] No samples found: somalier [2023-10-17 10:17:01,612] multiqc [DEBUG ] No samples found: methylQA [2023-10-17 10:17:01,618] multiqc [DEBUG ] No samples found: mosdepth [2023-10-17 10:17:01,622] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-10-17 10:17:01,625] multiqc [DEBUG ] No samples found: qualimap [2023-10-17 10:17:01,629] multiqc [DEBUG ] No samples found: preseq [2023-10-17 10:17:01,634] multiqc [DEBUG ] No samples found: quast [2023-10-17 10:17:01,638] multiqc [DEBUG ] No samples found: qorts [2023-10-17 10:17:01,642] multiqc [DEBUG ] No samples found: rna_seqc [2023-10-17 10:17:01,646] multiqc [DEBUG ] No samples found: rockhopper [2023-10-17 10:17:01,650] multiqc [DEBUG ] No samples found: rsem [2023-10-17 10:17:01,659] multiqc [DEBUG ] No samples found: rseqc [2023-10-17 10:17:01,663] multiqc [DEBUG ] No samples found: busco [2023-10-17 10:17:01,667] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-10-17 10:17:01,671] multiqc [DEBUG ] No samples found: disambiguate [2023-10-17 10:17:01,675] multiqc [DEBUG ] No samples found: supernova [2023-10-17 10:17:01,685] multiqc [DEBUG ] No samples found: deeptools [2023-10-17 10:17:01,689] multiqc [DEBUG ] No samples found: sargasso [2023-10-17 10:17:01,693] multiqc [DEBUG ] No samples found: verifybamid [2023-10-17 10:17:01,697] multiqc [DEBUG ] No samples found: mirtrace [2023-10-17 10:17:01,701] multiqc [DEBUG ] No samples found: happy [2023-10-17 10:17:01,705] multiqc [DEBUG ] No samples found: mirtop [2023-10-17 10:17:01,711] multiqc [DEBUG ] No samples found: homer [2023-10-17 10:17:01,715] multiqc [DEBUG ] No samples found: macs2 [2023-10-17 10:17:01,719] multiqc [DEBUG ] No samples found: theta2 [2023-10-17 10:17:01,723] multiqc [DEBUG ] No samples found: snpeff [2023-10-17 10:17:01,728] multiqc [DEBUG ] No samples found: gatk [2023-10-17 10:17:01,732] multiqc [DEBUG ] No samples found: htseq [2023-10-17 10:17:01,737] multiqc [DEBUG ] No samples found: bcftools [2023-10-17 10:17:01,741] multiqc [DEBUG ] No samples found: featureCounts [2023-10-17 10:17:01,747] multiqc [DEBUG ] No samples found: fgbio [2023-10-17 10:17:01,763] multiqc [DEBUG ] No samples found: dragen [2023-10-17 10:17:01,768] multiqc [DEBUG ] No samples found: dedup [2023-10-17 10:17:01,778] multiqc [DEBUG ] No samples found: damageprofiler [2023-10-17 10:17:01,798] multiqc [DEBUG ] No samples found: biobambam2 [2023-10-17 10:17:01,803] multiqc [DEBUG ] No samples found: mtnucratio [2023-10-17 10:17:01,805] multiqc [DEBUG ] No samples found: picard [2023-10-17 10:17:01,809] multiqc [DEBUG ] No samples found: prokka [2023-10-17 10:17:01,813] multiqc [DEBUG ] No samples found: samblaster [2023-10-17 10:17:01,820] multiqc [DEBUG ] No samples found: samtools [2023-10-17 10:17:01,824] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-10-17 10:17:01,828] multiqc [DEBUG ] No samples found: bamtools [2023-10-17 10:17:01,832] multiqc [DEBUG ] No samples found: jellyfish [2023-10-17 10:17:01,838] multiqc [DEBUG ] No samples found: vcftools [2023-10-17 10:17:01,842] multiqc [DEBUG ] No samples found: longranger [2023-10-17 10:17:01,846] multiqc [DEBUG ] No samples found: stacks [2023-10-17 10:17:01,850] multiqc [DEBUG ] No samples found: varscan2 [2023-10-17 10:17:01,861] multiqc [DEBUG ] No samples found: bbmap [2023-10-17 10:17:01,865] multiqc [DEBUG ] No samples found: bismark [2023-10-17 10:17:01,870] multiqc [DEBUG ] No samples found: biscuit [2023-10-17 10:17:01,874] multiqc [DEBUG ] No samples found: hicexplorer [2023-10-17 10:17:01,878] multiqc [DEBUG ] No samples found: hicup [2023-10-17 10:17:01,882] multiqc [DEBUG ] No samples found: hicpro [2023-10-17 10:17:01,886] multiqc [DEBUG ] No samples found: salmon [2023-10-17 10:17:01,890] multiqc [DEBUG ] No samples found: kallisto [2023-10-17 10:17:01,894] multiqc [DEBUG ] No samples found: slamdunk [2023-10-17 10:17:01,898] multiqc [DEBUG ] No samples found: star [2023-10-17 10:17:01,902] multiqc [DEBUG ] No samples found: hisat2 [2023-10-17 10:17:01,906] multiqc [DEBUG ] No samples found: tophat [2023-10-17 10:17:01,911] multiqc [DEBUG ] No samples found: bowtie2 [2023-10-17 10:17:01,915] multiqc [DEBUG ] No samples found: bowtie1 [2023-10-17 10:17:01,919] multiqc [DEBUG ] No samples found: snpsplit [2023-10-17 10:17:01,922] multiqc [DEBUG ] No samples found: kat [2023-10-17 10:17:01,926] multiqc [DEBUG ] No samples found: leehom [2023-10-17 10:17:01,930] multiqc [DEBUG ] No samples found: adapterRemoval [2023-10-17 10:17:01,934] multiqc [DEBUG ] No samples found: clipandmerge [2023-10-17 10:17:01,938] multiqc [DEBUG ] No samples found: cutadapt [2023-10-17 10:17:01,942] multiqc [DEBUG ] No samples found: flexbar [2023-10-17 10:17:01,946] multiqc [DEBUG ] No samples found: kaiju [2023-10-17 10:17:01,950] multiqc [DEBUG ] No samples found: kraken [2023-10-17 10:17:01,954] multiqc [DEBUG ] No samples found: malt [2023-10-17 10:17:01,958] multiqc [DEBUG ] No samples found: trimmomatic [2023-10-17 10:17:01,962] multiqc [DEBUG ] No samples found: sickle [2023-10-17 10:17:01,966] multiqc [DEBUG ] No samples found: skewer [2023-10-17 10:17:01,970] multiqc [DEBUG ] No samples found: sortmerna [2023-10-17 10:17:01,974] multiqc [DEBUG ] No samples found: biobloomtools [2023-10-17 10:17:01,978] multiqc [DEBUG ] No samples found: fastq_screen [2023-10-17 10:17:01,982] multiqc [DEBUG ] No samples found: afterqc [2023-10-17 10:17:01,986] multiqc [DEBUG ] No samples found: fastp [2023-10-17 10:17:02,450] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-10-17 10:17:02,568] multiqc [DEBUG ] No samples found: pycoqc [2023-10-17 10:17:02,572] multiqc [DEBUG ] No samples found: minionqc [2023-10-17 10:17:02,576] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-10-17 10:17:02,580] multiqc [DEBUG ] No samples found: clusterflow [2023-10-17 10:17:02,584] multiqc [DEBUG ] No samples found: bcl2fastq [2023-10-17 10:17:02,588] multiqc [DEBUG ] No samples found: interop [2023-10-17 10:17:02,592] multiqc [DEBUG ] No samples found: ivar [2023-10-17 10:17:02,597] multiqc [DEBUG ] No samples found: flash [2023-10-17 10:17:02,601] multiqc [DEBUG ] No samples found: seqyclean [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 10:17:02,601] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-10-17 10:17:02,602] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-10-17 10:17:02,615] multiqc [INFO ] Compressing plot data [2023-10-17 10:17:02,782] multiqc [INFO ] Report : multiqc_report.html [2023-10-17 10:17:02,782] multiqc [INFO ] Data : multiqc_data [2023-10-17 10:17:02,782] multiqc [DEBUG ] Moving data file from '/state/partition1/job-38952089/tmpbruj8pi5/multiqc_data' to '/vast/gencore/GENEFLOW/work/dc/dd772c2f757a86511c425ed8969a0a/merged/multiqc_data' [2023-10-17 10:17:02,965] multiqc [INFO ] MultiQC complete