[2024-07-13 10:19:31,831] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-07-13 10:19:31,831] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-07-13 10:19:31,833] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-07-13 10:19:31,835] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-07-13 10:19:31,836] 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}} [2024-07-13 10:19:31,836] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-13 10:19:31,942] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-07-13 10:19:31,942] multiqc [INFO ] This is MultiQC v1.9 [2024-07-13 10:19:31,942] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-13 10:19:31,943] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/64/423fdf09f91436fbbc8b4c9d7a3465/merged [2024-07-13 10:19:31,943] multiqc [INFO ] Template : default [2024-07-13 10:19:31,943] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-07-13 10:19:31,943] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/64/423fdf09f91436fbbc8b4c9d7a3465/merged [2024-07-13 10:19:31,943] 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 [2024-07-13 10:19:31,943] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-48459948/tmpy80w_3y0 [2024-07-13 10:19:32,080] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFGWFDRX5_n01_ARF7_CTL_01_fastqc.html [2024-07-13 10:19:32,090] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFGWFDRX5_n01_ARF7_CTL_01_fastqc.html [2024-07-13 10:19:32,190] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFGWFDRX5_n01_undetermined_fastqc.html [2024-07-13 10:19:32,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFGWFDRX5_n01_undetermined_fastqc.html [2024-07-13 10:19:32,257] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFGWFDRX5_n02_ARF7_CTL_01_fastqc.html [2024-07-13 10:19:32,266] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFGWFDRX5_n02_ARF7_CTL_01_fastqc.html [2024-07-13 10:19:32,358] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFGWFDRX5_n02_undetermined_fastqc.html [2024-07-13 10:19:32,371] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFGWFDRX5_n02_undetermined_fastqc.html [2024-07-13 10:19:32,794] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-13 10:19:32,796] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-13 10:19:32,804] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2024-07-13 10:19:32,807] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2024-07-13 10:19:32,808] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-07-13 10:19:32,814] multiqc [DEBUG ] No samples found: conpair [2024-07-13 10:19:32,820] multiqc [DEBUG ] No samples found: peddy [2024-07-13 10:19:32,826] multiqc [DEBUG ] No samples found: somalier [2024-07-13 10:19:32,832] multiqc [DEBUG ] No samples found: methylQA [2024-07-13 10:19:32,842] multiqc [DEBUG ] No samples found: mosdepth [2024-07-13 10:19:32,848] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-07-13 10:19:32,851] multiqc [DEBUG ] No samples found: qualimap [2024-07-13 10:19:32,857] multiqc [DEBUG ] No samples found: preseq [2024-07-13 10:19:32,863] multiqc [DEBUG ] No samples found: quast [2024-07-13 10:19:32,869] multiqc [DEBUG ] No samples found: qorts [2024-07-13 10:19:32,875] multiqc [DEBUG ] No samples found: rna_seqc [2024-07-13 10:19:32,880] multiqc [DEBUG ] No samples found: rockhopper [2024-07-13 10:19:32,886] multiqc [DEBUG ] No samples found: rsem [2024-07-13 10:19:32,899] multiqc [DEBUG ] No samples found: rseqc [2024-07-13 10:19:32,905] multiqc [DEBUG ] No samples found: busco [2024-07-13 10:19:32,910] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-07-13 10:19:32,916] multiqc [DEBUG ] No samples found: disambiguate [2024-07-13 10:19:32,921] multiqc [DEBUG ] No samples found: supernova [2024-07-13 10:19:32,937] multiqc [DEBUG ] No samples found: deeptools [2024-07-13 10:19:32,943] multiqc [DEBUG ] No samples found: sargasso [2024-07-13 10:19:32,948] multiqc [DEBUG ] No samples found: verifybamid [2024-07-13 10:19:32,954] multiqc [DEBUG ] No samples found: mirtrace [2024-07-13 10:19:32,960] multiqc [DEBUG ] No samples found: happy [2024-07-13 10:19:32,965] multiqc [DEBUG ] No samples found: mirtop [2024-07-13 10:19:32,972] multiqc [DEBUG ] No samples found: homer [2024-07-13 10:19:32,978] multiqc [DEBUG ] No samples found: macs2 [2024-07-13 10:19:32,983] multiqc [DEBUG ] No samples found: theta2 [2024-07-13 10:19:32,989] multiqc [DEBUG ] No samples found: snpeff [2024-07-13 10:19:32,997] multiqc [DEBUG ] No samples found: gatk [2024-07-13 10:19:33,003] multiqc [DEBUG ] No samples found: htseq [2024-07-13 10:19:33,010] multiqc [DEBUG ] No samples found: bcftools [2024-07-13 10:19:33,016] multiqc [DEBUG ] No samples found: featureCounts [2024-07-13 10:19:33,023] multiqc [DEBUG ] No samples found: fgbio [2024-07-13 10:19:33,038] multiqc [DEBUG ] No samples found: dragen [2024-07-13 10:19:33,044] multiqc [DEBUG ] No samples found: dedup [2024-07-13 10:19:33,050] multiqc [DEBUG ] No samples found: damageprofiler [2024-07-13 10:19:33,076] multiqc [DEBUG ] No samples found: biobambam2 [2024-07-13 10:19:33,082] multiqc [DEBUG ] No samples found: mtnucratio [2024-07-13 10:19:33,084] multiqc [DEBUG ] No samples found: picard [2024-07-13 10:19:33,090] multiqc [DEBUG ] No samples found: prokka [2024-07-13 10:19:33,095] multiqc [DEBUG ] No samples found: samblaster [2024-07-13 10:19:33,104] multiqc [DEBUG ] No samples found: samtools [2024-07-13 10:19:33,109] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-07-13 10:19:33,120] multiqc [DEBUG ] No samples found: bamtools [2024-07-13 10:19:33,125] multiqc [DEBUG ] No samples found: jellyfish [2024-07-13 10:19:33,134] multiqc [DEBUG ] No samples found: vcftools [2024-07-13 10:19:33,140] multiqc [DEBUG ] No samples found: longranger [2024-07-13 10:19:33,145] multiqc [DEBUG ] No samples found: stacks [2024-07-13 10:19:33,151] multiqc [DEBUG ] No samples found: varscan2 [2024-07-13 10:19:33,167] multiqc [DEBUG ] No samples found: bbmap [2024-07-13 10:19:33,173] multiqc [DEBUG ] No samples found: bismark [2024-07-13 10:19:33,186] multiqc [DEBUG ] No samples found: biscuit [2024-07-13 10:19:33,191] multiqc [DEBUG ] No samples found: hicexplorer [2024-07-13 10:19:33,197] multiqc [DEBUG ] No samples found: hicup [2024-07-13 10:19:33,202] multiqc [DEBUG ] No samples found: hicpro [2024-07-13 10:19:33,207] multiqc [DEBUG ] No samples found: salmon [2024-07-13 10:19:33,213] multiqc [DEBUG ] No samples found: kallisto [2024-07-13 10:19:33,218] multiqc [DEBUG ] No samples found: slamdunk [2024-07-13 10:19:33,224] multiqc [DEBUG ] No samples found: star [2024-07-13 10:19:33,230] multiqc [DEBUG ] No samples found: hisat2 [2024-07-13 10:19:33,235] multiqc [DEBUG ] No samples found: tophat [2024-07-13 10:19:33,240] multiqc [DEBUG ] No samples found: bowtie2 [2024-07-13 10:19:33,246] multiqc [DEBUG ] No samples found: bowtie1 [2024-07-13 10:19:33,251] multiqc [DEBUG ] No samples found: snpsplit [2024-07-13 10:19:33,256] multiqc [DEBUG ] No samples found: kat [2024-07-13 10:19:33,261] multiqc [DEBUG ] No samples found: leehom [2024-07-13 10:19:33,267] multiqc [DEBUG ] No samples found: adapterRemoval [2024-07-13 10:19:33,273] multiqc [DEBUG ] No samples found: clipandmerge [2024-07-13 10:19:33,278] multiqc [DEBUG ] No samples found: cutadapt [2024-07-13 10:19:33,283] multiqc [DEBUG ] No samples found: flexbar [2024-07-13 10:19:33,289] multiqc [DEBUG ] No samples found: kaiju [2024-07-13 10:19:33,294] multiqc [DEBUG ] No samples found: kraken [2024-07-13 10:19:33,301] multiqc [DEBUG ] No samples found: malt [2024-07-13 10:19:33,305] multiqc [DEBUG ] No samples found: trimmomatic [2024-07-13 10:19:33,311] multiqc [DEBUG ] No samples found: sickle [2024-07-13 10:19:33,316] multiqc [DEBUG ] No samples found: skewer [2024-07-13 10:19:33,321] multiqc [DEBUG ] No samples found: sortmerna [2024-07-13 10:19:33,326] multiqc [DEBUG ] No samples found: biobloomtools [2024-07-13 10:19:33,331] multiqc [DEBUG ] No samples found: fastq_screen [2024-07-13 10:19:33,337] multiqc [DEBUG ] No samples found: afterqc [2024-07-13 10:19:33,342] multiqc [DEBUG ] No samples found: fastp [2024-07-13 10:19:33,436] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-07-13 10:19:33,437] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HFGWFDRX5_n01_undetermined' [2024-07-13 10:19:33,437] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HFGWFDRX5_n02_undetermined' [2024-07-13 10:19:33,497] multiqc [DEBUG ] No samples found: pycoqc [2024-07-13 10:19:33,502] multiqc [DEBUG ] No samples found: minionqc [2024-07-13 10:19:33,508] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-07-13 10:19:33,513] multiqc [DEBUG ] No samples found: clusterflow [2024-07-13 10:19:33,519] multiqc [DEBUG ] No samples found: bcl2fastq [2024-07-13 10:19:33,525] multiqc [DEBUG ] No samples found: interop [2024-07-13 10:19:33,531] multiqc [DEBUG ] No samples found: ivar [2024-07-13 10:19:33,537] multiqc [DEBUG ] No samples found: flash [2024-07-13 10:19:33,542] multiqc [DEBUG ] No samples found: seqyclean [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-07-13 10:19:33,542] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-07-13 10:19:33,543] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-07-13 10:19:33,549] multiqc [INFO ] Compressing plot data [2024-07-13 10:19:33,614] multiqc [INFO ] Report : multiqc_report.html [2024-07-13 10:19:33,614] multiqc [INFO ] Data : multiqc_data [2024-07-13 10:19:33,614] multiqc [DEBUG ] Moving data file from '/state/partition1/job-48459948/tmpy80w_3y0/multiqc_data' to '/vast/gencore/GENEFLOW/work/64/423fdf09f91436fbbc8b4c9d7a3465/merged/multiqc_data' [2024-07-13 10:19:33,797] multiqc [INFO ] MultiQC complete