[2024-03-16 06:34:06,550] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-03-16 06:34:06,550] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-03-16 06:34:06,550] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-03-16 06:34:06,553] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-03-16 06:34:06,553] 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}} [2024-03-16 06:34:06,553] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-16 06:34:06,921] multiqc [WARNING] MultiQC Version v1.21 now available! [2024-03-16 06:34:06,921] multiqc [INFO ] This is MultiQC v1.9 [2024-03-16 06:34:06,921] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-16 06:34:06,921] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/e8/4b6c342145e14b6c52b80ebbd2d7de/merged [2024-03-16 06:34:06,921] multiqc [INFO ] Template : default [2024-03-16 06:34:06,921] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-03-16 06:34:06,921] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/e8/4b6c342145e14b6c52b80ebbd2d7de/merged [2024-03-16 06:34:06,921] 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 [2024-03-16 06:34:06,922] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-44179115/tmpv4xb1yfm [2024-03-16 06:34:07,062] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n01_Ath_Fresh_Sb_fastqc.html [2024-03-16 06:34:07,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n01_Ath_Fresh_Sb_fastqc.html [2024-03-16 06:34:07,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n01_Ath_Fresh_W5_fastqc.html [2024-03-16 06:34:07,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n01_Ath_Fresh_W5_fastqc.html [2024-03-16 06:34:07,231] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n01_Ath_Zm_Fresh_SB_fastqc.html [2024-03-16 06:34:07,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n01_Ath_Zm_Fresh_SB_fastqc.html [2024-03-16 06:34:07,314] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n01_undetermined_fastqc.html [2024-03-16 06:34:07,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n01_undetermined_fastqc.html [2024-03-16 06:34:07,397] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n02_Ath_Fresh_Sb_fastqc.html [2024-03-16 06:34:07,404] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n02_Ath_Fresh_Sb_fastqc.html [2024-03-16 06:34:07,470] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n02_Ath_Fresh_W5_fastqc.html [2024-03-16 06:34:07,477] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n02_Ath_Fresh_W5_fastqc.html [2024-03-16 06:34:07,557] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n02_Ath_Zm_Fresh_SB_fastqc.html [2024-03-16 06:34:07,566] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n02_Ath_Zm_Fresh_SB_fastqc.html [2024-03-16 06:34:07,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G77DRX5_n02_undetermined_fastqc.html [2024-03-16 06:34:07,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G77DRX5_n02_undetermined_fastqc.html [2024-03-16 06:34:07,705] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-16 06:34:07,711] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-16 06:34:08,466] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-16 06:34:08,468] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-16 06:34:08,479] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 4 samples (table) [2024-03-16 06:34:08,481] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-03-16 06:34:08,491] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-03-16 06:34:08,496] multiqc [DEBUG ] No samples found: conpair [2024-03-16 06:34:08,502] multiqc [DEBUG ] No samples found: peddy [2024-03-16 06:34:08,507] multiqc [DEBUG ] No samples found: somalier [2024-03-16 06:34:08,513] multiqc [DEBUG ] No samples found: methylQA [2024-03-16 06:34:08,522] multiqc [DEBUG ] No samples found: mosdepth [2024-03-16 06:34:08,527] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-03-16 06:34:08,532] multiqc [DEBUG ] No samples found: qualimap [2024-03-16 06:34:08,537] multiqc [DEBUG ] No samples found: preseq [2024-03-16 06:34:08,543] multiqc [DEBUG ] No samples found: quast [2024-03-16 06:34:08,548] multiqc [DEBUG ] No samples found: qorts [2024-03-16 06:34:08,553] multiqc [DEBUG ] No samples found: rna_seqc [2024-03-16 06:34:08,558] multiqc [DEBUG ] No samples found: rockhopper [2024-03-16 06:34:08,566] multiqc [DEBUG ] No samples found: rsem [2024-03-16 06:34:08,579] multiqc [DEBUG ] No samples found: rseqc [2024-03-16 06:34:08,584] multiqc [DEBUG ] No samples found: busco [2024-03-16 06:34:08,593] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-03-16 06:34:08,598] multiqc [DEBUG ] No samples found: disambiguate [2024-03-16 06:34:08,608] multiqc [DEBUG ] No samples found: supernova [2024-03-16 06:34:08,632] multiqc [DEBUG ] No samples found: deeptools [2024-03-16 06:34:08,638] multiqc [DEBUG ] No samples found: sargasso [2024-03-16 06:34:08,643] multiqc [DEBUG ] No samples found: verifybamid [2024-03-16 06:34:08,649] multiqc [DEBUG ] No samples found: mirtrace [2024-03-16 06:34:08,655] multiqc [DEBUG ] No samples found: happy [2024-03-16 06:34:08,661] multiqc [DEBUG ] No samples found: mirtop [2024-03-16 06:34:08,667] multiqc [DEBUG ] No samples found: homer [2024-03-16 06:34:08,673] multiqc [DEBUG ] No samples found: macs2 [2024-03-16 06:34:08,677] multiqc [DEBUG ] No samples found: theta2 [2024-03-16 06:34:08,682] multiqc [DEBUG ] No samples found: snpeff [2024-03-16 06:34:08,690] multiqc [DEBUG ] No samples found: gatk [2024-03-16 06:34:08,694] multiqc [DEBUG ] No samples found: htseq [2024-03-16 06:34:08,700] multiqc [DEBUG ] No samples found: bcftools [2024-03-16 06:34:08,705] multiqc [DEBUG ] No samples found: featureCounts [2024-03-16 06:34:08,713] multiqc [DEBUG ] No samples found: fgbio [2024-03-16 06:34:08,728] multiqc [DEBUG ] No samples found: dragen [2024-03-16 06:34:08,733] multiqc [DEBUG ] No samples found: dedup [2024-03-16 06:34:08,738] multiqc [DEBUG ] No samples found: damageprofiler [2024-03-16 06:34:08,763] multiqc [DEBUG ] No samples found: biobambam2 [2024-03-16 06:34:08,769] multiqc [DEBUG ] No samples found: mtnucratio [2024-03-16 06:34:08,771] multiqc [DEBUG ] No samples found: picard [2024-03-16 06:34:08,776] multiqc [DEBUG ] No samples found: prokka [2024-03-16 06:34:08,784] multiqc [DEBUG ] No samples found: samblaster [2024-03-16 06:34:08,793] multiqc [DEBUG ] No samples found: samtools [2024-03-16 06:34:08,799] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-03-16 06:34:08,804] multiqc [DEBUG ] No samples found: bamtools [2024-03-16 06:34:08,810] multiqc [DEBUG ] No samples found: jellyfish [2024-03-16 06:34:08,818] multiqc [DEBUG ] No samples found: vcftools [2024-03-16 06:34:08,825] multiqc [DEBUG ] No samples found: longranger [2024-03-16 06:34:08,831] multiqc [DEBUG ] No samples found: stacks [2024-03-16 06:34:08,837] multiqc [DEBUG ] No samples found: varscan2 [2024-03-16 06:34:08,853] multiqc [DEBUG ] No samples found: bbmap [2024-03-16 06:34:08,860] multiqc [DEBUG ] No samples found: bismark [2024-03-16 06:34:08,866] multiqc [DEBUG ] No samples found: biscuit [2024-03-16 06:34:08,871] multiqc [DEBUG ] No samples found: hicexplorer [2024-03-16 06:34:08,877] multiqc [DEBUG ] No samples found: hicup [2024-03-16 06:34:08,882] multiqc [DEBUG ] No samples found: hicpro [2024-03-16 06:34:08,887] multiqc [DEBUG ] No samples found: salmon [2024-03-16 06:34:08,892] multiqc [DEBUG ] No samples found: kallisto [2024-03-16 06:34:08,897] multiqc [DEBUG ] No samples found: slamdunk [2024-03-16 06:34:08,905] multiqc [DEBUG ] No samples found: star [2024-03-16 06:34:08,910] multiqc [DEBUG ] No samples found: hisat2 [2024-03-16 06:34:08,915] multiqc [DEBUG ] No samples found: tophat [2024-03-16 06:34:08,920] multiqc [DEBUG ] No samples found: bowtie2 [2024-03-16 06:34:08,925] multiqc [DEBUG ] No samples found: bowtie1 [2024-03-16 06:34:08,930] multiqc [DEBUG ] No samples found: snpsplit [2024-03-16 06:34:08,934] multiqc [DEBUG ] No samples found: kat [2024-03-16 06:34:08,939] multiqc [DEBUG ] No samples found: leehom [2024-03-16 06:34:08,944] multiqc [DEBUG ] No samples found: adapterRemoval [2024-03-16 06:34:08,948] multiqc [DEBUG ] No samples found: clipandmerge [2024-03-16 06:34:08,953] multiqc [DEBUG ] No samples found: cutadapt [2024-03-16 06:34:08,958] multiqc [DEBUG ] No samples found: flexbar [2024-03-16 06:34:08,963] multiqc [DEBUG ] No samples found: kaiju [2024-03-16 06:34:08,968] multiqc [DEBUG ] No samples found: kraken [2024-03-16 06:34:08,973] multiqc [DEBUG ] No samples found: malt [2024-03-16 06:34:08,978] multiqc [DEBUG ] No samples found: trimmomatic [2024-03-16 06:34:08,983] multiqc [DEBUG ] No samples found: sickle [2024-03-16 06:34:08,989] multiqc [DEBUG ] No samples found: skewer [2024-03-16 06:34:08,993] multiqc [DEBUG ] No samples found: sortmerna [2024-03-16 06:34:08,998] multiqc [DEBUG ] No samples found: biobloomtools [2024-03-16 06:34:09,003] multiqc [DEBUG ] No samples found: fastq_screen [2024-03-16 06:34:09,007] multiqc [DEBUG ] No samples found: afterqc [2024-03-16 06:34:09,012] multiqc [DEBUG ] No samples found: fastp [2024-03-16 06:34:09,290] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2024-03-16 06:34:09,422] multiqc [DEBUG ] No samples found: pycoqc [2024-03-16 06:34:09,426] multiqc [DEBUG ] No samples found: minionqc [2024-03-16 06:34:09,431] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-03-16 06:34:09,436] multiqc [DEBUG ] No samples found: clusterflow [2024-03-16 06:34:09,442] multiqc [DEBUG ] No samples found: bcl2fastq [2024-03-16 06:34:09,447] multiqc [DEBUG ] No samples found: interop [2024-03-16 06:34:09,452] multiqc [DEBUG ] No samples found: ivar [2024-03-16 06:34:09,457] multiqc [DEBUG ] No samples found: flash [2024-03-16 06:34:09,461] multiqc [DEBUG ] No samples found: seqyclean [2024-03-16 06:34:09,461] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-03-16 06:34:09,461] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-03-16 06:34:09,461] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-03-16 06:34:09,462] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-03-16 06:34:09,473] multiqc [INFO ] Compressing plot data [2024-03-16 06:34:09,651] multiqc [INFO ] Report : multiqc_report.html [2024-03-16 06:34:09,651] multiqc [INFO ] Data : multiqc_data [2024-03-16 06:34:09,651] multiqc [DEBUG ] Moving data file from '/state/partition1/job-44179115/tmpv4xb1yfm/multiqc_data' to '/vast/gencore/GENEFLOW/work/e8/4b6c342145e14b6c52b80ebbd2d7de/merged/multiqc_data' [2024-03-16 06:34:09,873] multiqc [INFO ] MultiQC complete