[2024-06-04 23:30:16,579] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-04 23:30:16,580] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-04 23:30:16,580] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-04 23:30:16,583] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-04 23:30:16,583] 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}} [2024-06-04 23:30:16,583] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-04 23:30:16,619] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-04 23:30:16,619] multiqc [INFO ] This is MultiQC v1.9 [2024-06-04 23:30:16,619] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-04 23:30:16,619] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/47/8474b9acc2c2fa860d600344b5916e/merged [2024-06-04 23:30:16,619] multiqc [INFO ] Template : default [2024-06-04 23:30:16,619] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-04 23:30:16,619] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/47/8474b9acc2c2fa860d600344b5916e/merged [2024-06-04 23:30:16,620] 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 [2024-06-04 23:30:16,620] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47254600/tmpq9bxym2o [2024-06-04 23:30:16,774] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_2-1_fastqc.html [2024-06-04 23:30:16,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_2-1_fastqc.html [2024-06-04 23:30:16,901] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_2-2_fastqc.html [2024-06-04 23:30:16,912] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_2-2_fastqc.html [2024-06-04 23:30:17,073] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_3-1_fastqc.html [2024-06-04 23:30:17,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_3-1_fastqc.html [2024-06-04 23:30:17,203] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_3-2_fastqc.html [2024-06-04 23:30:17,214] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n01_Rep_3-2_fastqc.html [2024-06-04 23:30:17,337] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n01_undetermined_fastqc.html [2024-06-04 23:30:17,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n01_undetermined_fastqc.html [2024-06-04 23:30:17,463] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_2-1_fastqc.html [2024-06-04 23:30:17,474] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_2-1_fastqc.html [2024-06-04 23:30:17,576] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_2-2_fastqc.html [2024-06-04 23:30:17,585] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_2-2_fastqc.html [2024-06-04 23:30:17,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_3-1_fastqc.html [2024-06-04 23:30:17,708] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_3-1_fastqc.html [2024-06-04 23:30:17,836] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_3-2_fastqc.html [2024-06-04 23:30:17,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n02_Rep_3-2_fastqc.html [2024-06-04 23:30:17,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5TVHDRX5_n02_undetermined_fastqc.html [2024-06-04 23:30:17,959] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5TVHDRX5_n02_undetermined_fastqc.html [2024-06-04 23:30:18,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-04 23:30:18,070] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-04 23:30:18,534] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-04 23:30:18,536] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-04 23:30:18,550] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2024-06-04 23:30:18,551] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-04 23:30:18,562] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-04 23:30:18,568] multiqc [DEBUG ] No samples found: conpair [2024-06-04 23:30:18,574] multiqc [DEBUG ] No samples found: peddy [2024-06-04 23:30:18,579] multiqc [DEBUG ] No samples found: somalier [2024-06-04 23:30:18,584] multiqc [DEBUG ] No samples found: methylQA [2024-06-04 23:30:18,593] multiqc [DEBUG ] No samples found: mosdepth [2024-06-04 23:30:18,598] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-04 23:30:18,602] multiqc [DEBUG ] No samples found: qualimap [2024-06-04 23:30:18,607] multiqc [DEBUG ] No samples found: preseq [2024-06-04 23:30:18,612] multiqc [DEBUG ] No samples found: quast [2024-06-04 23:30:18,617] multiqc [DEBUG ] No samples found: qorts [2024-06-04 23:30:18,622] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-04 23:30:18,628] multiqc [DEBUG ] No samples found: rockhopper [2024-06-04 23:30:18,633] multiqc [DEBUG ] No samples found: rsem [2024-06-04 23:30:18,645] multiqc [DEBUG ] No samples found: rseqc [2024-06-04 23:30:18,650] multiqc [DEBUG ] No samples found: busco [2024-06-04 23:30:18,655] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-04 23:30:18,660] multiqc [DEBUG ] No samples found: disambiguate [2024-06-04 23:30:18,665] multiqc [DEBUG ] No samples found: supernova [2024-06-04 23:30:18,679] multiqc [DEBUG ] No samples found: deeptools [2024-06-04 23:30:18,684] multiqc [DEBUG ] No samples found: sargasso [2024-06-04 23:30:18,689] multiqc [DEBUG ] No samples found: verifybamid [2024-06-04 23:30:18,695] multiqc [DEBUG ] No samples found: mirtrace [2024-06-04 23:30:18,700] multiqc [DEBUG ] No samples found: happy [2024-06-04 23:30:18,705] multiqc [DEBUG ] No samples found: mirtop [2024-06-04 23:30:18,712] multiqc [DEBUG ] No samples found: homer [2024-06-04 23:30:18,719] multiqc [DEBUG ] No samples found: macs2 [2024-06-04 23:30:18,724] multiqc [DEBUG ] No samples found: theta2 [2024-06-04 23:30:18,729] multiqc [DEBUG ] No samples found: snpeff [2024-06-04 23:30:18,736] multiqc [DEBUG ] No samples found: gatk [2024-06-04 23:30:18,741] multiqc [DEBUG ] No samples found: htseq [2024-06-04 23:30:18,747] multiqc [DEBUG ] No samples found: bcftools [2024-06-04 23:30:18,752] multiqc [DEBUG ] No samples found: featureCounts [2024-06-04 23:30:18,758] multiqc [DEBUG ] No samples found: fgbio [2024-06-04 23:30:18,774] multiqc [DEBUG ] No samples found: dragen [2024-06-04 23:30:18,779] multiqc [DEBUG ] No samples found: dedup [2024-06-04 23:30:18,784] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-04 23:30:18,808] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-04 23:30:18,814] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-04 23:30:18,817] multiqc [DEBUG ] No samples found: picard [2024-06-04 23:30:18,822] multiqc [DEBUG ] No samples found: prokka [2024-06-04 23:30:18,827] multiqc [DEBUG ] No samples found: samblaster [2024-06-04 23:30:18,836] multiqc [DEBUG ] No samples found: samtools [2024-06-04 23:30:18,842] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-04 23:30:18,847] multiqc [DEBUG ] No samples found: bamtools [2024-06-04 23:30:18,852] multiqc [DEBUG ] No samples found: jellyfish [2024-06-04 23:30:18,862] multiqc [DEBUG ] No samples found: vcftools [2024-06-04 23:30:18,867] multiqc [DEBUG ] No samples found: longranger [2024-06-04 23:30:18,872] multiqc [DEBUG ] No samples found: stacks [2024-06-04 23:30:18,878] multiqc [DEBUG ] No samples found: varscan2 [2024-06-04 23:30:18,894] multiqc [DEBUG ] No samples found: bbmap [2024-06-04 23:30:18,900] multiqc [DEBUG ] No samples found: bismark [2024-06-04 23:30:18,905] multiqc [DEBUG ] No samples found: biscuit [2024-06-04 23:30:18,910] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-04 23:30:18,916] multiqc [DEBUG ] No samples found: hicup [2024-06-04 23:30:18,921] multiqc [DEBUG ] No samples found: hicpro [2024-06-04 23:30:18,926] multiqc [DEBUG ] No samples found: salmon [2024-06-04 23:30:18,931] multiqc [DEBUG ] No samples found: kallisto [2024-06-04 23:30:18,936] multiqc [DEBUG ] No samples found: slamdunk [2024-06-04 23:30:18,941] multiqc [DEBUG ] No samples found: star [2024-06-04 23:30:18,947] multiqc [DEBUG ] No samples found: hisat2 [2024-06-04 23:30:18,952] multiqc [DEBUG ] No samples found: tophat [2024-06-04 23:30:18,957] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-04 23:30:18,962] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-04 23:30:18,967] multiqc [DEBUG ] No samples found: snpsplit [2024-06-04 23:30:18,972] multiqc [DEBUG ] No samples found: kat [2024-06-04 23:30:18,978] multiqc [DEBUG ] No samples found: leehom [2024-06-04 23:30:18,983] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-04 23:30:18,988] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-04 23:30:18,995] multiqc [DEBUG ] No samples found: cutadapt [2024-06-04 23:30:19,000] multiqc [DEBUG ] No samples found: flexbar [2024-06-04 23:30:19,005] multiqc [DEBUG ] No samples found: kaiju [2024-06-04 23:30:19,010] multiqc [DEBUG ] No samples found: kraken [2024-06-04 23:30:19,015] multiqc [DEBUG ] No samples found: malt [2024-06-04 23:30:19,021] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-04 23:30:19,028] multiqc [DEBUG ] No samples found: sickle [2024-06-04 23:30:19,033] multiqc [DEBUG ] No samples found: skewer [2024-06-04 23:30:19,039] multiqc [DEBUG ] No samples found: sortmerna [2024-06-04 23:30:19,044] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-04 23:30:19,049] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-04 23:30:19,055] multiqc [DEBUG ] No samples found: afterqc [2024-06-04 23:30:19,060] multiqc [DEBUG ] No samples found: fastp [2024-06-04 23:30:19,751] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2024-06-04 23:30:19,899] multiqc [DEBUG ] No samples found: pycoqc [2024-06-04 23:30:19,904] multiqc [DEBUG ] No samples found: minionqc [2024-06-04 23:30:19,909] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-04 23:30:19,914] multiqc [DEBUG ] No samples found: clusterflow [2024-06-04 23:30:19,921] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-04 23:30:19,927] multiqc [DEBUG ] No samples found: interop [2024-06-04 23:30:19,932] multiqc [DEBUG ] No samples found: ivar [2024-06-04 23:30:19,937] multiqc [DEBUG ] No samples found: flash [2024-06-04 23:30:19,942] multiqc [DEBUG ] No samples found: seqyclean [2024-06-04 23:30:19,942] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-04 23:30:19,942] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-04 23:30:19,942] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-04 23:30:19,942] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-04 23:30:19,943] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-04 23:30:19,958] multiqc [INFO ] Compressing plot data [2024-06-04 23:30:20,164] multiqc [INFO ] Report : multiqc_report.html [2024-06-04 23:30:20,164] multiqc [INFO ] Data : multiqc_data [2024-06-04 23:30:20,164] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47254600/tmpq9bxym2o/multiqc_data' to '/vast/gencore/GENEFLOW/work/47/8474b9acc2c2fa860d600344b5916e/merged/multiqc_data' [2024-06-04 23:30:20,421] multiqc [INFO ] MultiQC complete