[2024-02-22 02:34:54,053] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-22 02:34:54,053] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-22 02:34:54,053] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-22 02:34:54,056] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-22 02:34:54,056] 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}} [2024-02-22 02:34:54,056] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-22 02:34:54,224] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-22 02:34:54,224] multiqc [INFO ] This is MultiQC v1.9 [2024-02-22 02:34:54,224] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-22 02:34:54,224] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/48/7ec48c36fcd61aaeb3c15c00025a1a/1 [2024-02-22 02:34:54,224] multiqc [INFO ] Template : default [2024-02-22 02:34:54,224] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-22 02:34:54,224] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/48/7ec48c36fcd61aaeb3c15c00025a1a/1 [2024-02-22 02:34:54,224] 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 [2024-02-22 02:34:54,225] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43274077/tmp03ewnidm [2024-02-22 02:34:54,345] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_BS_CR_21_fastqc.html [2024-02-22 02:34:54,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_BS_CR_21_fastqc.html [2024-02-22 02:34:54,423] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_BS_CR_22_fastqc.html [2024-02-22 02:34:54,430] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_BS_CR_22_fastqc.html [2024-02-22 02:34:54,496] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_BS_CR_24_fastqc.html [2024-02-22 02:34:54,503] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_BS_CR_24_fastqc.html [2024-02-22 02:34:54,567] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_undetermined_fastqc.html [2024-02-22 02:34:54,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n01_undetermined_fastqc.html [2024-02-22 02:34:54,643] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_BS_CR_21_fastqc.html [2024-02-22 02:34:54,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_BS_CR_21_fastqc.html [2024-02-22 02:34:54,717] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_BS_CR_22_fastqc.html [2024-02-22 02:34:54,724] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_BS_CR_22_fastqc.html [2024-02-22 02:34:54,788] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_BS_CR_24_fastqc.html [2024-02-22 02:34:54,795] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_BS_CR_24_fastqc.html [2024-02-22 02:34:54,876] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_undetermined_fastqc.html [2024-02-22 02:34:54,894] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFMD3_l01_n02_undetermined_fastqc.html [2024-02-22 02:34:54,967] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:54,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:54,974] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:54,974] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:54,975] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:54,975] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:54,975] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:54,993] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-22 02:34:56,095] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-22 02:34:56,097] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-22 02:34:56,108] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 4 samples (table) [2024-02-22 02:34:56,110] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-22 02:34:56,120] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-22 02:34:56,126] multiqc [DEBUG ] No samples found: conpair [2024-02-22 02:34:56,131] multiqc [DEBUG ] No samples found: peddy [2024-02-22 02:34:56,137] multiqc [DEBUG ] No samples found: somalier [2024-02-22 02:34:56,143] multiqc [DEBUG ] No samples found: methylQA [2024-02-22 02:34:56,152] multiqc [DEBUG ] No samples found: mosdepth [2024-02-22 02:34:56,157] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-22 02:34:56,160] multiqc [DEBUG ] No samples found: qualimap [2024-02-22 02:34:56,166] multiqc [DEBUG ] No samples found: preseq [2024-02-22 02:34:56,171] multiqc [DEBUG ] No samples found: quast [2024-02-22 02:34:56,176] multiqc [DEBUG ] No samples found: qorts [2024-02-22 02:34:56,182] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-22 02:34:56,187] multiqc [DEBUG ] No samples found: rockhopper [2024-02-22 02:34:56,192] multiqc [DEBUG ] No samples found: rsem [2024-02-22 02:34:56,205] multiqc [DEBUG ] No samples found: rseqc [2024-02-22 02:34:56,210] multiqc [DEBUG ] No samples found: busco [2024-02-22 02:34:56,216] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-22 02:34:56,220] multiqc [DEBUG ] No samples found: disambiguate [2024-02-22 02:34:56,226] multiqc [DEBUG ] No samples found: supernova [2024-02-22 02:34:56,241] multiqc [DEBUG ] No samples found: deeptools [2024-02-22 02:34:56,246] multiqc [DEBUG ] No samples found: sargasso [2024-02-22 02:34:56,251] multiqc [DEBUG ] No samples found: verifybamid [2024-02-22 02:34:56,256] multiqc [DEBUG ] No samples found: mirtrace [2024-02-22 02:34:56,261] multiqc [DEBUG ] No samples found: happy [2024-02-22 02:34:56,266] multiqc [DEBUG ] No samples found: mirtop [2024-02-22 02:34:56,274] multiqc [DEBUG ] No samples found: homer [2024-02-22 02:34:56,279] multiqc [DEBUG ] No samples found: macs2 [2024-02-22 02:34:56,284] multiqc [DEBUG ] No samples found: theta2 [2024-02-22 02:34:56,290] multiqc [DEBUG ] No samples found: snpeff [2024-02-22 02:34:56,298] multiqc [DEBUG ] No samples found: gatk [2024-02-22 02:34:56,304] multiqc [DEBUG ] No samples found: htseq [2024-02-22 02:34:56,309] multiqc [DEBUG ] No samples found: bcftools [2024-02-22 02:34:56,315] multiqc [DEBUG ] No samples found: featureCounts [2024-02-22 02:34:56,322] multiqc [DEBUG ] No samples found: fgbio [2024-02-22 02:34:56,337] multiqc [DEBUG ] No samples found: dragen [2024-02-22 02:34:56,342] multiqc [DEBUG ] No samples found: dedup [2024-02-22 02:34:56,348] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-22 02:34:56,374] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-22 02:34:56,380] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-22 02:34:56,382] multiqc [DEBUG ] No samples found: picard [2024-02-22 02:34:56,387] multiqc [DEBUG ] No samples found: prokka [2024-02-22 02:34:56,392] multiqc [DEBUG ] No samples found: samblaster [2024-02-22 02:34:56,401] multiqc [DEBUG ] No samples found: samtools [2024-02-22 02:34:56,407] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-22 02:34:56,414] multiqc [DEBUG ] No samples found: bamtools [2024-02-22 02:34:56,419] multiqc [DEBUG ] No samples found: jellyfish [2024-02-22 02:34:56,428] multiqc [DEBUG ] No samples found: vcftools [2024-02-22 02:34:56,434] multiqc [DEBUG ] No samples found: longranger [2024-02-22 02:34:56,439] multiqc [DEBUG ] No samples found: stacks [2024-02-22 02:34:56,445] multiqc [DEBUG ] No samples found: varscan2 [2024-02-22 02:34:56,462] multiqc [DEBUG ] No samples found: bbmap [2024-02-22 02:34:56,467] multiqc [DEBUG ] No samples found: bismark [2024-02-22 02:34:56,473] multiqc [DEBUG ] No samples found: biscuit [2024-02-22 02:34:56,479] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-22 02:34:56,484] multiqc [DEBUG ] No samples found: hicup [2024-02-22 02:34:56,489] multiqc [DEBUG ] No samples found: hicpro [2024-02-22 02:34:56,494] multiqc [DEBUG ] No samples found: salmon [2024-02-22 02:34:56,499] multiqc [DEBUG ] No samples found: kallisto [2024-02-22 02:34:56,505] multiqc [DEBUG ] No samples found: slamdunk [2024-02-22 02:34:56,510] multiqc [DEBUG ] No samples found: star [2024-02-22 02:34:56,515] multiqc [DEBUG ] No samples found: hisat2 [2024-02-22 02:34:56,521] multiqc [DEBUG ] No samples found: tophat [2024-02-22 02:34:56,527] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-22 02:34:56,532] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-22 02:34:56,537] multiqc [DEBUG ] No samples found: snpsplit [2024-02-22 02:34:56,541] multiqc [DEBUG ] No samples found: kat [2024-02-22 02:34:56,546] multiqc [DEBUG ] No samples found: leehom [2024-02-22 02:34:56,552] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-22 02:34:56,557] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-22 02:34:56,563] multiqc [DEBUG ] No samples found: cutadapt [2024-02-22 02:34:56,568] multiqc [DEBUG ] No samples found: flexbar [2024-02-22 02:34:56,573] multiqc [DEBUG ] No samples found: kaiju [2024-02-22 02:34:56,578] multiqc [DEBUG ] No samples found: kraken [2024-02-22 02:34:56,583] multiqc [DEBUG ] No samples found: malt [2024-02-22 02:34:56,589] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-22 02:34:56,594] multiqc [DEBUG ] No samples found: sickle [2024-02-22 02:34:56,599] multiqc [DEBUG ] No samples found: skewer [2024-02-22 02:34:56,604] multiqc [DEBUG ] No samples found: sortmerna [2024-02-22 02:34:56,609] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-22 02:34:56,614] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-22 02:34:56,619] multiqc [DEBUG ] No samples found: afterqc [2024-02-22 02:34:56,624] multiqc [DEBUG ] No samples found: fastp [2024-02-22 02:34:56,709] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2024-02-22 02:34:56,809] multiqc [DEBUG ] No samples found: pycoqc [2024-02-22 02:34:56,815] multiqc [DEBUG ] No samples found: minionqc [2024-02-22 02:34:56,820] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-22 02:34:56,826] multiqc [DEBUG ] No samples found: clusterflow [2024-02-22 02:34:56,831] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-22 02:34:56,838] multiqc [DEBUG ] No samples found: interop [2024-02-22 02:34:56,843] multiqc [DEBUG ] No samples found: ivar [2024-02-22 02:34:56,848] multiqc [DEBUG ] No samples found: flash [2024-02-22 02:34:56,853] multiqc [DEBUG ] No samples found: seqyclean [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-22 02:34:56,853] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-22 02:34:56,854] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-22 02:34:56,865] multiqc [INFO ] Compressing plot data [2024-02-22 02:34:57,019] multiqc [INFO ] Report : multiqc_report.html [2024-02-22 02:34:57,019] multiqc [INFO ] Data : multiqc_data [2024-02-22 02:34:57,019] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43274077/tmp03ewnidm/multiqc_data' to '/vast/gencore/GENEFLOW/work/48/7ec48c36fcd61aaeb3c15c00025a1a/1/multiqc_data' [2024-02-22 02:34:57,221] multiqc [INFO ] MultiQC complete