[2023-12-01 02:53:06,910] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-01 02:53:06,910] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-01 02:53:06,911] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-01 02:53:06,913] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-12-01 02:53:06,913] 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}} [2023-12-01 02:53:06,913] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-01 02:53:07,885] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-01 02:53:07,886] multiqc [INFO ] This is MultiQC v1.9 [2023-12-01 02:53:07,886] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-01 02:53:07,886] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/dc/449ef784dadf945dd0535c9f50d365/merged [2023-12-01 02:53:07,886] multiqc [INFO ] Template : default [2023-12-01 02:53:07,886] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-01 02:53:07,886] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/dc/449ef784dadf945dd0535c9f50d365/merged [2023-12-01 02:53:07,886] 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 [2023-12-01 02:53:07,886] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40472244/tmpx1srqlgm [2023-12-01 02:53:08,005] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2T7JBGXV_n01_BS_F23_fastqc.html [2023-12-01 02:53:08,012] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2T7JBGXV_n01_BS_F23_fastqc.html [2023-12-01 02:53:08,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2T7JBGXV_n01_undetermined_fastqc.html [2023-12-01 02:53:08,097] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2T7JBGXV_n01_undetermined_fastqc.html [2023-12-01 02:53:08,572] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-01 02:53:08,573] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-01 02:53:08,580] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-12-01 02:53:08,582] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2023-12-01 02:53:08,583] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-01 02:53:08,588] multiqc [DEBUG ] No samples found: conpair [2023-12-01 02:53:08,592] multiqc [DEBUG ] No samples found: peddy [2023-12-01 02:53:08,597] multiqc [DEBUG ] No samples found: somalier [2023-12-01 02:53:08,602] multiqc [DEBUG ] No samples found: methylQA [2023-12-01 02:53:08,609] multiqc [DEBUG ] No samples found: mosdepth [2023-12-01 02:53:08,613] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-01 02:53:08,616] multiqc [DEBUG ] No samples found: qualimap [2023-12-01 02:53:08,621] multiqc [DEBUG ] No samples found: preseq [2023-12-01 02:53:08,626] multiqc [DEBUG ] No samples found: quast [2023-12-01 02:53:08,630] multiqc [DEBUG ] No samples found: qorts [2023-12-01 02:53:08,635] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-01 02:53:08,639] multiqc [DEBUG ] No samples found: rockhopper [2023-12-01 02:53:08,644] multiqc [DEBUG ] No samples found: rsem [2023-12-01 02:53:08,654] multiqc [DEBUG ] No samples found: rseqc [2023-12-01 02:53:08,658] multiqc [DEBUG ] No samples found: busco [2023-12-01 02:53:08,663] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-01 02:53:08,667] multiqc [DEBUG ] No samples found: disambiguate [2023-12-01 02:53:08,672] multiqc [DEBUG ] No samples found: supernova [2023-12-01 02:53:08,684] multiqc [DEBUG ] No samples found: deeptools [2023-12-01 02:53:08,688] multiqc [DEBUG ] No samples found: sargasso [2023-12-01 02:53:08,693] multiqc [DEBUG ] No samples found: verifybamid [2023-12-01 02:53:08,697] multiqc [DEBUG ] No samples found: mirtrace [2023-12-01 02:53:08,702] multiqc [DEBUG ] No samples found: happy [2023-12-01 02:53:08,706] multiqc [DEBUG ] No samples found: mirtop [2023-12-01 02:53:08,712] multiqc [DEBUG ] No samples found: homer [2023-12-01 02:53:08,716] multiqc [DEBUG ] No samples found: macs2 [2023-12-01 02:53:08,721] multiqc [DEBUG ] No samples found: theta2 [2023-12-01 02:53:08,725] multiqc [DEBUG ] No samples found: snpeff [2023-12-01 02:53:08,732] multiqc [DEBUG ] No samples found: gatk [2023-12-01 02:53:08,736] multiqc [DEBUG ] No samples found: htseq [2023-12-01 02:53:08,741] multiqc [DEBUG ] No samples found: bcftools [2023-12-01 02:53:08,746] multiqc [DEBUG ] No samples found: featureCounts [2023-12-01 02:53:08,751] multiqc [DEBUG ] No samples found: fgbio [2023-12-01 02:53:08,763] multiqc [DEBUG ] No samples found: dragen [2023-12-01 02:53:08,768] multiqc [DEBUG ] No samples found: dedup [2023-12-01 02:53:08,772] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-01 02:53:08,793] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-01 02:53:08,798] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-01 02:53:08,800] multiqc [DEBUG ] No samples found: picard [2023-12-01 02:53:08,804] multiqc [DEBUG ] No samples found: prokka [2023-12-01 02:53:08,808] multiqc [DEBUG ] No samples found: samblaster [2023-12-01 02:53:08,817] multiqc [DEBUG ] No samples found: samtools [2023-12-01 02:53:08,821] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-01 02:53:08,826] multiqc [DEBUG ] No samples found: bamtools [2023-12-01 02:53:08,830] multiqc [DEBUG ] No samples found: jellyfish [2023-12-01 02:53:08,837] multiqc [DEBUG ] No samples found: vcftools [2023-12-01 02:53:08,844] multiqc [DEBUG ] No samples found: longranger [2023-12-01 02:53:08,849] multiqc [DEBUG ] No samples found: stacks [2023-12-01 02:53:08,855] multiqc [DEBUG ] No samples found: varscan2 [2023-12-01 02:53:08,870] multiqc [DEBUG ] No samples found: bbmap [2023-12-01 02:53:08,877] multiqc [DEBUG ] No samples found: bismark [2023-12-01 02:53:08,882] multiqc [DEBUG ] No samples found: biscuit [2023-12-01 02:53:08,888] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-01 02:53:08,893] multiqc [DEBUG ] No samples found: hicup [2023-12-01 02:53:08,898] multiqc [DEBUG ] No samples found: hicpro [2023-12-01 02:53:08,902] multiqc [DEBUG ] No samples found: salmon [2023-12-01 02:53:08,906] multiqc [DEBUG ] No samples found: kallisto [2023-12-01 02:53:08,911] multiqc [DEBUG ] No samples found: slamdunk [2023-12-01 02:53:08,915] multiqc [DEBUG ] No samples found: star [2023-12-01 02:53:08,920] multiqc [DEBUG ] No samples found: hisat2 [2023-12-01 02:53:08,924] multiqc [DEBUG ] No samples found: tophat [2023-12-01 02:53:08,928] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-01 02:53:08,933] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-01 02:53:08,937] multiqc [DEBUG ] No samples found: snpsplit [2023-12-01 02:53:08,942] multiqc [DEBUG ] No samples found: kat [2023-12-01 02:53:08,946] multiqc [DEBUG ] No samples found: leehom [2023-12-01 02:53:08,950] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-01 02:53:08,955] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-01 02:53:08,959] multiqc [DEBUG ] No samples found: cutadapt [2023-12-01 02:53:08,963] multiqc [DEBUG ] No samples found: flexbar [2023-12-01 02:53:08,968] multiqc [DEBUG ] No samples found: kaiju [2023-12-01 02:53:08,972] multiqc [DEBUG ] No samples found: kraken [2023-12-01 02:53:08,977] multiqc [DEBUG ] No samples found: malt [2023-12-01 02:53:08,981] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-01 02:53:08,986] multiqc [DEBUG ] No samples found: sickle [2023-12-01 02:53:08,990] multiqc [DEBUG ] No samples found: skewer [2023-12-01 02:53:08,994] multiqc [DEBUG ] No samples found: sortmerna [2023-12-01 02:53:08,999] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-01 02:53:09,003] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-01 02:53:09,008] multiqc [DEBUG ] No samples found: afterqc [2023-12-01 02:53:09,012] multiqc [DEBUG ] No samples found: fastp [2023-12-01 02:53:09,093] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2023-12-01 02:53:09,094] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H2T7JBGXV_n01_undetermined' [2023-12-01 02:53:09,144] multiqc [DEBUG ] No samples found: pycoqc [2023-12-01 02:53:09,148] multiqc [DEBUG ] No samples found: minionqc [2023-12-01 02:53:09,153] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-01 02:53:09,157] multiqc [DEBUG ] No samples found: clusterflow [2023-12-01 02:53:09,162] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-01 02:53:09,167] multiqc [DEBUG ] No samples found: interop [2023-12-01 02:53:09,171] multiqc [DEBUG ] No samples found: ivar [2023-12-01 02:53:09,175] multiqc [DEBUG ] No samples found: flash [2023-12-01 02:53:09,180] multiqc [DEBUG ] No samples found: seqyclean [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-01 02:53:09,180] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-01 02:53:09,181] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-01 02:53:09,184] multiqc [INFO ] Compressing plot data [2023-12-01 02:53:09,216] multiqc [INFO ] Report : multiqc_report.html [2023-12-01 02:53:09,216] multiqc [INFO ] Data : multiqc_data [2023-12-01 02:53:09,216] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40472244/tmpx1srqlgm/multiqc_data' to '/vast/gencore/GENEFLOW/work/dc/449ef784dadf945dd0535c9f50d365/merged/multiqc_data' [2023-12-01 02:53:09,371] multiqc [INFO ] MultiQC complete