[2023-09-01 09:57:42,597] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-09-01 09:57:42,597] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-09-01 09:57:42,597] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-09-01 09:57:42,600] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-09-01 09:57:42,600] 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}} [2023-09-01 09:57:42,600] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-09-01 09:57:42,773] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-09-01 09:57:42,773] multiqc [INFO ] This is MultiQC v1.9 [2023-09-01 09:57:42,773] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-09-01 09:57:42,773] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/7e/ed0bf972081ec3a00e8671462c68cc/merged [2023-09-01 09:57:42,773] multiqc [INFO ] Template : default [2023-09-01 09:57:42,773] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-09-01 09:57:42,773] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/7e/ed0bf972081ec3a00e8671462c68cc/merged [2023-09-01 09:57:42,774] 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 [2023-09-01 09:57:42,774] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-37117824/tmp56rv2v2u [2023-09-01 09:57:42,942] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLFKDRX3_1_fastqc.html [2023-09-01 09:57:42,949] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLFKDRX3_1_fastqc.html [2023-09-01 09:57:43,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLFKDRX3_2_fastqc.html [2023-09-01 09:57:43,027] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLFKDRX3_2_fastqc.html [2023-09-01 09:57:43,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLFKDRX3_3_fastqc.html [2023-09-01 09:57:43,104] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLFKDRX3_3_fastqc.html [2023-09-01 09:57:43,855] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-01 09:57:43,856] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-01 09:57:43,862] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-09-01 09:57:43,867] multiqc [DEBUG ] No samples found: conpair [2023-09-01 09:57:43,872] multiqc [DEBUG ] No samples found: peddy [2023-09-01 09:57:43,877] multiqc [DEBUG ] No samples found: somalier [2023-09-01 09:57:43,882] multiqc [DEBUG ] No samples found: methylQA [2023-09-01 09:57:43,891] multiqc [DEBUG ] No samples found: mosdepth [2023-09-01 09:57:43,895] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-09-01 09:57:43,899] multiqc [DEBUG ] No samples found: qualimap [2023-09-01 09:57:43,904] multiqc [DEBUG ] No samples found: preseq [2023-09-01 09:57:43,909] multiqc [DEBUG ] No samples found: quast [2023-09-01 09:57:43,914] multiqc [DEBUG ] No samples found: qorts [2023-09-01 09:57:43,919] multiqc [DEBUG ] No samples found: rna_seqc [2023-09-01 09:57:43,924] multiqc [DEBUG ] No samples found: rockhopper [2023-09-01 09:57:43,929] multiqc [DEBUG ] No samples found: rsem [2023-09-01 09:57:43,941] multiqc [DEBUG ] No samples found: rseqc [2023-09-01 09:57:43,945] multiqc [DEBUG ] No samples found: busco [2023-09-01 09:57:43,951] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-09-01 09:57:43,955] multiqc [DEBUG ] No samples found: disambiguate [2023-09-01 09:57:43,960] multiqc [DEBUG ] No samples found: supernova [2023-09-01 09:57:43,973] multiqc [DEBUG ] No samples found: deeptools [2023-09-01 09:57:43,978] multiqc [DEBUG ] No samples found: sargasso [2023-09-01 09:57:43,983] multiqc [DEBUG ] No samples found: verifybamid [2023-09-01 09:57:43,988] multiqc [DEBUG ] No samples found: mirtrace [2023-09-01 09:57:43,993] multiqc [DEBUG ] No samples found: happy [2023-09-01 09:57:43,998] multiqc [DEBUG ] No samples found: mirtop [2023-09-01 09:57:44,005] multiqc [DEBUG ] No samples found: homer [2023-09-01 09:57:44,010] multiqc [DEBUG ] No samples found: macs2 [2023-09-01 09:57:44,014] multiqc [DEBUG ] No samples found: theta2 [2023-09-01 09:57:44,019] multiqc [DEBUG ] No samples found: snpeff [2023-09-01 09:57:44,027] multiqc [DEBUG ] No samples found: gatk [2023-09-01 09:57:44,032] multiqc [DEBUG ] No samples found: htseq [2023-09-01 09:57:44,037] multiqc [DEBUG ] No samples found: bcftools [2023-09-01 09:57:44,042] multiqc [DEBUG ] No samples found: featureCounts [2023-09-01 09:57:44,049] multiqc [DEBUG ] No samples found: fgbio [2023-09-01 09:57:44,062] multiqc [DEBUG ] No samples found: dragen [2023-09-01 09:57:44,067] multiqc [DEBUG ] No samples found: dedup [2023-09-01 09:57:44,072] multiqc [DEBUG ] No samples found: damageprofiler [2023-09-01 09:57:44,095] multiqc [DEBUG ] No samples found: biobambam2 [2023-09-01 09:57:44,100] multiqc [DEBUG ] No samples found: mtnucratio [2023-09-01 09:57:44,103] multiqc [DEBUG ] No samples found: picard [2023-09-01 09:57:44,108] multiqc [DEBUG ] No samples found: prokka [2023-09-01 09:57:44,112] multiqc [DEBUG ] No samples found: samblaster [2023-09-01 09:57:44,121] multiqc [DEBUG ] No samples found: samtools [2023-09-01 09:57:44,126] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-09-01 09:57:44,132] multiqc [DEBUG ] No samples found: bamtools [2023-09-01 09:57:44,136] multiqc [DEBUG ] No samples found: jellyfish [2023-09-01 09:57:44,144] multiqc [DEBUG ] No samples found: vcftools [2023-09-01 09:57:44,149] multiqc [DEBUG ] No samples found: longranger [2023-09-01 09:57:44,154] multiqc [DEBUG ] No samples found: stacks [2023-09-01 09:57:44,159] multiqc [DEBUG ] No samples found: varscan2 [2023-09-01 09:57:44,173] multiqc [DEBUG ] No samples found: bbmap [2023-09-01 09:57:44,178] multiqc [DEBUG ] No samples found: bismark [2023-09-01 09:57:44,183] multiqc [DEBUG ] No samples found: biscuit [2023-09-01 09:57:44,188] multiqc [DEBUG ] No samples found: hicexplorer [2023-09-01 09:57:44,193] multiqc [DEBUG ] No samples found: hicup [2023-09-01 09:57:44,198] multiqc [DEBUG ] No samples found: hicpro [2023-09-01 09:57:44,203] multiqc [DEBUG ] No samples found: salmon [2023-09-01 09:57:44,208] multiqc [DEBUG ] No samples found: kallisto [2023-09-01 09:57:44,213] multiqc [DEBUG ] No samples found: slamdunk [2023-09-01 09:57:44,218] multiqc [DEBUG ] No samples found: star [2023-09-01 09:57:44,226] multiqc [DEBUG ] No samples found: hisat2 [2023-09-01 09:57:44,231] multiqc [DEBUG ] No samples found: tophat [2023-09-01 09:57:44,238] multiqc [DEBUG ] No samples found: bowtie2 [2023-09-01 09:57:44,246] multiqc [DEBUG ] No samples found: bowtie1 [2023-09-01 09:57:44,252] multiqc [DEBUG ] No samples found: snpsplit [2023-09-01 09:57:44,261] multiqc [DEBUG ] No samples found: kat [2023-09-01 09:57:44,270] multiqc [DEBUG ] No samples found: leehom [2023-09-01 09:57:44,278] multiqc [DEBUG ] No samples found: adapterRemoval [2023-09-01 09:57:44,289] multiqc [DEBUG ] No samples found: clipandmerge [2023-09-01 09:57:44,294] multiqc [DEBUG ] No samples found: cutadapt [2023-09-01 09:57:44,299] multiqc [DEBUG ] No samples found: flexbar [2023-09-01 09:57:44,304] multiqc [DEBUG ] No samples found: kaiju [2023-09-01 09:57:44,309] multiqc [DEBUG ] No samples found: kraken [2023-09-01 09:57:44,314] multiqc [DEBUG ] No samples found: malt [2023-09-01 09:57:44,319] multiqc [DEBUG ] No samples found: trimmomatic [2023-09-01 09:57:44,324] multiqc [DEBUG ] No samples found: sickle [2023-09-01 09:57:44,329] multiqc [DEBUG ] No samples found: skewer [2023-09-01 09:57:44,334] multiqc [DEBUG ] No samples found: sortmerna [2023-09-01 09:57:44,338] multiqc [DEBUG ] No samples found: biobloomtools [2023-09-01 09:57:44,343] multiqc [DEBUG ] No samples found: fastq_screen [2023-09-01 09:57:44,348] multiqc [DEBUG ] No samples found: afterqc [2023-09-01 09:57:44,353] multiqc [DEBUG ] No samples found: fastp [2023-09-01 09:57:44,417] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2023-09-01 09:57:44,462] multiqc [DEBUG ] No samples found: pycoqc [2023-09-01 09:57:44,468] multiqc [DEBUG ] No samples found: minionqc [2023-09-01 09:57:44,472] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-09-01 09:57:44,477] multiqc [DEBUG ] No samples found: clusterflow [2023-09-01 09:57:44,482] multiqc [DEBUG ] No samples found: bcl2fastq [2023-09-01 09:57:44,487] multiqc [DEBUG ] No samples found: interop [2023-09-01 09:57:44,493] multiqc [DEBUG ] No samples found: ivar [2023-09-01 09:57:44,498] multiqc [DEBUG ] No samples found: flash [2023-09-01 09:57:44,503] multiqc [DEBUG ] No samples found: seqyclean [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-09-01 09:57:44,503] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-09-01 09:57:44,508] multiqc [INFO ] Compressing plot data [2023-09-01 09:57:44,567] multiqc [INFO ] Report : multiqc_report.html [2023-09-01 09:57:44,567] multiqc [INFO ] Data : multiqc_data [2023-09-01 09:57:44,567] multiqc [DEBUG ] Moving data file from '/state/partition1/job-37117824/tmp56rv2v2u/multiqc_data' to '/vast/gencore/GENEFLOW/work/7e/ed0bf972081ec3a00e8671462c68cc/merged/multiqc_data' [2023-09-01 09:57:44,720] multiqc [INFO ] MultiQC complete