[2023-08-16 22:04:11,653] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-08-16 22:04:11,653] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-08-16 22:04:11,653] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-08-16 22:04:11,656] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-08-16 22:04:11,656] 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}} [2023-08-16 22:04:11,656] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-08-16 22:04:11,829] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-08-16 22:04:11,830] multiqc [INFO ] This is MultiQC v1.9 [2023-08-16 22:04:11,830] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-08-16 22:04:11,830] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/3b/1750adcbd1d42d5d73d747b09aea7b/merged [2023-08-16 22:04:11,830] multiqc [INFO ] Template : default [2023-08-16 22:04:11,830] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-08-16 22:04:11,830] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/3b/1750adcbd1d42d5d73d747b09aea7b/merged [2023-08-16 22:04:11,830] 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 [2023-08-16 22:04:11,830] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-36560054/tmpzgwt52yw [2023-08-16 22:04:11,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NJNDRX3_1_fastqc.html [2023-08-16 22:04:11,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NJNDRX3_1_fastqc.html [2023-08-16 22:04:12,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NJNDRX3_2_fastqc.html [2023-08-16 22:04:12,113] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NJNDRX3_2_fastqc.html [2023-08-16 22:04:12,208] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NJNDRX3_3_fastqc.html [2023-08-16 22:04:12,220] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NJNDRX3_3_fastqc.html [2023-08-16 22:04:12,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NJNDRX3_4_fastqc.html [2023-08-16 22:04:12,334] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NJNDRX3_4_fastqc.html [2023-08-16 22:04:13,007] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-16 22:04:13,009] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-16 22:04:13,016] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-08-16 22:04:13,021] multiqc [DEBUG ] No samples found: conpair [2023-08-16 22:04:13,027] multiqc [DEBUG ] No samples found: peddy [2023-08-16 22:04:13,033] multiqc [DEBUG ] No samples found: somalier [2023-08-16 22:04:13,039] multiqc [DEBUG ] No samples found: methylQA [2023-08-16 22:04:13,049] multiqc [DEBUG ] No samples found: mosdepth [2023-08-16 22:04:13,054] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-08-16 22:04:13,057] multiqc [DEBUG ] No samples found: qualimap [2023-08-16 22:04:13,063] multiqc [DEBUG ] No samples found: preseq [2023-08-16 22:04:13,069] multiqc [DEBUG ] No samples found: quast [2023-08-16 22:04:13,075] multiqc [DEBUG ] No samples found: qorts [2023-08-16 22:04:13,081] multiqc [DEBUG ] No samples found: rna_seqc [2023-08-16 22:04:13,086] multiqc [DEBUG ] No samples found: rockhopper [2023-08-16 22:04:13,092] multiqc [DEBUG ] No samples found: rsem [2023-08-16 22:04:13,105] multiqc [DEBUG ] No samples found: rseqc [2023-08-16 22:04:13,111] multiqc [DEBUG ] No samples found: busco [2023-08-16 22:04:13,117] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-08-16 22:04:13,122] multiqc [DEBUG ] No samples found: disambiguate [2023-08-16 22:04:13,128] multiqc [DEBUG ] No samples found: supernova [2023-08-16 22:04:13,143] multiqc [DEBUG ] No samples found: deeptools [2023-08-16 22:04:13,148] multiqc [DEBUG ] No samples found: sargasso [2023-08-16 22:04:13,154] multiqc [DEBUG ] No samples found: verifybamid [2023-08-16 22:04:13,159] multiqc [DEBUG ] No samples found: mirtrace [2023-08-16 22:04:13,165] multiqc [DEBUG ] No samples found: happy [2023-08-16 22:04:13,171] multiqc [DEBUG ] No samples found: mirtop [2023-08-16 22:04:13,179] multiqc [DEBUG ] No samples found: homer [2023-08-16 22:04:13,184] multiqc [DEBUG ] No samples found: macs2 [2023-08-16 22:04:13,190] multiqc [DEBUG ] No samples found: theta2 [2023-08-16 22:04:13,195] multiqc [DEBUG ] No samples found: snpeff [2023-08-16 22:04:13,203] multiqc [DEBUG ] No samples found: gatk [2023-08-16 22:04:13,209] multiqc [DEBUG ] No samples found: htseq [2023-08-16 22:04:13,215] multiqc [DEBUG ] No samples found: bcftools [2023-08-16 22:04:13,220] multiqc [DEBUG ] No samples found: featureCounts [2023-08-16 22:04:13,227] multiqc [DEBUG ] No samples found: fgbio [2023-08-16 22:04:13,242] multiqc [DEBUG ] No samples found: dragen [2023-08-16 22:04:13,248] multiqc [DEBUG ] No samples found: dedup [2023-08-16 22:04:13,254] multiqc [DEBUG ] No samples found: damageprofiler [2023-08-16 22:04:13,281] multiqc [DEBUG ] No samples found: biobambam2 [2023-08-16 22:04:13,287] multiqc [DEBUG ] No samples found: mtnucratio [2023-08-16 22:04:13,289] multiqc [DEBUG ] No samples found: picard [2023-08-16 22:04:13,295] multiqc [DEBUG ] No samples found: prokka [2023-08-16 22:04:13,300] multiqc [DEBUG ] No samples found: samblaster [2023-08-16 22:04:13,310] multiqc [DEBUG ] No samples found: samtools [2023-08-16 22:04:13,315] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-08-16 22:04:13,322] multiqc [DEBUG ] No samples found: bamtools [2023-08-16 22:04:13,327] multiqc [DEBUG ] No samples found: jellyfish [2023-08-16 22:04:13,337] multiqc [DEBUG ] No samples found: vcftools [2023-08-16 22:04:13,343] multiqc [DEBUG ] No samples found: longranger [2023-08-16 22:04:13,349] multiqc [DEBUG ] No samples found: stacks [2023-08-16 22:04:13,355] multiqc [DEBUG ] No samples found: varscan2 [2023-08-16 22:04:13,372] multiqc [DEBUG ] No samples found: bbmap [2023-08-16 22:04:13,378] multiqc [DEBUG ] No samples found: bismark [2023-08-16 22:04:13,384] multiqc [DEBUG ] No samples found: biscuit [2023-08-16 22:04:13,389] multiqc [DEBUG ] No samples found: hicexplorer [2023-08-16 22:04:13,394] multiqc [DEBUG ] No samples found: hicup [2023-08-16 22:04:13,400] multiqc [DEBUG ] No samples found: hicpro [2023-08-16 22:04:13,405] multiqc [DEBUG ] No samples found: salmon [2023-08-16 22:04:13,410] multiqc [DEBUG ] No samples found: kallisto [2023-08-16 22:04:13,416] multiqc [DEBUG ] No samples found: slamdunk [2023-08-16 22:04:13,423] multiqc [DEBUG ] No samples found: star [2023-08-16 22:04:13,429] multiqc [DEBUG ] No samples found: hisat2 [2023-08-16 22:04:13,436] multiqc [DEBUG ] No samples found: tophat [2023-08-16 22:04:13,441] multiqc [DEBUG ] No samples found: bowtie2 [2023-08-16 22:04:13,447] multiqc [DEBUG ] No samples found: bowtie1 [2023-08-16 22:04:13,452] multiqc [DEBUG ] No samples found: snpsplit [2023-08-16 22:04:13,457] multiqc [DEBUG ] No samples found: kat [2023-08-16 22:04:13,462] multiqc [DEBUG ] No samples found: leehom [2023-08-16 22:04:13,469] multiqc [DEBUG ] No samples found: adapterRemoval [2023-08-16 22:04:13,474] multiqc [DEBUG ] No samples found: clipandmerge [2023-08-16 22:04:13,479] multiqc [DEBUG ] No samples found: cutadapt [2023-08-16 22:04:13,484] multiqc [DEBUG ] No samples found: flexbar [2023-08-16 22:04:13,489] multiqc [DEBUG ] No samples found: kaiju [2023-08-16 22:04:13,496] multiqc [DEBUG ] No samples found: kraken [2023-08-16 22:04:13,501] multiqc [DEBUG ] No samples found: malt [2023-08-16 22:04:13,507] multiqc [DEBUG ] No samples found: trimmomatic [2023-08-16 22:04:13,512] multiqc [DEBUG ] No samples found: sickle [2023-08-16 22:04:13,518] multiqc [DEBUG ] No samples found: skewer [2023-08-16 22:04:13,523] multiqc [DEBUG ] No samples found: sortmerna [2023-08-16 22:04:13,529] multiqc [DEBUG ] No samples found: biobloomtools [2023-08-16 22:04:13,535] multiqc [DEBUG ] No samples found: fastq_screen [2023-08-16 22:04:13,540] multiqc [DEBUG ] No samples found: afterqc [2023-08-16 22:04:13,546] multiqc [DEBUG ] No samples found: fastp [2023-08-16 22:04:13,671] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-08-16 22:04:13,728] multiqc [DEBUG ] No samples found: pycoqc [2023-08-16 22:04:13,738] multiqc [DEBUG ] No samples found: minionqc [2023-08-16 22:04:13,744] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-08-16 22:04:13,750] multiqc [DEBUG ] No samples found: clusterflow [2023-08-16 22:04:13,756] multiqc [DEBUG ] No samples found: bcl2fastq [2023-08-16 22:04:13,762] multiqc [DEBUG ] No samples found: interop [2023-08-16 22:04:13,769] multiqc [DEBUG ] No samples found: ivar [2023-08-16 22:04:13,776] multiqc [DEBUG ] No samples found: flash [2023-08-16 22:04:13,782] multiqc [DEBUG ] No samples found: seqyclean [2023-08-16 22:04:13,782] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-08-16 22:04:13,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-08-16 22:04:13,783] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-08-16 22:04:13,789] multiqc [INFO ] Compressing plot data [2023-08-16 22:04:13,867] multiqc [INFO ] Report : multiqc_report.html [2023-08-16 22:04:13,867] multiqc [INFO ] Data : multiqc_data [2023-08-16 22:04:13,867] multiqc [DEBUG ] Moving data file from '/state/partition1/job-36560054/tmpzgwt52yw/multiqc_data' to '/vast/gencore/GENEFLOW/work/3b/1750adcbd1d42d5d73d747b09aea7b/merged/multiqc_data' [2023-08-16 22:04:14,210] multiqc [INFO ] MultiQC complete