[2024-06-03 16:51:21,921] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-03 16:51:21,922] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-03 16:51:21,922] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-03 16:51:21,924] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-03 16:51:21,924] 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}} [2024-06-03 16:51:21,925] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-03 16:51:21,975] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-03 16:51:21,975] multiqc [INFO ] This is MultiQC v1.9 [2024-06-03 16:51:21,975] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-03 16:51:21,975] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/83/905a76a32a575c920ee09abb2b7c24/1 [2024-06-03 16:51:21,975] multiqc [INFO ] Template : default [2024-06-03 16:51:21,975] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-03 16:51:21,975] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/83/905a76a32a575c920ee09abb2b7c24/1 [2024-06-03 16:51:21,975] 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 [2024-06-03 16:51:21,975] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47221260/tmpu7_rhv1m [2024-06-03 16:51:22,113] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_51_fastqc.html [2024-06-03 16:51:22,121] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_51_fastqc.html [2024-06-03 16:51:22,194] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_52_fastqc.html [2024-06-03 16:51:22,201] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_52_fastqc.html [2024-06-03 16:51:22,272] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_53_fastqc.html [2024-06-03 16:51:22,283] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_53_fastqc.html [2024-06-03 16:51:22,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_54_fastqc.html [2024-06-03 16:51:22,361] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_54_fastqc.html [2024-06-03 16:51:22,430] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_55_fastqc.html [2024-06-03 16:51:22,440] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_BS_CR_55_fastqc.html [2024-06-03 16:51:22,510] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_undetermined_fastqc.html [2024-06-03 16:51:22,516] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n01_undetermined_fastqc.html [2024-06-03 16:51:22,586] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_51_fastqc.html [2024-06-03 16:51:22,598] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_51_fastqc.html [2024-06-03 16:51:22,673] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_52_fastqc.html [2024-06-03 16:51:22,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_52_fastqc.html [2024-06-03 16:51:22,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_53_fastqc.html [2024-06-03 16:51:22,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_53_fastqc.html [2024-06-03 16:51:22,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_54_fastqc.html [2024-06-03 16:51:22,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_54_fastqc.html [2024-06-03 16:51:22,903] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_55_fastqc.html [2024-06-03 16:51:22,911] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_BS_CR_55_fastqc.html [2024-06-03 16:51:22,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_undetermined_fastqc.html [2024-06-03 16:51:22,987] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJMMB_l01_n02_undetermined_fastqc.html [2024-06-03 16:51:23,054] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:23,061] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:23,061] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:23,061] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:23,061] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:23,061] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:23,061] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:23,097] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-03 16:51:24,937] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-03 16:51:24,940] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-03 16:51:24,952] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2024-06-03 16:51:24,954] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-03 16:51:24,964] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-03 16:51:24,971] multiqc [DEBUG ] No samples found: conpair [2024-06-03 16:51:24,978] multiqc [DEBUG ] No samples found: peddy [2024-06-03 16:51:24,987] multiqc [DEBUG ] No samples found: somalier [2024-06-03 16:51:24,993] multiqc [DEBUG ] No samples found: methylQA [2024-06-03 16:51:25,004] multiqc [DEBUG ] No samples found: mosdepth [2024-06-03 16:51:25,010] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-03 16:51:25,014] multiqc [DEBUG ] No samples found: qualimap [2024-06-03 16:51:25,019] multiqc [DEBUG ] No samples found: preseq [2024-06-03 16:51:25,026] multiqc [DEBUG ] No samples found: quast [2024-06-03 16:51:25,031] multiqc [DEBUG ] No samples found: qorts [2024-06-03 16:51:25,037] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-03 16:51:25,043] multiqc [DEBUG ] No samples found: rockhopper [2024-06-03 16:51:25,048] multiqc [DEBUG ] No samples found: rsem [2024-06-03 16:51:25,064] multiqc [DEBUG ] No samples found: rseqc [2024-06-03 16:51:25,069] multiqc [DEBUG ] No samples found: busco [2024-06-03 16:51:25,074] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-03 16:51:25,079] multiqc [DEBUG ] No samples found: disambiguate [2024-06-03 16:51:25,085] multiqc [DEBUG ] No samples found: supernova [2024-06-03 16:51:25,104] multiqc [DEBUG ] No samples found: deeptools [2024-06-03 16:51:25,111] multiqc [DEBUG ] No samples found: sargasso [2024-06-03 16:51:25,117] multiqc [DEBUG ] No samples found: verifybamid [2024-06-03 16:51:25,122] multiqc [DEBUG ] No samples found: mirtrace [2024-06-03 16:51:25,128] multiqc [DEBUG ] No samples found: happy [2024-06-03 16:51:25,134] multiqc [DEBUG ] No samples found: mirtop [2024-06-03 16:51:25,141] multiqc [DEBUG ] No samples found: homer [2024-06-03 16:51:25,147] multiqc [DEBUG ] No samples found: macs2 [2024-06-03 16:51:25,152] multiqc [DEBUG ] No samples found: theta2 [2024-06-03 16:51:25,158] multiqc [DEBUG ] No samples found: snpeff [2024-06-03 16:51:25,166] multiqc [DEBUG ] No samples found: gatk [2024-06-03 16:51:25,172] multiqc [DEBUG ] No samples found: htseq [2024-06-03 16:51:25,178] multiqc [DEBUG ] No samples found: bcftools [2024-06-03 16:51:25,184] multiqc [DEBUG ] No samples found: featureCounts [2024-06-03 16:51:25,192] multiqc [DEBUG ] No samples found: fgbio [2024-06-03 16:51:25,208] multiqc [DEBUG ] No samples found: dragen [2024-06-03 16:51:25,214] multiqc [DEBUG ] No samples found: dedup [2024-06-03 16:51:25,220] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-03 16:51:25,246] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-03 16:51:25,252] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-03 16:51:25,255] multiqc [DEBUG ] No samples found: picard [2024-06-03 16:51:25,260] multiqc [DEBUG ] No samples found: prokka [2024-06-03 16:51:25,265] multiqc [DEBUG ] No samples found: samblaster [2024-06-03 16:51:25,277] multiqc [DEBUG ] No samples found: samtools [2024-06-03 16:51:25,283] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-03 16:51:25,290] multiqc [DEBUG ] No samples found: bamtools [2024-06-03 16:51:25,295] multiqc [DEBUG ] No samples found: jellyfish [2024-06-03 16:51:25,304] multiqc [DEBUG ] No samples found: vcftools [2024-06-03 16:51:25,310] multiqc [DEBUG ] No samples found: longranger [2024-06-03 16:51:25,316] multiqc [DEBUG ] No samples found: stacks [2024-06-03 16:51:25,322] multiqc [DEBUG ] No samples found: varscan2 [2024-06-03 16:51:25,342] multiqc [DEBUG ] No samples found: bbmap [2024-06-03 16:51:25,348] multiqc [DEBUG ] No samples found: bismark [2024-06-03 16:51:25,354] multiqc [DEBUG ] No samples found: biscuit [2024-06-03 16:51:25,360] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-03 16:51:25,366] multiqc [DEBUG ] No samples found: hicup [2024-06-03 16:51:25,372] multiqc [DEBUG ] No samples found: hicpro [2024-06-03 16:51:25,377] multiqc [DEBUG ] No samples found: salmon [2024-06-03 16:51:25,384] multiqc [DEBUG ] No samples found: kallisto [2024-06-03 16:51:25,390] multiqc [DEBUG ] No samples found: slamdunk [2024-06-03 16:51:25,395] multiqc [DEBUG ] No samples found: star [2024-06-03 16:51:25,401] multiqc [DEBUG ] No samples found: hisat2 [2024-06-03 16:51:25,407] multiqc [DEBUG ] No samples found: tophat [2024-06-03 16:51:25,413] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-03 16:51:25,418] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-03 16:51:25,424] multiqc [DEBUG ] No samples found: snpsplit [2024-06-03 16:51:25,430] multiqc [DEBUG ] No samples found: kat [2024-06-03 16:51:25,435] multiqc [DEBUG ] No samples found: leehom [2024-06-03 16:51:25,441] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-03 16:51:25,447] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-03 16:51:25,453] multiqc [DEBUG ] No samples found: cutadapt [2024-06-03 16:51:25,458] multiqc [DEBUG ] No samples found: flexbar [2024-06-03 16:51:25,464] multiqc [DEBUG ] No samples found: kaiju [2024-06-03 16:51:25,469] multiqc [DEBUG ] No samples found: kraken [2024-06-03 16:51:25,475] multiqc [DEBUG ] No samples found: malt [2024-06-03 16:51:25,481] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-03 16:51:25,487] multiqc [DEBUG ] No samples found: sickle [2024-06-03 16:51:25,492] multiqc [DEBUG ] No samples found: skewer [2024-06-03 16:51:25,498] multiqc [DEBUG ] No samples found: sortmerna [2024-06-03 16:51:25,504] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-03 16:51:25,510] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-03 16:51:25,516] multiqc [DEBUG ] No samples found: afterqc [2024-06-03 16:51:25,523] multiqc [DEBUG ] No samples found: fastp [2024-06-03 16:51:25,636] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2024-06-03 16:51:25,765] multiqc [DEBUG ] No samples found: pycoqc [2024-06-03 16:51:25,771] multiqc [DEBUG ] No samples found: minionqc [2024-06-03 16:51:25,776] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-03 16:51:25,782] multiqc [DEBUG ] No samples found: clusterflow [2024-06-03 16:51:25,788] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-03 16:51:25,794] multiqc [DEBUG ] No samples found: interop [2024-06-03 16:51:25,800] multiqc [DEBUG ] No samples found: ivar [2024-06-03 16:51:25,805] multiqc [DEBUG ] No samples found: flash [2024-06-03 16:51:25,811] multiqc [DEBUG ] No samples found: seqyclean [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-03 16:51:25,811] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-03 16:51:25,812] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-03 16:51:25,827] multiqc [INFO ] Compressing plot data [2024-06-03 16:51:26,046] multiqc [INFO ] Report : multiqc_report.html [2024-06-03 16:51:26,046] multiqc [INFO ] Data : multiqc_data [2024-06-03 16:51:26,047] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47221260/tmpu7_rhv1m/multiqc_data' to '/vast/gencore/GENEFLOW/work/83/905a76a32a575c920ee09abb2b7c24/1/multiqc_data' [2024-06-03 16:51:26,248] multiqc [INFO ] MultiQC complete