[2024-05-02 16:59:32,617] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-05-02 16:59:32,617] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-05-02 16:59:32,617] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-05-02 16:59:32,620] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-05-02 16:59:32,620] 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}} [2024-05-02 16:59:32,620] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-02 16:59:32,664] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-05-02 16:59:32,664] multiqc [INFO ] This is MultiQC v1.9 [2024-05-02 16:59:32,664] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-02 16:59:32,664] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/04/f7a4138d1da374cbd53df89df934f7/merged [2024-05-02 16:59:32,664] multiqc [INFO ] Template : default [2024-05-02 16:59:32,664] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-05-02 16:59:32,664] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/04/f7a4138d1da374cbd53df89df934f7/merged [2024-05-02 16:59:32,664] 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 [2024-05-02 16:59:32,665] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-45998478/tmp00d1_ru9 [2024-05-02 16:59:32,790] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4628r_fastqc.html [2024-05-02 16:59:32,800] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4628r_fastqc.html [2024-05-02 16:59:32,877] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4644r_fastqc.html [2024-05-02 16:59:32,885] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4644r_fastqc.html [2024-05-02 16:59:32,956] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4708r_fastqc.html [2024-05-02 16:59:32,962] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4708r_fastqc.html [2024-05-02 16:59:33,031] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4797r_fastqc.html [2024-05-02 16:59:33,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4797r_fastqc.html [2024-05-02 16:59:33,117] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4848r_fastqc.html [2024-05-02 16:59:33,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n01_QG4848r_fastqc.html [2024-05-02 16:59:33,200] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n01_undetermined_fastqc.html [2024-05-02 16:59:33,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n01_undetermined_fastqc.html [2024-05-02 16:59:33,280] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4628r_fastqc.html [2024-05-02 16:59:33,287] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4628r_fastqc.html [2024-05-02 16:59:33,358] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4644r_fastqc.html [2024-05-02 16:59:33,364] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4644r_fastqc.html [2024-05-02 16:59:33,445] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4708r_fastqc.html [2024-05-02 16:59:33,457] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4708r_fastqc.html [2024-05-02 16:59:33,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4797r_fastqc.html [2024-05-02 16:59:33,531] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4797r_fastqc.html [2024-05-02 16:59:33,598] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4848r_fastqc.html [2024-05-02 16:59:33,606] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n02_QG4848r_fastqc.html [2024-05-02 16:59:33,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2YAFX5_n02_undetermined_fastqc.html [2024-05-02 16:59:33,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2YAFX5_n02_undetermined_fastqc.html [2024-05-02 16:59:33,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:33,750] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:33,750] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:33,750] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:33,750] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:33,750] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:33,751] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:33,793] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-02 16:59:36,065] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-02 16:59:36,067] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-02 16:59:36,080] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2024-05-02 16:59:36,082] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-05-02 16:59:36,092] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-05-02 16:59:36,097] multiqc [DEBUG ] No samples found: conpair [2024-05-02 16:59:36,102] multiqc [DEBUG ] No samples found: peddy [2024-05-02 16:59:36,107] multiqc [DEBUG ] No samples found: somalier [2024-05-02 16:59:36,113] multiqc [DEBUG ] No samples found: methylQA [2024-05-02 16:59:36,121] multiqc [DEBUG ] No samples found: mosdepth [2024-05-02 16:59:36,126] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-05-02 16:59:36,130] multiqc [DEBUG ] No samples found: qualimap [2024-05-02 16:59:36,135] multiqc [DEBUG ] No samples found: preseq [2024-05-02 16:59:36,140] multiqc [DEBUG ] No samples found: quast [2024-05-02 16:59:36,145] multiqc [DEBUG ] No samples found: qorts [2024-05-02 16:59:36,150] multiqc [DEBUG ] No samples found: rna_seqc [2024-05-02 16:59:36,155] multiqc [DEBUG ] No samples found: rockhopper [2024-05-02 16:59:36,159] multiqc [DEBUG ] No samples found: rsem [2024-05-02 16:59:36,172] multiqc [DEBUG ] No samples found: rseqc [2024-05-02 16:59:36,177] multiqc [DEBUG ] No samples found: busco [2024-05-02 16:59:36,182] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-05-02 16:59:36,186] multiqc [DEBUG ] No samples found: disambiguate [2024-05-02 16:59:36,192] multiqc [DEBUG ] No samples found: supernova [2024-05-02 16:59:36,205] multiqc [DEBUG ] No samples found: deeptools [2024-05-02 16:59:36,210] multiqc [DEBUG ] No samples found: sargasso [2024-05-02 16:59:36,215] multiqc [DEBUG ] No samples found: verifybamid [2024-05-02 16:59:36,220] multiqc [DEBUG ] No samples found: mirtrace [2024-05-02 16:59:36,225] multiqc [DEBUG ] No samples found: happy [2024-05-02 16:59:36,230] multiqc [DEBUG ] No samples found: mirtop [2024-05-02 16:59:36,237] multiqc [DEBUG ] No samples found: homer [2024-05-02 16:59:36,242] multiqc [DEBUG ] No samples found: macs2 [2024-05-02 16:59:36,246] multiqc [DEBUG ] No samples found: theta2 [2024-05-02 16:59:36,251] multiqc [DEBUG ] No samples found: snpeff [2024-05-02 16:59:36,259] multiqc [DEBUG ] No samples found: gatk [2024-05-02 16:59:36,263] multiqc [DEBUG ] No samples found: htseq [2024-05-02 16:59:36,269] multiqc [DEBUG ] No samples found: bcftools [2024-05-02 16:59:36,274] multiqc [DEBUG ] No samples found: featureCounts [2024-05-02 16:59:36,281] multiqc [DEBUG ] No samples found: fgbio [2024-05-02 16:59:36,294] multiqc [DEBUG ] No samples found: dragen [2024-05-02 16:59:36,299] multiqc [DEBUG ] No samples found: dedup [2024-05-02 16:59:36,304] multiqc [DEBUG ] No samples found: damageprofiler [2024-05-02 16:59:36,336] multiqc [DEBUG ] No samples found: biobambam2 [2024-05-02 16:59:36,341] multiqc [DEBUG ] No samples found: mtnucratio [2024-05-02 16:59:36,344] multiqc [DEBUG ] No samples found: picard [2024-05-02 16:59:36,349] multiqc [DEBUG ] No samples found: prokka [2024-05-02 16:59:36,353] multiqc [DEBUG ] No samples found: samblaster [2024-05-02 16:59:36,362] multiqc [DEBUG ] No samples found: samtools [2024-05-02 16:59:36,368] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-05-02 16:59:36,374] multiqc [DEBUG ] No samples found: bamtools [2024-05-02 16:59:36,379] multiqc [DEBUG ] No samples found: jellyfish [2024-05-02 16:59:36,387] multiqc [DEBUG ] No samples found: vcftools [2024-05-02 16:59:36,392] multiqc [DEBUG ] No samples found: longranger [2024-05-02 16:59:36,397] multiqc [DEBUG ] No samples found: stacks [2024-05-02 16:59:36,402] multiqc [DEBUG ] No samples found: varscan2 [2024-05-02 16:59:36,417] multiqc [DEBUG ] No samples found: bbmap [2024-05-02 16:59:36,422] multiqc [DEBUG ] No samples found: bismark [2024-05-02 16:59:36,427] multiqc [DEBUG ] No samples found: biscuit [2024-05-02 16:59:36,432] multiqc [DEBUG ] No samples found: hicexplorer [2024-05-02 16:59:36,437] multiqc [DEBUG ] No samples found: hicup [2024-05-02 16:59:36,443] multiqc [DEBUG ] No samples found: hicpro [2024-05-02 16:59:36,447] multiqc [DEBUG ] No samples found: salmon [2024-05-02 16:59:36,452] multiqc [DEBUG ] No samples found: kallisto [2024-05-02 16:59:36,457] multiqc [DEBUG ] No samples found: slamdunk [2024-05-02 16:59:36,462] multiqc [DEBUG ] No samples found: star [2024-05-02 16:59:36,467] multiqc [DEBUG ] No samples found: hisat2 [2024-05-02 16:59:36,471] multiqc [DEBUG ] No samples found: tophat [2024-05-02 16:59:36,476] multiqc [DEBUG ] No samples found: bowtie2 [2024-05-02 16:59:36,481] multiqc [DEBUG ] No samples found: bowtie1 [2024-05-02 16:59:36,486] multiqc [DEBUG ] No samples found: snpsplit [2024-05-02 16:59:36,490] multiqc [DEBUG ] No samples found: kat [2024-05-02 16:59:36,495] multiqc [DEBUG ] No samples found: leehom [2024-05-02 16:59:36,499] multiqc [DEBUG ] No samples found: adapterRemoval [2024-05-02 16:59:36,504] multiqc [DEBUG ] No samples found: clipandmerge [2024-05-02 16:59:36,509] multiqc [DEBUG ] No samples found: cutadapt [2024-05-02 16:59:36,514] multiqc [DEBUG ] No samples found: flexbar [2024-05-02 16:59:36,518] multiqc [DEBUG ] No samples found: kaiju [2024-05-02 16:59:36,523] multiqc [DEBUG ] No samples found: kraken [2024-05-02 16:59:36,528] multiqc [DEBUG ] No samples found: malt [2024-05-02 16:59:36,534] multiqc [DEBUG ] No samples found: trimmomatic [2024-05-02 16:59:36,539] multiqc [DEBUG ] No samples found: sickle [2024-05-02 16:59:36,544] multiqc [DEBUG ] No samples found: skewer [2024-05-02 16:59:36,549] multiqc [DEBUG ] No samples found: sortmerna [2024-05-02 16:59:36,554] multiqc [DEBUG ] No samples found: biobloomtools [2024-05-02 16:59:36,558] multiqc [DEBUG ] No samples found: fastq_screen [2024-05-02 16:59:36,563] multiqc [DEBUG ] No samples found: afterqc [2024-05-02 16:59:36,568] multiqc [DEBUG ] No samples found: fastp [2024-05-02 16:59:36,857] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2024-05-02 16:59:37,079] multiqc [DEBUG ] No samples found: pycoqc [2024-05-02 16:59:37,084] multiqc [DEBUG ] No samples found: minionqc [2024-05-02 16:59:37,089] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-05-02 16:59:37,094] multiqc [DEBUG ] No samples found: clusterflow [2024-05-02 16:59:37,099] multiqc [DEBUG ] No samples found: bcl2fastq [2024-05-02 16:59:37,104] multiqc [DEBUG ] No samples found: interop [2024-05-02 16:59:37,108] multiqc [DEBUG ] No samples found: ivar [2024-05-02 16:59:37,114] multiqc [DEBUG ] No samples found: flash [2024-05-02 16:59:37,118] multiqc [DEBUG ] No samples found: seqyclean [2024-05-02 16:59:37,118] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-05-02 16:59:37,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-05-02 16:59:37,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-05-02 16:59:37,118] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-05-02 16:59:37,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-05-02 16:59:37,119] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-05-02 16:59:37,135] multiqc [INFO ] Compressing plot data [2024-05-02 16:59:37,376] multiqc [INFO ] Report : multiqc_report.html [2024-05-02 16:59:37,376] multiqc [INFO ] Data : multiqc_data [2024-05-02 16:59:37,376] multiqc [DEBUG ] Moving data file from '/state/partition1/job-45998478/tmp00d1_ru9/multiqc_data' to '/vast/gencore/GENEFLOW/work/04/f7a4138d1da374cbd53df89df934f7/merged/multiqc_data' [2024-05-02 16:59:37,595] multiqc [INFO ] MultiQC complete