[2023-10-17 09:28:58,089] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-10-17 09:28:58,090] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-10-17 09:28:58,090] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-10-17 09:28:58,093] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-10-17 09:28:58,093] 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}} [2023-10-17 09:28:58,093] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-17 09:28:58,318] multiqc [WARNING] MultiQC Version v1.16 now available! [2023-10-17 09:28:58,319] multiqc [INFO ] This is MultiQC v1.9 [2023-10-17 09:28:58,319] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-17 09:28:58,319] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/43/d986ec79ced333ddb7b6ee2d816345/1 [2023-10-17 09:28:58,319] multiqc [INFO ] Template : default [2023-10-17 09:28:58,319] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-10-17 09:28:58,319] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/43/d986ec79ced333ddb7b6ee2d816345/1 [2023-10-17 09:28:58,319] 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 [2023-10-17 09:28:58,319] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-38949297/tmpwk_130u4 [2023-10-17 09:28:58,439] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.1_fastqc.html [2023-10-17 09:28:58,448] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.1_fastqc.html [2023-10-17 09:28:58,448] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.1_fastqc.html [2023-10-17 09:28:58,448] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.1_fastqc.html [2023-10-17 09:28:58,448] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.1_fastqc.html [2023-10-17 09:28:58,448] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.1_fastqc.html [2023-10-17 09:28:58,448] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.1_fastqc.html [2023-10-17 09:28:58,567] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.2_fastqc.html [2023-10-17 09:28:58,581] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GHTTR_l01.2_fastqc.html [2023-10-17 09:28:59,048] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 09:28:59,049] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 09:28:59,054] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-10-17 09:28:59,058] multiqc [DEBUG ] No samples found: conpair [2023-10-17 09:28:59,061] multiqc [DEBUG ] No samples found: peddy [2023-10-17 09:28:59,065] multiqc [DEBUG ] No samples found: somalier [2023-10-17 09:28:59,068] multiqc [DEBUG ] No samples found: methylQA [2023-10-17 09:28:59,072] multiqc [DEBUG ] No samples found: mosdepth [2023-10-17 09:28:59,075] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-10-17 09:28:59,077] multiqc [DEBUG ] No samples found: qualimap [2023-10-17 09:28:59,080] multiqc [DEBUG ] No samples found: preseq [2023-10-17 09:28:59,083] multiqc [DEBUG ] No samples found: quast [2023-10-17 09:28:59,086] multiqc [DEBUG ] No samples found: qorts [2023-10-17 09:28:59,089] multiqc [DEBUG ] No samples found: rna_seqc [2023-10-17 09:28:59,092] multiqc [DEBUG ] No samples found: rockhopper [2023-10-17 09:28:59,095] multiqc [DEBUG ] No samples found: rsem [2023-10-17 09:28:59,100] multiqc [DEBUG ] No samples found: rseqc [2023-10-17 09:28:59,103] multiqc [DEBUG ] No samples found: busco [2023-10-17 09:28:59,106] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-10-17 09:28:59,109] multiqc [DEBUG ] No samples found: disambiguate [2023-10-17 09:28:59,112] multiqc [DEBUG ] No samples found: supernova [2023-10-17 09:28:59,118] multiqc [DEBUG ] No samples found: deeptools [2023-10-17 09:28:59,120] multiqc [DEBUG ] No samples found: sargasso [2023-10-17 09:28:59,123] multiqc [DEBUG ] No samples found: verifybamid [2023-10-17 09:28:59,127] multiqc [DEBUG ] No samples found: mirtrace [2023-10-17 09:28:59,130] multiqc [DEBUG ] No samples found: happy [2023-10-17 09:28:59,132] multiqc [DEBUG ] No samples found: mirtop [2023-10-17 09:28:59,136] multiqc [DEBUG ] No samples found: homer [2023-10-17 09:28:59,139] multiqc [DEBUG ] No samples found: macs2 [2023-10-17 09:28:59,142] multiqc [DEBUG ] No samples found: theta2 [2023-10-17 09:28:59,145] multiqc [DEBUG ] No samples found: snpeff [2023-10-17 09:28:59,149] multiqc [DEBUG ] No samples found: gatk [2023-10-17 09:28:59,152] multiqc [DEBUG ] No samples found: htseq [2023-10-17 09:28:59,155] multiqc [DEBUG ] No samples found: bcftools [2023-10-17 09:28:59,158] multiqc [DEBUG ] No samples found: featureCounts [2023-10-17 09:28:59,161] multiqc [DEBUG ] No samples found: fgbio [2023-10-17 09:28:59,167] multiqc [DEBUG ] No samples found: dragen [2023-10-17 09:28:59,169] multiqc [DEBUG ] No samples found: dedup [2023-10-17 09:28:59,172] multiqc [DEBUG ] No samples found: damageprofiler [2023-10-17 09:28:59,181] multiqc [DEBUG ] No samples found: biobambam2 [2023-10-17 09:28:59,185] multiqc [DEBUG ] No samples found: mtnucratio [2023-10-17 09:28:59,187] multiqc [DEBUG ] No samples found: picard [2023-10-17 09:28:59,191] multiqc [DEBUG ] No samples found: prokka [2023-10-17 09:28:59,194] multiqc [DEBUG ] No samples found: samblaster [2023-10-17 09:28:59,197] multiqc [DEBUG ] No samples found: samtools [2023-10-17 09:28:59,200] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-10-17 09:28:59,204] multiqc [DEBUG ] No samples found: bamtools [2023-10-17 09:28:59,206] multiqc [DEBUG ] No samples found: jellyfish [2023-10-17 09:28:59,210] multiqc [DEBUG ] No samples found: vcftools [2023-10-17 09:28:59,213] multiqc [DEBUG ] No samples found: longranger [2023-10-17 09:28:59,216] multiqc [DEBUG ] No samples found: stacks [2023-10-17 09:28:59,219] multiqc [DEBUG ] No samples found: varscan2 [2023-10-17 09:28:59,225] multiqc [DEBUG ] No samples found: bbmap [2023-10-17 09:28:59,227] multiqc [DEBUG ] No samples found: bismark [2023-10-17 09:28:59,231] multiqc [DEBUG ] No samples found: biscuit [2023-10-17 09:28:59,237] multiqc [DEBUG ] No samples found: hicexplorer [2023-10-17 09:28:59,240] multiqc [DEBUG ] No samples found: hicup [2023-10-17 09:28:59,243] multiqc [DEBUG ] No samples found: hicpro [2023-10-17 09:28:59,246] multiqc [DEBUG ] No samples found: salmon [2023-10-17 09:28:59,249] multiqc [DEBUG ] No samples found: kallisto [2023-10-17 09:28:59,252] multiqc [DEBUG ] No samples found: slamdunk [2023-10-17 09:28:59,255] multiqc [DEBUG ] No samples found: star [2023-10-17 09:28:59,259] multiqc [DEBUG ] No samples found: hisat2 [2023-10-17 09:28:59,263] multiqc [DEBUG ] No samples found: tophat [2023-10-17 09:28:59,267] multiqc [DEBUG ] No samples found: bowtie2 [2023-10-17 09:28:59,270] multiqc [DEBUG ] No samples found: bowtie1 [2023-10-17 09:28:59,273] multiqc [DEBUG ] No samples found: snpsplit [2023-10-17 09:28:59,276] multiqc [DEBUG ] No samples found: kat [2023-10-17 09:28:59,280] multiqc [DEBUG ] No samples found: leehom [2023-10-17 09:28:59,283] multiqc [DEBUG ] No samples found: adapterRemoval [2023-10-17 09:28:59,287] multiqc [DEBUG ] No samples found: clipandmerge [2023-10-17 09:28:59,291] multiqc [DEBUG ] No samples found: cutadapt [2023-10-17 09:28:59,297] multiqc [DEBUG ] No samples found: flexbar [2023-10-17 09:28:59,301] multiqc [DEBUG ] No samples found: kaiju [2023-10-17 09:28:59,304] multiqc [DEBUG ] No samples found: kraken [2023-10-17 09:28:59,307] multiqc [DEBUG ] No samples found: malt [2023-10-17 09:28:59,311] multiqc [DEBUG ] No samples found: trimmomatic [2023-10-17 09:28:59,314] multiqc [DEBUG ] No samples found: sickle [2023-10-17 09:28:59,317] multiqc [DEBUG ] No samples found: skewer [2023-10-17 09:28:59,320] multiqc [DEBUG ] No samples found: sortmerna [2023-10-17 09:28:59,323] multiqc [DEBUG ] No samples found: biobloomtools [2023-10-17 09:28:59,326] multiqc [DEBUG ] No samples found: fastq_screen [2023-10-17 09:28:59,329] multiqc [DEBUG ] No samples found: afterqc [2023-10-17 09:28:59,332] multiqc [DEBUG ] No samples found: fastp [2023-10-17 09:28:59,348] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2023-10-17 09:28:59,403] multiqc [DEBUG ] No samples found: pycoqc [2023-10-17 09:28:59,406] multiqc [DEBUG ] No samples found: minionqc [2023-10-17 09:28:59,409] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-10-17 09:28:59,412] multiqc [DEBUG ] No samples found: clusterflow [2023-10-17 09:28:59,415] multiqc [DEBUG ] No samples found: bcl2fastq [2023-10-17 09:28:59,418] multiqc [DEBUG ] No samples found: interop [2023-10-17 09:28:59,421] multiqc [DEBUG ] No samples found: ivar [2023-10-17 09:28:59,425] multiqc [DEBUG ] No samples found: flash [2023-10-17 09:28:59,428] multiqc [DEBUG ] No samples found: seqyclean [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-10-17 09:28:59,428] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-10-17 09:28:59,429] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-10-17 09:28:59,429] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-10-17 09:28:59,432] multiqc [INFO ] Compressing plot data [2023-10-17 09:28:59,481] multiqc [INFO ] Report : multiqc_report.html [2023-10-17 09:28:59,481] multiqc [INFO ] Data : multiqc_data [2023-10-17 09:28:59,481] multiqc [DEBUG ] Moving data file from '/state/partition1/job-38949297/tmpwk_130u4/multiqc_data' to '/vast/gencore/GENEFLOW/work/43/d986ec79ced333ddb7b6ee2d816345/1/multiqc_data' [2023-10-17 09:28:59,646] multiqc [INFO ] MultiQC complete