[2024-04-10 20:07:54,737] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-04-10 20:07:54,737] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-04-10 20:07:54,737] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-04-10 20:07:54,740] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-04-10 20:07:54,740] 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}} [2024-04-10 20:07:54,740] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-10 20:07:54,771] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-04-10 20:07:54,771] multiqc [INFO ] This is MultiQC v1.9 [2024-04-10 20:07:54,771] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-10 20:07:54,771] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/71/8deae5ca5f516fe9b23f908a947c5e/merged [2024-04-10 20:07:54,771] multiqc [INFO ] Template : default [2024-04-10 20:07:54,771] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-04-10 20:07:54,771] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/71/8deae5ca5f516fe9b23f908a947c5e/merged [2024-04-10 20:07:54,772] 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 [2024-04-10 20:07:54,772] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-45174110/tmpbyh7p24q [2024-04-10 20:07:54,944] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G7GDRX5_1_fastqc.html [2024-04-10 20:07:54,954] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G7GDRX5_1_fastqc.html [2024-04-10 20:07:55,068] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G7GDRX5_2_fastqc.html [2024-04-10 20:07:55,076] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G7GDRX5_2_fastqc.html [2024-04-10 20:07:55,165] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G7GDRX5_3_fastqc.html [2024-04-10 20:07:55,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G7GDRX5_3_fastqc.html [2024-04-10 20:07:55,283] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2G7GDRX5_4_fastqc.html [2024-04-10 20:07:55,297] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2G7GDRX5_4_fastqc.html [2024-04-10 20:07:55,870] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-10 20:07:55,872] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-10 20:07:55,881] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-04-10 20:07:55,887] multiqc [DEBUG ] No samples found: conpair [2024-04-10 20:07:55,893] multiqc [DEBUG ] No samples found: peddy [2024-04-10 20:07:55,900] multiqc [DEBUG ] No samples found: somalier [2024-04-10 20:07:55,905] multiqc [DEBUG ] No samples found: methylQA [2024-04-10 20:07:55,917] multiqc [DEBUG ] No samples found: mosdepth [2024-04-10 20:07:55,923] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-04-10 20:07:55,926] multiqc [DEBUG ] No samples found: qualimap [2024-04-10 20:07:55,933] multiqc [DEBUG ] No samples found: preseq [2024-04-10 20:07:55,939] multiqc [DEBUG ] No samples found: quast [2024-04-10 20:07:55,946] multiqc [DEBUG ] No samples found: qorts [2024-04-10 20:07:55,951] multiqc [DEBUG ] No samples found: rna_seqc [2024-04-10 20:07:55,957] multiqc [DEBUG ] No samples found: rockhopper [2024-04-10 20:07:55,963] multiqc [DEBUG ] No samples found: rsem [2024-04-10 20:07:55,978] multiqc [DEBUG ] No samples found: rseqc [2024-04-10 20:07:55,984] multiqc [DEBUG ] No samples found: busco [2024-04-10 20:07:55,990] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-04-10 20:07:55,996] multiqc [DEBUG ] No samples found: disambiguate [2024-04-10 20:07:56,002] multiqc [DEBUG ] No samples found: supernova [2024-04-10 20:07:56,020] multiqc [DEBUG ] No samples found: deeptools [2024-04-10 20:07:56,026] multiqc [DEBUG ] No samples found: sargasso [2024-04-10 20:07:56,032] multiqc [DEBUG ] No samples found: verifybamid [2024-04-10 20:07:56,038] multiqc [DEBUG ] No samples found: mirtrace [2024-04-10 20:07:56,044] multiqc [DEBUG ] No samples found: happy [2024-04-10 20:07:56,050] multiqc [DEBUG ] No samples found: mirtop [2024-04-10 20:07:56,058] multiqc [DEBUG ] No samples found: homer [2024-04-10 20:07:56,064] multiqc [DEBUG ] No samples found: macs2 [2024-04-10 20:07:56,070] multiqc [DEBUG ] No samples found: theta2 [2024-04-10 20:07:56,075] multiqc [DEBUG ] No samples found: snpeff [2024-04-10 20:07:56,084] multiqc [DEBUG ] No samples found: gatk [2024-04-10 20:07:56,089] multiqc [DEBUG ] No samples found: htseq [2024-04-10 20:07:56,096] multiqc [DEBUG ] No samples found: bcftools [2024-04-10 20:07:56,103] multiqc [DEBUG ] No samples found: featureCounts [2024-04-10 20:07:56,111] multiqc [DEBUG ] No samples found: fgbio [2024-04-10 20:07:56,127] multiqc [DEBUG ] No samples found: dragen [2024-04-10 20:07:56,133] multiqc [DEBUG ] No samples found: dedup [2024-04-10 20:07:56,139] multiqc [DEBUG ] No samples found: damageprofiler [2024-04-10 20:07:56,170] multiqc [DEBUG ] No samples found: biobambam2 [2024-04-10 20:07:56,176] multiqc [DEBUG ] No samples found: mtnucratio [2024-04-10 20:07:56,178] multiqc [DEBUG ] No samples found: picard [2024-04-10 20:07:56,184] multiqc [DEBUG ] No samples found: prokka [2024-04-10 20:07:56,190] multiqc [DEBUG ] No samples found: samblaster [2024-04-10 20:07:56,200] multiqc [DEBUG ] No samples found: samtools [2024-04-10 20:07:56,206] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-04-10 20:07:56,213] multiqc [DEBUG ] No samples found: bamtools [2024-04-10 20:07:56,219] multiqc [DEBUG ] No samples found: jellyfish [2024-04-10 20:07:56,229] multiqc [DEBUG ] No samples found: vcftools [2024-04-10 20:07:56,235] multiqc [DEBUG ] No samples found: longranger [2024-04-10 20:07:56,242] multiqc [DEBUG ] No samples found: stacks [2024-04-10 20:07:56,247] multiqc [DEBUG ] No samples found: varscan2 [2024-04-10 20:07:56,267] multiqc [DEBUG ] No samples found: bbmap [2024-04-10 20:07:56,273] multiqc [DEBUG ] No samples found: bismark [2024-04-10 20:07:56,280] multiqc [DEBUG ] No samples found: biscuit [2024-04-10 20:07:56,286] multiqc [DEBUG ] No samples found: hicexplorer [2024-04-10 20:07:56,292] multiqc [DEBUG ] No samples found: hicup [2024-04-10 20:07:56,298] multiqc [DEBUG ] No samples found: hicpro [2024-04-10 20:07:56,303] multiqc [DEBUG ] No samples found: salmon [2024-04-10 20:07:56,309] multiqc [DEBUG ] No samples found: kallisto [2024-04-10 20:07:56,315] multiqc [DEBUG ] No samples found: slamdunk [2024-04-10 20:07:56,320] multiqc [DEBUG ] No samples found: star [2024-04-10 20:07:56,325] multiqc [DEBUG ] No samples found: hisat2 [2024-04-10 20:07:56,331] multiqc [DEBUG ] No samples found: tophat [2024-04-10 20:07:56,336] multiqc [DEBUG ] No samples found: bowtie2 [2024-04-10 20:07:56,342] multiqc [DEBUG ] No samples found: bowtie1 [2024-04-10 20:07:56,348] multiqc [DEBUG ] No samples found: snpsplit [2024-04-10 20:07:56,353] multiqc [DEBUG ] No samples found: kat [2024-04-10 20:07:56,359] multiqc [DEBUG ] No samples found: leehom [2024-04-10 20:07:56,365] multiqc [DEBUG ] No samples found: adapterRemoval [2024-04-10 20:07:56,371] multiqc [DEBUG ] No samples found: clipandmerge [2024-04-10 20:07:56,376] multiqc [DEBUG ] No samples found: cutadapt [2024-04-10 20:07:56,382] multiqc [DEBUG ] No samples found: flexbar [2024-04-10 20:07:56,388] multiqc [DEBUG ] No samples found: kaiju [2024-04-10 20:07:56,393] multiqc [DEBUG ] No samples found: kraken [2024-04-10 20:07:56,398] multiqc [DEBUG ] No samples found: malt [2024-04-10 20:07:56,404] multiqc [DEBUG ] No samples found: trimmomatic [2024-04-10 20:07:56,410] multiqc [DEBUG ] No samples found: sickle [2024-04-10 20:07:56,415] multiqc [DEBUG ] No samples found: skewer [2024-04-10 20:07:56,420] multiqc [DEBUG ] No samples found: sortmerna [2024-04-10 20:07:56,426] multiqc [DEBUG ] No samples found: biobloomtools [2024-04-10 20:07:56,432] multiqc [DEBUG ] No samples found: fastq_screen [2024-04-10 20:07:56,437] multiqc [DEBUG ] No samples found: afterqc [2024-04-10 20:07:56,443] multiqc [DEBUG ] No samples found: fastp [2024-04-10 20:07:56,523] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-04-10 20:07:56,585] multiqc [DEBUG ] No samples found: pycoqc [2024-04-10 20:07:56,591] multiqc [DEBUG ] No samples found: minionqc [2024-04-10 20:07:56,596] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-04-10 20:07:56,602] multiqc [DEBUG ] No samples found: clusterflow [2024-04-10 20:07:56,608] multiqc [DEBUG ] No samples found: bcl2fastq [2024-04-10 20:07:56,614] multiqc [DEBUG ] No samples found: interop [2024-04-10 20:07:56,619] multiqc [DEBUG ] No samples found: ivar [2024-04-10 20:07:56,624] multiqc [DEBUG ] No samples found: flash [2024-04-10 20:07:56,630] multiqc [DEBUG ] No samples found: seqyclean [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-04-10 20:07:56,630] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-04-10 20:07:56,631] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-04-10 20:07:56,631] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-04-10 20:07:56,631] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-04-10 20:07:56,631] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-04-10 20:07:56,636] multiqc [INFO ] Compressing plot data [2024-04-10 20:07:56,708] multiqc [INFO ] Report : multiqc_report.html [2024-04-10 20:07:56,708] multiqc [INFO ] Data : multiqc_data [2024-04-10 20:07:56,708] multiqc [DEBUG ] Moving data file from '/state/partition1/job-45174110/tmpbyh7p24q/multiqc_data' to '/vast/gencore/GENEFLOW/work/71/8deae5ca5f516fe9b23f908a947c5e/merged/multiqc_data' [2024-04-10 20:07:57,068] multiqc [INFO ] MultiQC complete