[2023-09-08 22:05:16,973] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-09-08 22:05:16,973] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-09-08 22:05:16,973] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-09-08 22:05:16,976] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-09-08 22:05:16,976] 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}} [2023-09-08 22:05:16,976] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-09-08 22:05:17,155] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-09-08 22:05:17,155] multiqc [INFO ] This is MultiQC v1.9 [2023-09-08 22:05:17,155] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-09-08 22:05:17,155] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/b9/9940dfb505ae8deb596b4c5c730847/merged [2023-09-08 22:05:17,155] multiqc [INFO ] Template : default [2023-09-08 22:05:17,155] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-09-08 22:05:17,155] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/b9/9940dfb505ae8deb596b4c5c730847/merged [2023-09-08 22:05:17,156] 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 [2023-09-08 22:05:17,156] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-37501229/tmp_sp5g0q_ [2023-09-08 22:05:17,278] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_D_O1_A_fastqc.html [2023-09-08 22:05:17,286] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_D_O1_A_fastqc.html [2023-09-08 22:05:17,361] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HJ5HKDRX3_n01_H_W1_C_fastqc.html [2023-09-08 22:05:18,577] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_H_W1_E_fastqc.html [2023-09-08 22:05:18,583] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_H_W1_E_fastqc.html [2023-09-08 22:05:18,663] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_H_W8_A_fastqc.html [2023-09-08 22:05:18,670] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_H_W8_A_fastqc.html [2023-09-08 22:05:18,741] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_H_W8_B_fastqc.html [2023-09-08 22:05:18,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_H_W8_B_fastqc.html [2023-09-08 22:05:18,818] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_Z_O8_B_fastqc.html [2023-09-08 22:05:18,825] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_Z_O8_B_fastqc.html [2023-09-08 22:05:18,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_Z_W8_B_fastqc.html [2023-09-08 22:05:18,879] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_Z_W8_B_fastqc.html [2023-09-08 22:05:18,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_undetermined_fastqc.html [2023-09-08 22:05:18,931] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5HKDRX3_n01_undetermined_fastqc.html [2023-09-08 22:05:19,292] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-08 22:05:19,292] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-08 22:05:19,313] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2023-09-08 22:05:19,315] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-09-08 22:05:19,326] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-09-08 22:05:19,330] multiqc [DEBUG ] No samples found: conpair [2023-09-08 22:05:19,334] multiqc [DEBUG ] No samples found: peddy [2023-09-08 22:05:19,337] multiqc [DEBUG ] No samples found: somalier [2023-09-08 22:05:19,341] multiqc [DEBUG ] No samples found: methylQA [2023-09-08 22:05:19,345] multiqc [DEBUG ] No samples found: mosdepth [2023-09-08 22:05:19,351] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-09-08 22:05:19,354] multiqc [DEBUG ] No samples found: qualimap [2023-09-08 22:05:19,358] multiqc [DEBUG ] No samples found: preseq [2023-09-08 22:05:19,365] multiqc [DEBUG ] No samples found: quast [2023-09-08 22:05:19,369] multiqc [DEBUG ] No samples found: qorts [2023-09-08 22:05:19,375] multiqc [DEBUG ] No samples found: rna_seqc [2023-09-08 22:05:19,379] multiqc [DEBUG ] No samples found: rockhopper [2023-09-08 22:05:19,383] multiqc [DEBUG ] No samples found: rsem [2023-09-08 22:05:19,399] multiqc [DEBUG ] No samples found: rseqc [2023-09-08 22:05:19,403] multiqc [DEBUG ] No samples found: busco [2023-09-08 22:05:19,407] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-09-08 22:05:19,413] multiqc [DEBUG ] No samples found: disambiguate [2023-09-08 22:05:19,417] multiqc [DEBUG ] No samples found: supernova [2023-09-08 22:05:19,424] multiqc [DEBUG ] No samples found: deeptools [2023-09-08 22:05:19,427] multiqc [DEBUG ] No samples found: sargasso [2023-09-08 22:05:19,431] multiqc [DEBUG ] No samples found: verifybamid [2023-09-08 22:05:19,435] multiqc [DEBUG ] No samples found: mirtrace [2023-09-08 22:05:19,439] multiqc [DEBUG ] No samples found: happy [2023-09-08 22:05:19,442] multiqc [DEBUG ] No samples found: mirtop [2023-09-08 22:05:19,446] multiqc [DEBUG ] No samples found: homer [2023-09-08 22:05:19,450] multiqc [DEBUG ] No samples found: macs2 [2023-09-08 22:05:19,453] multiqc [DEBUG ] No samples found: theta2 [2023-09-08 22:05:19,456] multiqc [DEBUG ] No samples found: snpeff [2023-09-08 22:05:19,461] multiqc [DEBUG ] No samples found: gatk [2023-09-08 22:05:19,464] multiqc [DEBUG ] No samples found: htseq [2023-09-08 22:05:19,468] multiqc [DEBUG ] No samples found: bcftools [2023-09-08 22:05:19,471] multiqc [DEBUG ] No samples found: featureCounts [2023-09-08 22:05:19,475] multiqc [DEBUG ] No samples found: fgbio [2023-09-08 22:05:19,481] multiqc [DEBUG ] No samples found: dragen [2023-09-08 22:05:19,485] multiqc [DEBUG ] No samples found: dedup [2023-09-08 22:05:19,488] multiqc [DEBUG ] No samples found: damageprofiler [2023-09-08 22:05:19,498] multiqc [DEBUG ] No samples found: biobambam2 [2023-09-08 22:05:19,501] multiqc [DEBUG ] No samples found: mtnucratio [2023-09-08 22:05:19,504] multiqc [DEBUG ] No samples found: picard [2023-09-08 22:05:19,507] multiqc [DEBUG ] No samples found: prokka [2023-09-08 22:05:19,511] multiqc [DEBUG ] No samples found: samblaster [2023-09-08 22:05:19,515] multiqc [DEBUG ] No samples found: samtools [2023-09-08 22:05:19,519] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-09-08 22:05:19,522] multiqc [DEBUG ] No samples found: bamtools [2023-09-08 22:05:19,526] multiqc [DEBUG ] No samples found: jellyfish [2023-09-08 22:05:19,530] multiqc [DEBUG ] No samples found: vcftools [2023-09-08 22:05:19,533] multiqc [DEBUG ] No samples found: longranger [2023-09-08 22:05:19,537] multiqc [DEBUG ] No samples found: stacks [2023-09-08 22:05:19,540] multiqc [DEBUG ] No samples found: varscan2 [2023-09-08 22:05:19,547] multiqc [DEBUG ] No samples found: bbmap [2023-09-08 22:05:19,550] multiqc [DEBUG ] No samples found: bismark [2023-09-08 22:05:19,554] multiqc [DEBUG ] No samples found: biscuit [2023-09-08 22:05:19,558] multiqc [DEBUG ] No samples found: hicexplorer [2023-09-08 22:05:19,561] multiqc [DEBUG ] No samples found: hicup [2023-09-08 22:05:19,564] multiqc [DEBUG ] No samples found: hicpro [2023-09-08 22:05:19,568] multiqc [DEBUG ] No samples found: salmon [2023-09-08 22:05:19,571] multiqc [DEBUG ] No samples found: kallisto [2023-09-08 22:05:19,575] multiqc [DEBUG ] No samples found: slamdunk [2023-09-08 22:05:19,578] multiqc [DEBUG ] No samples found: star [2023-09-08 22:05:19,581] multiqc [DEBUG ] No samples found: hisat2 [2023-09-08 22:05:19,585] multiqc [DEBUG ] No samples found: tophat [2023-09-08 22:05:19,588] multiqc [DEBUG ] No samples found: bowtie2 [2023-09-08 22:05:19,591] multiqc [DEBUG ] No samples found: bowtie1 [2023-09-08 22:05:19,595] multiqc [DEBUG ] No samples found: snpsplit [2023-09-08 22:05:19,598] multiqc [DEBUG ] No samples found: kat [2023-09-08 22:05:19,601] multiqc [DEBUG ] No samples found: leehom [2023-09-08 22:05:19,605] multiqc [DEBUG ] No samples found: adapterRemoval [2023-09-08 22:05:19,608] multiqc [DEBUG ] No samples found: clipandmerge [2023-09-08 22:05:19,611] multiqc [DEBUG ] No samples found: cutadapt [2023-09-08 22:05:19,615] multiqc [DEBUG ] No samples found: flexbar [2023-09-08 22:05:19,618] multiqc [DEBUG ] No samples found: kaiju [2023-09-08 22:05:19,621] multiqc [DEBUG ] No samples found: kraken [2023-09-08 22:05:19,625] multiqc [DEBUG ] No samples found: malt [2023-09-08 22:05:19,628] multiqc [DEBUG ] No samples found: trimmomatic [2023-09-08 22:05:19,631] multiqc [DEBUG ] No samples found: sickle [2023-09-08 22:05:19,635] multiqc [DEBUG ] No samples found: skewer [2023-09-08 22:05:19,638] multiqc [DEBUG ] No samples found: sortmerna [2023-09-08 22:05:19,641] multiqc [DEBUG ] No samples found: biobloomtools [2023-09-08 22:05:19,644] multiqc [DEBUG ] No samples found: fastq_screen [2023-09-08 22:05:19,648] multiqc [DEBUG ] No samples found: afterqc [2023-09-08 22:05:19,651] multiqc [DEBUG ] No samples found: fastp [2023-09-08 22:05:20,810] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2023-09-08 22:05:20,812] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJ5HKDRX3_n01_D_O8_A' [2023-09-08 22:05:20,812] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJ5HKDRX3_n01_D_W8_A' [2023-09-08 22:05:20,812] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJ5HKDRX3_n01_H_O1_E' [2023-09-08 22:05:20,812] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJ5HKDRX3_n01_H_W1_C' [2023-09-08 22:05:20,812] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJ5HKDRX3_n01_Z_O8_B' [2023-09-08 22:05:20,812] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HJ5HKDRX3_n01_Z_W8_B' [2023-09-08 22:05:21,116] multiqc [DEBUG ] No samples found: pycoqc [2023-09-08 22:05:21,119] multiqc [DEBUG ] No samples found: minionqc [2023-09-08 22:05:21,122] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-09-08 22:05:21,126] multiqc [DEBUG ] No samples found: clusterflow [2023-09-08 22:05:21,129] multiqc [DEBUG ] No samples found: bcl2fastq [2023-09-08 22:05:21,133] multiqc [DEBUG ] No samples found: interop [2023-09-08 22:05:21,136] multiqc [DEBUG ] No samples found: ivar [2023-09-08 22:05:21,140] multiqc [DEBUG ] No samples found: flash [2023-09-08 22:05:21,143] multiqc [DEBUG ] No samples found: seqyclean [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-09-08 22:05:21,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-09-08 22:05:21,144] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-09-08 22:05:21,174] multiqc [INFO ] Compressing plot data [2023-09-08 22:05:21,481] multiqc [INFO ] Report : multiqc_report.html [2023-09-08 22:05:21,481] multiqc [INFO ] Data : multiqc_data [2023-09-08 22:05:21,482] multiqc [DEBUG ] Moving data file from '/state/partition1/job-37501229/tmp_sp5g0q_/multiqc_data' to '/vast/gencore/GENEFLOW/work/b9/9940dfb505ae8deb596b4c5c730847/merged/multiqc_data' [2023-09-08 22:05:21,629] multiqc [INFO ] MultiQC complete