[2023-05-14 21:24:47,068] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-14 21:24:47,068] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-14 21:24:47,068] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-14 21:24:47,071] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-14 21:24:47,071] 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}} [2023-05-14 21:24:47,071] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/3 [2023-05-14 21:24:47,254] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-14 21:24:47,255] multiqc [INFO ] This is MultiQC v1.9 [2023-05-14 21:24:47,255] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/3 [2023-05-14 21:24:47,255] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H52YHDSX7/3 [2023-05-14 21:24:47,255] multiqc [INFO ] Template : default [2023-05-14 21:24:47,255] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-14 21:24:47,255] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H52YHDSX7/3 [2023-05-14 21:24:47,255] 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 [2023-05-14 21:24:47,256] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33331815/tmpce_e_yy7 [2023-05-14 21:24:47,359] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_2G_1-9_fastqc.html [2023-05-14 21:24:47,362] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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H52YHDSX7_l03_n02_5G_1-15_fastqc.html [2023-05-14 21:25:00,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_3R_1-9_fastqc.html [2023-05-14 21:25:00,348] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_3R_1-9_fastqc.html [2023-05-14 21:25:00,411] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n02_13R_1-10_fastqc.html [2023-05-14 21:25:00,413] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n02_13R_1-10_fastqc.html [2023-05-14 21:25:00,478] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10R_1-9_fastqc.html [2023-05-14 21:25:00,481] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_10R_1-9_fastqc.html [2023-05-14 21:25:00,548] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_5R_1-11_fastqc.html [2023-05-14 21:25:00,550] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_5R_1-11_fastqc.html [2023-05-14 21:25:00,601] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n02_4R_1-10_fastqc.html [2023-05-14 21:25:00,603] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n02_4R_1-10_fastqc.html [2023-05-14 21:25:00,669] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_5G_1-10_fastqc.html [2023-05-14 21:25:00,672] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l03_n01_5G_1-10_fastqc.html [2023-05-14 21:25:00,984] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 21:25:00,984] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 21:25:01,034] multiqc.modules.custom_content.custom_content [INFO ] demux_report-3: Found 98 samples (table) [2023-05-14 21:25:01,044] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-14 21:25:01,045] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-14 21:25:01,048] multiqc [DEBUG ] No samples found: conpair [2023-05-14 21:25:01,051] multiqc [DEBUG ] No samples found: peddy [2023-05-14 21:25:01,054] multiqc [DEBUG ] No samples found: somalier [2023-05-14 21:25:01,057] multiqc [DEBUG ] No samples found: methylQA [2023-05-14 21:25:01,060] multiqc [DEBUG ] No samples found: mosdepth [2023-05-14 21:25:01,063] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-14 21:25:01,066] multiqc [DEBUG ] No samples found: qualimap [2023-05-14 21:25:01,068] multiqc [DEBUG ] No samples found: preseq [2023-05-14 21:25:01,071] multiqc [DEBUG ] No samples found: quast [2023-05-14 21:25:01,074] multiqc [DEBUG ] No samples found: qorts [2023-05-14 21:25:01,077] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-14 21:25:01,079] multiqc [DEBUG ] No samples found: rockhopper [2023-05-14 21:25:01,082] multiqc [DEBUG ] No samples found: rsem [2023-05-14 21:25:01,087] multiqc [DEBUG ] No samples found: rseqc [2023-05-14 21:25:01,090] multiqc [DEBUG ] No samples found: busco [2023-05-14 21:25:01,092] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-14 21:25:01,095] multiqc [DEBUG ] No samples found: disambiguate [2023-05-14 21:25:01,098] multiqc [DEBUG ] No samples found: supernova [2023-05-14 21:25:01,103] multiqc [DEBUG ] No samples found: deeptools [2023-05-14 21:25:01,105] multiqc [DEBUG ] No samples found: sargasso [2023-05-14 21:25:01,108] multiqc [DEBUG ] No samples found: verifybamid [2023-05-14 21:25:01,111] multiqc [DEBUG ] No samples found: mirtrace [2023-05-14 21:25:01,114] multiqc [DEBUG ] No samples found: happy [2023-05-14 21:25:01,117] multiqc [DEBUG ] No samples found: mirtop [2023-05-14 21:25:01,120] multiqc [DEBUG ] No samples found: homer [2023-05-14 21:25:01,123] multiqc [DEBUG ] No samples found: macs2 [2023-05-14 21:25:01,126] multiqc [DEBUG ] No samples found: theta2 [2023-05-14 21:25:01,128] multiqc [DEBUG ] No samples found: snpeff [2023-05-14 21:25:01,132] multiqc [DEBUG ] No samples found: gatk [2023-05-14 21:25:01,134] multiqc [DEBUG ] No samples found: htseq [2023-05-14 21:25:01,137] multiqc [DEBUG ] No samples found: bcftools [2023-05-14 21:25:01,140] multiqc [DEBUG ] No samples found: featureCounts [2023-05-14 21:25:01,143] multiqc [DEBUG ] No samples found: fgbio [2023-05-14 21:25:01,148] multiqc [DEBUG ] No samples found: dragen [2023-05-14 21:25:01,151] multiqc [DEBUG ] No samples found: dedup [2023-05-14 21:25:01,154] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-14 21:25:01,162] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-14 21:25:01,165] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-14 21:25:01,167] multiqc [DEBUG ] No samples found: picard [2023-05-14 21:25:01,170] multiqc [DEBUG ] No samples found: prokka [2023-05-14 21:25:01,172] multiqc [DEBUG ] No samples found: samblaster [2023-05-14 21:25:01,176] multiqc [DEBUG ] No samples found: samtools [2023-05-14 21:25:01,179] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-14 21:25:01,181] multiqc [DEBUG ] No samples found: bamtools [2023-05-14 21:25:01,184] multiqc [DEBUG ] No samples found: jellyfish [2023-05-14 21:25:01,188] multiqc [DEBUG ] No samples found: vcftools [2023-05-14 21:25:01,190] multiqc [DEBUG ] No samples found: longranger [2023-05-14 21:25:01,193] multiqc [DEBUG ] No samples found: stacks [2023-05-14 21:25:01,196] multiqc [DEBUG ] No samples found: varscan2 [2023-05-14 21:25:01,201] multiqc [DEBUG ] No samples found: bbmap [2023-05-14 21:25:01,204] multiqc [DEBUG ] No samples found: bismark [2023-05-14 21:25:01,207] multiqc [DEBUG ] No samples found: biscuit [2023-05-14 21:25:01,210] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-14 21:25:01,213] multiqc [DEBUG ] No samples found: hicup [2023-05-14 21:25:01,216] multiqc [DEBUG ] No samples found: hicpro [2023-05-14 21:25:01,219] multiqc [DEBUG ] No samples found: salmon [2023-05-14 21:25:01,221] multiqc [DEBUG ] No samples found: kallisto [2023-05-14 21:25:01,224] multiqc [DEBUG ] No samples found: slamdunk [2023-05-14 21:25:01,227] multiqc [DEBUG ] No samples found: star [2023-05-14 21:25:01,230] multiqc [DEBUG ] No samples found: hisat2 [2023-05-14 21:25:01,232] multiqc [DEBUG ] No samples found: tophat [2023-05-14 21:25:01,235] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-14 21:25:01,238] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-14 21:25:01,241] multiqc [DEBUG ] No samples found: snpsplit [2023-05-14 21:25:01,243] multiqc [DEBUG ] No samples found: kat [2023-05-14 21:25:01,246] multiqc [DEBUG ] No samples found: leehom [2023-05-14 21:25:01,249] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-14 21:25:01,252] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-14 21:25:01,254] multiqc [DEBUG ] No samples found: cutadapt [2023-05-14 21:25:01,257] multiqc [DEBUG ] No samples found: flexbar [2023-05-14 21:25:01,260] multiqc [DEBUG ] No samples found: kaiju [2023-05-14 21:25:01,262] multiqc [DEBUG ] No samples found: kraken [2023-05-14 21:25:01,265] multiqc [DEBUG ] No samples found: malt [2023-05-14 21:25:01,268] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-14 21:25:01,271] multiqc [DEBUG ] No samples found: sickle [2023-05-14 21:25:01,273] multiqc [DEBUG ] No samples found: skewer [2023-05-14 21:25:01,276] multiqc [DEBUG ] No samples found: sortmerna [2023-05-14 21:25:01,279] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-14 21:25:01,282] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-14 21:25:01,284] multiqc [DEBUG ] No samples found: afterqc [2023-05-14 21:25:01,287] multiqc [DEBUG ] No samples found: fastp [2023-05-14 21:25:44,408] multiqc.modules.fastqc.fastqc [INFO ] Found 196 reports [2023-05-14 21:26:06,782] multiqc [DEBUG ] No samples found: pycoqc [2023-05-14 21:26:06,784] multiqc [DEBUG ] No samples found: minionqc [2023-05-14 21:26:06,787] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-14 21:26:06,790] multiqc [DEBUG ] No samples found: clusterflow [2023-05-14 21:26:06,793] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-14 21:26:06,796] multiqc [DEBUG ] No samples found: interop [2023-05-14 21:26:06,799] multiqc [DEBUG ] No samples found: ivar [2023-05-14 21:26:06,802] multiqc [DEBUG ] No samples found: flash [2023-05-14 21:26:06,804] multiqc [DEBUG ] No samples found: seqyclean [2023-05-14 21:26:06,804] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-14 21:26:06,804] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-14 21:26:06,804] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-14 21:26:06,804] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 3 Demultiplexing Report'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 3 Demultiplexing Report'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 3 Demultiplexing Report'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 3 Demultiplexing Report'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 3 Demultiplexing Report'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 3 Demultiplexing Report'. [2023-05-14 21:26:06,805] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 3 Demultiplexing Report'. [2023-05-14 21:26:07,028] multiqc [INFO ] Compressing plot data [2023-05-14 21:26:07,097] multiqc [INFO ] Report : multiqc_report.html [2023-05-14 21:26:07,097] multiqc [INFO ] Data : multiqc_data [2023-05-14 21:26:07,097] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33331815/tmpce_e_yy7/multiqc_data' to '/scratch/gencore/logs/html/H52YHDSX7/3/multiqc_data' [2023-05-14 21:26:07,222] multiqc [INFO ] MultiQC complete