[2023-05-14 16:25:35,594] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-14 16:25:35,594] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-14 16:25:35,595] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-14 16:25:35,597] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-14 16:25:35,597] 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 16:25:35,597] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/1 [2023-05-14 16:25:35,756] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-14 16:25:35,757] multiqc [INFO ] This is MultiQC v1.9 [2023-05-14 16:25:35,757] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/1 [2023-05-14 16:25:35,757] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H52YHDSX7/1 [2023-05-14 16:25:35,757] multiqc [INFO ] Template : default [2023-05-14 16:25:35,769] 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 16:25:35,770] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H52YHDSX7/1 [2023-05-14 16:25:35,770] 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 16:25:35,770] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33331815/tmpmhkdavpc [2023-05-14 16:25:35,902] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_15G_1-16_fastqc.html [2023-05-14 16:25:35,904] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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H52YHDSX7_l01_n01_7R_1-16_fastqc.html [2023-05-14 16:25:48,016] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_13R_1-16_fastqc.html [2023-05-14 16:25:48,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_13R_1-16_fastqc.html [2023-05-14 16:25:48,081] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_12R_1-3_fastqc.html [2023-05-14 16:25:48,083] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_12R_1-3_fastqc.html [2023-05-14 16:25:48,142] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_8G_1-3_fastqc.html [2023-05-14 16:25:48,144] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_8G_1-3_fastqc.html [2023-05-14 16:25:48,210] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_14R_1-3_fastqc.html [2023-05-14 16:25:48,212] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_14R_1-3_fastqc.html [2023-05-14 16:25:48,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_9R_1-2_fastqc.html [2023-05-14 16:25:48,273] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_9R_1-2_fastqc.html [2023-05-14 16:25:48,344] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_8G_1-16_fastqc.html [2023-05-14 16:25:48,346] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n01_8G_1-16_fastqc.html [2023-05-14 16:25:48,394] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_10G_1-2_fastqc.html [2023-05-14 16:25:48,396] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_10G_1-2_fastqc.html [2023-05-14 16:25:48,451] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_14G_1-16_fastqc.html [2023-05-14 16:25:48,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_14G_1-16_fastqc.html [2023-05-14 16:25:48,508] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_4R_1-14_fastqc.html [2023-05-14 16:25:48,509] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l01_n02_4R_1-14_fastqc.html [2023-05-14 16:25:48,969] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 16:25:48,970] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 16:25:49,021] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 98 samples (table) [2023-05-14 16:25:49,022] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-14 16:25:49,032] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-14 16:25:49,036] multiqc [DEBUG ] No samples found: conpair [2023-05-14 16:25:49,040] multiqc [DEBUG ] No samples found: peddy [2023-05-14 16:25:49,044] multiqc [DEBUG ] No samples found: somalier [2023-05-14 16:25:49,048] multiqc [DEBUG ] No samples found: methylQA [2023-05-14 16:25:49,055] multiqc [DEBUG ] No samples found: mosdepth [2023-05-14 16:25:49,059] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-14 16:25:49,062] multiqc [DEBUG ] No samples found: qualimap [2023-05-14 16:25:49,066] multiqc [DEBUG ] No samples found: preseq [2023-05-14 16:25:49,070] multiqc [DEBUG ] No samples found: quast [2023-05-14 16:25:49,074] multiqc [DEBUG ] No samples found: qorts [2023-05-14 16:25:49,078] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-14 16:25:49,082] multiqc [DEBUG ] No samples found: rockhopper [2023-05-14 16:25:49,086] multiqc [DEBUG ] No samples found: rsem [2023-05-14 16:25:49,095] multiqc [DEBUG ] No samples found: rseqc [2023-05-14 16:25:49,099] multiqc [DEBUG ] No samples found: busco [2023-05-14 16:25:49,103] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-14 16:25:49,107] multiqc [DEBUG ] No samples found: disambiguate [2023-05-14 16:25:49,111] multiqc [DEBUG ] No samples found: supernova [2023-05-14 16:25:49,122] multiqc [DEBUG ] No samples found: deeptools [2023-05-14 16:25:49,127] multiqc [DEBUG ] No samples found: sargasso [2023-05-14 16:25:49,131] multiqc [DEBUG ] No samples found: verifybamid [2023-05-14 16:25:49,135] multiqc [DEBUG ] No samples found: mirtrace [2023-05-14 16:25:49,139] multiqc [DEBUG ] No samples found: happy [2023-05-14 16:25:49,142] multiqc [DEBUG ] No samples found: mirtop [2023-05-14 16:25:49,148] multiqc [DEBUG ] No samples found: homer [2023-05-14 16:25:49,152] multiqc [DEBUG ] No samples found: macs2 [2023-05-14 16:25:49,155] multiqc [DEBUG ] No samples found: theta2 [2023-05-14 16:25:49,159] multiqc [DEBUG ] No samples found: snpeff [2023-05-14 16:25:49,165] multiqc [DEBUG ] No samples found: gatk [2023-05-14 16:25:49,169] multiqc [DEBUG ] No samples found: htseq [2023-05-14 16:25:49,174] multiqc [DEBUG ] No samples found: bcftools [2023-05-14 16:25:49,177] multiqc [DEBUG ] No samples found: featureCounts [2023-05-14 16:25:49,183] multiqc [DEBUG ] No samples found: fgbio [2023-05-14 16:25:49,193] multiqc [DEBUG ] No samples found: dragen [2023-05-14 16:25:49,197] multiqc [DEBUG ] No samples found: dedup [2023-05-14 16:25:49,201] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-14 16:25:49,220] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-14 16:25:49,224] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-14 16:25:49,226] multiqc [DEBUG ] No samples found: picard [2023-05-14 16:25:49,230] multiqc [DEBUG ] No samples found: prokka [2023-05-14 16:25:49,234] multiqc [DEBUG ] No samples found: samblaster [2023-05-14 16:25:49,241] multiqc [DEBUG ] No samples found: samtools [2023-05-14 16:25:49,245] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-14 16:25:49,249] multiqc [DEBUG ] No samples found: bamtools [2023-05-14 16:25:49,252] multiqc [DEBUG ] No samples found: jellyfish [2023-05-14 16:25:49,258] multiqc [DEBUG ] No samples found: vcftools [2023-05-14 16:25:49,262] multiqc [DEBUG ] No samples found: longranger [2023-05-14 16:25:49,266] multiqc [DEBUG ] No samples found: stacks [2023-05-14 16:25:49,270] multiqc [DEBUG ] No samples found: varscan2 [2023-05-14 16:25:49,281] multiqc [DEBUG ] No samples found: bbmap [2023-05-14 16:25:49,285] multiqc [DEBUG ] No samples found: bismark [2023-05-14 16:25:49,290] multiqc [DEBUG ] No samples found: biscuit [2023-05-14 16:25:49,294] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-14 16:25:49,298] multiqc [DEBUG ] No samples found: hicup [2023-05-14 16:25:49,302] multiqc [DEBUG ] No samples found: hicpro [2023-05-14 16:25:49,306] multiqc [DEBUG ] No samples found: salmon [2023-05-14 16:25:49,309] multiqc [DEBUG ] No samples found: kallisto [2023-05-14 16:25:49,314] multiqc [DEBUG ] No samples found: slamdunk [2023-05-14 16:25:49,317] multiqc [DEBUG ] No samples found: star [2023-05-14 16:25:49,321] multiqc [DEBUG ] No samples found: hisat2 [2023-05-14 16:25:49,325] multiqc [DEBUG ] No samples found: tophat [2023-05-14 16:25:49,329] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-14 16:25:49,333] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-14 16:25:49,337] multiqc [DEBUG ] No samples found: snpsplit [2023-05-14 16:25:49,341] multiqc [DEBUG ] No samples found: kat [2023-05-14 16:25:49,345] multiqc [DEBUG ] No samples found: leehom [2023-05-14 16:25:49,349] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-14 16:25:49,352] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-14 16:25:49,356] multiqc [DEBUG ] No samples found: cutadapt [2023-05-14 16:25:49,360] multiqc [DEBUG ] No samples found: flexbar [2023-05-14 16:25:49,364] multiqc [DEBUG ] No samples found: kaiju [2023-05-14 16:25:49,368] multiqc [DEBUG ] No samples found: kraken [2023-05-14 16:25:49,372] multiqc [DEBUG ] No samples found: malt [2023-05-14 16:25:49,376] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-14 16:25:49,380] multiqc [DEBUG ] No samples found: sickle [2023-05-14 16:25:49,384] multiqc [DEBUG ] No samples found: skewer [2023-05-14 16:25:49,387] multiqc [DEBUG ] No samples found: sortmerna [2023-05-14 16:25:49,391] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-14 16:25:49,395] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-14 16:25:49,399] multiqc [DEBUG ] No samples found: afterqc [2023-05-14 16:25:49,403] multiqc [DEBUG ] No samples found: fastp [2023-05-14 16:26:31,236] multiqc.modules.fastqc.fastqc [INFO ] Found 196 reports [2023-05-14 16:26:53,363] multiqc [DEBUG ] No samples found: pycoqc [2023-05-14 16:26:53,367] multiqc [DEBUG ] No samples found: minionqc [2023-05-14 16:26:53,371] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-14 16:26:53,375] multiqc [DEBUG ] No samples found: clusterflow [2023-05-14 16:26:53,379] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-14 16:26:53,383] multiqc [DEBUG ] No samples found: interop [2023-05-14 16:26:53,387] multiqc [DEBUG ] No samples found: ivar [2023-05-14 16:26:53,391] multiqc [DEBUG ] No samples found: flash [2023-05-14 16:26:53,395] multiqc [DEBUG ] No samples found: seqyclean [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-14 16:26:53,395] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-14 16:26:53,396] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-14 16:26:53,618] multiqc [INFO ] Compressing plot data [2023-05-14 16:26:53,687] multiqc [INFO ] Report : multiqc_report.html [2023-05-14 16:26:53,687] multiqc [INFO ] Data : multiqc_data [2023-05-14 16:26:53,687] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33331815/tmpmhkdavpc/multiqc_data' to '/scratch/gencore/logs/html/H52YHDSX7/1/multiqc_data' [2023-05-14 16:26:53,810] multiqc [INFO ] MultiQC complete