[2023-06-03 17:30:20,545] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-06-03 17:30:20,546] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-06-03 17:30:20,546] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-03 17:30:20,548] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-06-03 17:30:20,548] 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}} [2023-06-03 17:30:20,548] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7GY3DRX3/merged [2023-06-03 17:30:21,535] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-06-03 17:30:21,535] multiqc [INFO ] This is MultiQC v1.9 [2023-06-03 17:30:21,535] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7GY3DRX3/merged [2023-06-03 17:30:21,535] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7GY3DRX3/merged [2023-06-03 17:30:21,535] multiqc [INFO ] Template : default [2023-06-03 17:30:21,535] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-06-03 17:30:21,535] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7GY3DRX3/merged [2023-06-03 17:30:21,536] 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 [2023-06-03 17:30:21,536] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-34163321/tmp69xfdq4h [2023-06-03 17:30:21,642] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:21,645] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-03 17:30:25,661] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n01_undetermined_fastqc.html [2023-06-03 17:30:25,663] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n01_undetermined_fastqc.html [2023-06-03 17:30:25,720] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n02_undetermined_fastqc.html [2023-06-03 17:30:25,722] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n02_undetermined_fastqc.html [2023-06-03 17:30:25,776] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n01_IR64-1.2_fastqc.html [2023-06-03 17:30:25,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n01_IR64-1.2_fastqc.html [2023-06-03 17:30:25,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n01_NPB-4.2_fastqc.html [2023-06-03 17:30:25,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n01_NPB-4.2_fastqc.html [2023-06-03 17:30:25,907] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n02_AZUCENA-2.2_fastqc.html [2023-06-03 17:30:25,909] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n02_AZUCENA-2.2_fastqc.html [2023-06-03 17:30:25,989] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n01_AZUCENA-2.2_fastqc.html [2023-06-03 17:30:25,991] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n01_AZUCENA-2.2_fastqc.html [2023-06-03 17:30:26,054] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n02_NPB-4.2_fastqc.html [2023-06-03 17:30:26,056] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n02_NPB-4.2_fastqc.html [2023-06-03 17:30:26,113] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7GY3DRX3_n02_IR64-1.2_fastqc.html [2023-06-03 17:30:26,115] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7GY3DRX3_n02_IR64-1.2_fastqc.html [2023-06-03 17:30:26,437] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-03 17:30:26,438] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-03 17:30:26,446] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-06-03 17:30:26,456] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-06-03 17:30:26,458] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 4 samples (table) [2023-06-03 17:30:26,462] multiqc [DEBUG ] No samples found: conpair [2023-06-03 17:30:26,467] multiqc [DEBUG ] No samples found: peddy [2023-06-03 17:30:26,472] multiqc [DEBUG ] No samples found: somalier [2023-06-03 17:30:26,476] multiqc [DEBUG ] No samples found: methylQA [2023-06-03 17:30:26,484] multiqc [DEBUG ] No samples found: mosdepth [2023-06-03 17:30:26,489] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-03 17:30:26,492] multiqc [DEBUG ] No samples found: qualimap [2023-06-03 17:30:26,496] multiqc [DEBUG ] No samples found: preseq [2023-06-03 17:30:26,501] multiqc [DEBUG ] No samples found: quast [2023-06-03 17:30:26,505] multiqc [DEBUG ] No samples found: qorts [2023-06-03 17:30:26,510] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-03 17:30:26,514] multiqc [DEBUG ] No samples found: rockhopper [2023-06-03 17:30:26,519] multiqc [DEBUG ] No samples found: rsem [2023-06-03 17:30:26,530] multiqc [DEBUG ] No samples found: rseqc [2023-06-03 17:30:26,534] multiqc [DEBUG ] No samples found: busco [2023-06-03 17:30:26,538] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-03 17:30:26,542] multiqc [DEBUG ] No samples found: disambiguate [2023-06-03 17:30:26,547] multiqc [DEBUG ] No samples found: supernova [2023-06-03 17:30:26,558] multiqc [DEBUG ] No samples found: deeptools [2023-06-03 17:30:26,563] multiqc [DEBUG ] No samples found: sargasso [2023-06-03 17:30:26,567] multiqc [DEBUG ] No samples found: verifybamid [2023-06-03 17:30:26,572] multiqc [DEBUG ] No samples found: mirtrace [2023-06-03 17:30:26,576] multiqc [DEBUG ] No samples found: happy [2023-06-03 17:30:26,580] multiqc [DEBUG ] No samples found: mirtop [2023-06-03 17:30:26,586] multiqc [DEBUG ] No samples found: homer [2023-06-03 17:30:26,590] multiqc [DEBUG ] No samples found: macs2 [2023-06-03 17:30:26,594] multiqc [DEBUG ] No samples found: theta2 [2023-06-03 17:30:26,599] multiqc [DEBUG ] No samples found: snpeff [2023-06-03 17:30:26,605] multiqc [DEBUG ] No samples found: gatk [2023-06-03 17:30:26,609] multiqc [DEBUG ] No samples found: htseq [2023-06-03 17:30:26,614] multiqc [DEBUG ] No samples found: bcftools [2023-06-03 17:30:26,618] multiqc [DEBUG ] No samples found: featureCounts [2023-06-03 17:30:26,624] multiqc [DEBUG ] No samples found: fgbio [2023-06-03 17:30:26,635] multiqc [DEBUG ] No samples found: dragen [2023-06-03 17:30:26,640] multiqc [DEBUG ] No samples found: dedup [2023-06-03 17:30:26,644] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-03 17:30:26,664] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-03 17:30:26,669] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-03 17:30:26,672] multiqc [DEBUG ] No samples found: picard [2023-06-03 17:30:26,676] multiqc [DEBUG ] No samples found: prokka [2023-06-03 17:30:26,680] multiqc [DEBUG ] No samples found: samblaster [2023-06-03 17:30:26,688] multiqc [DEBUG ] No samples found: samtools [2023-06-03 17:30:26,692] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-03 17:30:26,697] multiqc [DEBUG ] No samples found: bamtools [2023-06-03 17:30:26,701] multiqc [DEBUG ] No samples found: jellyfish [2023-06-03 17:30:26,708] multiqc [DEBUG ] No samples found: vcftools [2023-06-03 17:30:26,712] multiqc [DEBUG ] No samples found: longranger [2023-06-03 17:30:26,716] multiqc [DEBUG ] No samples found: stacks [2023-06-03 17:30:26,721] multiqc [DEBUG ] No samples found: varscan2 [2023-06-03 17:30:26,734] multiqc [DEBUG ] No samples found: bbmap [2023-06-03 17:30:26,738] multiqc [DEBUG ] No samples found: bismark [2023-06-03 17:30:26,743] multiqc [DEBUG ] No samples found: biscuit [2023-06-03 17:30:26,748] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-03 17:30:26,752] multiqc [DEBUG ] No samples found: hicup [2023-06-03 17:30:26,756] multiqc [DEBUG ] No samples found: hicpro [2023-06-03 17:30:26,760] multiqc [DEBUG ] No samples found: salmon [2023-06-03 17:30:26,765] multiqc [DEBUG ] No samples found: kallisto [2023-06-03 17:30:26,769] multiqc [DEBUG ] No samples found: slamdunk [2023-06-03 17:30:26,773] multiqc [DEBUG ] No samples found: star [2023-06-03 17:30:26,778] multiqc [DEBUG ] No samples found: hisat2 [2023-06-03 17:30:26,782] multiqc [DEBUG ] No samples found: tophat [2023-06-03 17:30:26,787] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-03 17:30:26,791] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-03 17:30:26,795] multiqc [DEBUG ] No samples found: snpsplit [2023-06-03 17:30:26,799] multiqc [DEBUG ] No samples found: kat [2023-06-03 17:30:26,803] multiqc [DEBUG ] No samples found: leehom [2023-06-03 17:30:26,808] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-03 17:30:26,812] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-03 17:30:26,817] multiqc [DEBUG ] No samples found: cutadapt [2023-06-03 17:30:26,821] multiqc [DEBUG ] No samples found: flexbar [2023-06-03 17:30:26,825] multiqc [DEBUG ] No samples found: kaiju [2023-06-03 17:30:26,829] multiqc [DEBUG ] No samples found: kraken [2023-06-03 17:30:26,834] multiqc [DEBUG ] No samples found: malt [2023-06-03 17:30:26,838] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-03 17:30:26,842] multiqc [DEBUG ] No samples found: sickle [2023-06-03 17:30:26,847] multiqc [DEBUG ] No samples found: skewer [2023-06-03 17:30:26,851] multiqc [DEBUG ] No samples found: sortmerna [2023-06-03 17:30:26,855] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-03 17:30:26,859] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-03 17:30:26,863] multiqc [DEBUG ] No samples found: afterqc [2023-06-03 17:30:26,868] multiqc [DEBUG ] No samples found: fastp [2023-06-03 17:30:27,429] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2023-06-03 17:30:27,512] multiqc [DEBUG ] No samples found: pycoqc [2023-06-03 17:30:27,517] multiqc [DEBUG ] No samples found: minionqc [2023-06-03 17:30:27,521] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-06-03 17:30:27,526] multiqc [DEBUG ] No samples found: clusterflow [2023-06-03 17:30:27,530] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-03 17:30:27,535] multiqc [DEBUG ] No samples found: interop [2023-06-03 17:30:27,539] multiqc [DEBUG ] No samples found: ivar [2023-06-03 17:30:27,544] multiqc [DEBUG ] No samples found: flash [2023-06-03 17:30:27,548] multiqc [DEBUG ] No samples found: seqyclean [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-06-03 17:30:27,548] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-06-03 17:30:27,549] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-06-03 17:30:27,559] multiqc [INFO ] Compressing plot data [2023-06-03 17:30:27,707] multiqc [INFO ] Report : multiqc_report.html [2023-06-03 17:30:27,707] multiqc [INFO ] Data : multiqc_data [2023-06-03 17:30:27,707] multiqc [DEBUG ] Moving data file from '/state/partition1/job-34163321/tmp69xfdq4h/multiqc_data' to '/scratch/gencore/logs/html/H7GY3DRX3/merged/multiqc_data' [2023-06-03 17:30:27,863] multiqc [INFO ] MultiQC complete