[2023-08-15 19:29:56,322] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-08-15 19:29:56,322] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-08-15 19:29:56,322] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-08-15 19:29:56,324] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-08-15 19:29:56,324] 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}} [2023-08-15 19:29:56,325] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HW22CDRX2/2 [2023-08-15 19:29:56,473] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-08-15 19:29:56,473] multiqc [INFO ] This is MultiQC v1.9 [2023-08-15 19:29:56,473] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HW22CDRX2/2 [2023-08-15 19:29:56,473] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HW22CDRX2/2 [2023-08-15 19:29:56,473] multiqc [INFO ] Template : default [2023-08-15 19:29:56,473] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-08-15 19:29:56,473] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HW22CDRX2/2 [2023-08-15 19:29:56,473] 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 [2023-08-15 19:29:56,474] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-36508951/tmpallotu8m [2023-08-15 19:29:56,564] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:29:56,567] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-15 19:30:01,206] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l02_n01_scN3updated_fastqc.html [2023-08-15 19:30:01,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l02_n01_scN3updated_fastqc.html [2023-08-15 19:30:01,229] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l02_n01_undetermined_fastqc.html [2023-08-15 19:30:01,231] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l02_n01_undetermined_fastqc.html [2023-08-15 19:30:01,272] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l02_n02_scN2updated_fastqc.html [2023-08-15 19:30:01,274] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l02_n02_scN2updated_fastqc.html [2023-08-15 19:30:01,294] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l02_n02_scN3updated_fastqc.html [2023-08-15 19:30:01,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l02_n02_scN3updated_fastqc.html [2023-08-15 19:30:01,316] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l02_n01_scN2updated_fastqc.html [2023-08-15 19:30:01,318] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l02_n01_scN2updated_fastqc.html [2023-08-15 19:30:01,338] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l02_n02_undetermined_fastqc.html [2023-08-15 19:30:01,340] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l02_n02_undetermined_fastqc.html [2023-08-15 19:30:01,652] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-15 19:30:01,653] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-15 19:30:01,660] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 3 samples (table) [2023-08-15 19:30:01,670] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-08-15 19:30:01,672] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-08-15 19:30:01,675] multiqc [DEBUG ] No samples found: conpair [2023-08-15 19:30:01,678] multiqc [DEBUG ] No samples found: peddy [2023-08-15 19:30:01,681] multiqc [DEBUG ] No samples found: somalier [2023-08-15 19:30:01,684] multiqc [DEBUG ] No samples found: methylQA [2023-08-15 19:30:01,688] multiqc [DEBUG ] No samples found: mosdepth [2023-08-15 19:30:01,690] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-08-15 19:30:01,693] multiqc [DEBUG ] No samples found: qualimap [2023-08-15 19:30:01,696] multiqc [DEBUG ] No samples found: preseq [2023-08-15 19:30:01,698] multiqc [DEBUG ] No samples found: quast [2023-08-15 19:30:01,701] multiqc [DEBUG ] No samples found: qorts [2023-08-15 19:30:01,704] multiqc [DEBUG ] No samples found: rna_seqc [2023-08-15 19:30:01,707] multiqc [DEBUG ] No samples found: rockhopper [2023-08-15 19:30:01,710] multiqc [DEBUG ] No samples found: rsem [2023-08-15 19:30:01,714] multiqc [DEBUG ] No samples found: rseqc [2023-08-15 19:30:01,717] multiqc [DEBUG ] No samples found: busco [2023-08-15 19:30:01,720] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-08-15 19:30:01,723] multiqc [DEBUG ] No samples found: disambiguate [2023-08-15 19:30:01,726] multiqc [DEBUG ] No samples found: supernova [2023-08-15 19:30:01,730] multiqc [DEBUG ] No samples found: deeptools [2023-08-15 19:30:01,733] multiqc [DEBUG ] No samples found: sargasso [2023-08-15 19:30:01,736] multiqc [DEBUG ] No samples found: verifybamid [2023-08-15 19:30:01,739] multiqc [DEBUG ] No samples found: mirtrace [2023-08-15 19:30:01,741] multiqc [DEBUG ] No samples found: happy [2023-08-15 19:30:01,744] multiqc [DEBUG ] No samples found: mirtop [2023-08-15 19:30:01,747] multiqc [DEBUG ] No samples found: homer [2023-08-15 19:30:01,750] multiqc [DEBUG ] No samples found: macs2 [2023-08-15 19:30:01,753] multiqc [DEBUG ] No samples found: theta2 [2023-08-15 19:30:01,756] multiqc [DEBUG ] No samples found: snpeff [2023-08-15 19:30:01,759] multiqc [DEBUG ] No samples found: gatk [2023-08-15 19:30:01,762] multiqc [DEBUG ] No samples found: htseq [2023-08-15 19:30:01,765] multiqc [DEBUG ] No samples found: bcftools [2023-08-15 19:30:01,768] multiqc [DEBUG ] No samples found: featureCounts [2023-08-15 19:30:01,771] multiqc [DEBUG ] No samples found: fgbio [2023-08-15 19:30:01,776] multiqc [DEBUG ] No samples found: dragen [2023-08-15 19:30:01,779] multiqc [DEBUG ] No samples found: dedup [2023-08-15 19:30:01,782] multiqc [DEBUG ] No samples found: damageprofiler [2023-08-15 19:30:01,790] multiqc [DEBUG ] No samples found: biobambam2 [2023-08-15 19:30:01,793] multiqc [DEBUG ] No samples found: mtnucratio [2023-08-15 19:30:01,795] multiqc [DEBUG ] No samples found: picard [2023-08-15 19:30:01,798] multiqc [DEBUG ] No samples found: prokka [2023-08-15 19:30:01,801] multiqc [DEBUG ] No samples found: samblaster [2023-08-15 19:30:01,805] multiqc [DEBUG ] No samples found: samtools [2023-08-15 19:30:01,807] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-08-15 19:30:01,811] multiqc [DEBUG ] No samples found: bamtools [2023-08-15 19:30:01,813] multiqc [DEBUG ] No samples found: jellyfish [2023-08-15 19:30:01,817] multiqc [DEBUG ] No samples found: vcftools [2023-08-15 19:30:01,820] multiqc [DEBUG ] No samples found: longranger [2023-08-15 19:30:01,822] multiqc [DEBUG ] No samples found: stacks [2023-08-15 19:30:01,825] multiqc [DEBUG ] No samples found: varscan2 [2023-08-15 19:30:01,830] multiqc [DEBUG ] No samples found: bbmap [2023-08-15 19:30:01,833] multiqc [DEBUG ] No samples found: bismark [2023-08-15 19:30:01,836] multiqc [DEBUG ] No samples found: biscuit [2023-08-15 19:30:01,839] multiqc [DEBUG ] No samples found: hicexplorer [2023-08-15 19:30:01,842] multiqc [DEBUG ] No samples found: hicup [2023-08-15 19:30:01,845] multiqc [DEBUG ] No samples found: hicpro [2023-08-15 19:30:01,847] multiqc [DEBUG ] No samples found: salmon [2023-08-15 19:30:01,850] multiqc [DEBUG ] No samples found: kallisto [2023-08-15 19:30:01,853] multiqc [DEBUG ] No samples found: slamdunk [2023-08-15 19:30:01,856] multiqc [DEBUG ] No samples found: star [2023-08-15 19:30:01,859] multiqc [DEBUG ] No samples found: hisat2 [2023-08-15 19:30:01,861] multiqc [DEBUG ] No samples found: tophat [2023-08-15 19:30:01,864] multiqc [DEBUG ] No samples found: bowtie2 [2023-08-15 19:30:01,867] multiqc [DEBUG ] No samples found: bowtie1 [2023-08-15 19:30:01,870] multiqc [DEBUG ] No samples found: snpsplit [2023-08-15 19:30:01,872] multiqc [DEBUG ] No samples found: kat [2023-08-15 19:30:01,875] multiqc [DEBUG ] No samples found: leehom [2023-08-15 19:30:01,878] multiqc [DEBUG ] No samples found: adapterRemoval [2023-08-15 19:30:01,881] multiqc [DEBUG ] No samples found: clipandmerge [2023-08-15 19:30:01,883] multiqc [DEBUG ] No samples found: cutadapt [2023-08-15 19:30:01,886] multiqc [DEBUG ] No samples found: flexbar [2023-08-15 19:30:01,889] multiqc [DEBUG ] No samples found: kaiju [2023-08-15 19:30:01,892] multiqc [DEBUG ] No samples found: kraken [2023-08-15 19:30:01,894] multiqc [DEBUG ] No samples found: malt [2023-08-15 19:30:01,897] multiqc [DEBUG ] No samples found: trimmomatic [2023-08-15 19:30:01,900] multiqc [DEBUG ] No samples found: sickle [2023-08-15 19:30:01,903] multiqc [DEBUG ] No samples found: skewer [2023-08-15 19:30:01,905] multiqc [DEBUG ] No samples found: sortmerna [2023-08-15 19:30:01,908] multiqc [DEBUG ] No samples found: biobloomtools [2023-08-15 19:30:01,911] multiqc [DEBUG ] No samples found: fastq_screen [2023-08-15 19:30:01,914] multiqc [DEBUG ] No samples found: afterqc [2023-08-15 19:30:01,916] multiqc [DEBUG ] No samples found: fastp [2023-08-15 19:30:02,011] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-08-15 19:30:02,012] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HW22CDRX2_l02_n02_scN2updated' [2023-08-15 19:30:02,012] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HW22CDRX2_l02_n01_scN2updated' [2023-08-15 19:30:02,012] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HW22CDRX2_l02_n02_scN3updated' [2023-08-15 19:30:02,012] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HW22CDRX2_l02_n01_scN3updated' [2023-08-15 19:30:02,054] multiqc [DEBUG ] No samples found: pycoqc [2023-08-15 19:30:02,057] multiqc [DEBUG ] No samples found: minionqc [2023-08-15 19:30:02,060] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-08-15 19:30:02,063] multiqc [DEBUG ] No samples found: clusterflow [2023-08-15 19:30:02,066] multiqc [DEBUG ] No samples found: bcl2fastq [2023-08-15 19:30:02,069] multiqc [DEBUG ] No samples found: interop [2023-08-15 19:30:02,071] multiqc [DEBUG ] No samples found: ivar [2023-08-15 19:30:02,074] multiqc [DEBUG ] No samples found: flash [2023-08-15 19:30:02,077] multiqc [DEBUG ] No samples found: seqyclean [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 2 Demultiplexing Report'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 2 Demultiplexing Report'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 2 Demultiplexing Report'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 2 Demultiplexing Report'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 2 Demultiplexing Report'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 2 Demultiplexing Report'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-08-15 19:30:02,077] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-08-15 19:30:02,078] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-08-15 19:30:02,086] multiqc [INFO ] Compressing plot data [2023-08-15 19:30:02,149] multiqc [INFO ] Report : multiqc_report.html [2023-08-15 19:30:02,149] multiqc [INFO ] Data : multiqc_data [2023-08-15 19:30:02,149] multiqc [DEBUG ] Moving data file from '/state/partition1/job-36508951/tmpallotu8m/multiqc_data' to '/scratch/gencore/logs/html/HW22CDRX2/2/multiqc_data' [2023-08-15 19:30:02,244] multiqc [INFO ] MultiQC complete