[2023-01-27 03:13:49,167] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-01-27 03:13:49,167] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-01-27 03:13:49,167] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-01-27 03:13:49,170] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-01-27 03:13:49,170] 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}} [2023-01-27 03:13:49,170] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKTFTDRX2/merged [2023-01-27 03:13:49,696] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-01-27 03:13:49,696] multiqc [INFO ] This is MultiQC v1.9 [2023-01-27 03:13:49,696] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKTFTDRX2/merged [2023-01-27 03:13:49,696] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKTFTDRX2/merged [2023-01-27 03:13:49,696] multiqc [INFO ] Template : default [2023-01-27 03:13:49,696] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-01-27 03:13:49,697] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKTFTDRX2/merged [2023-01-27 03:13:49,697] 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 [2023-01-27 03:13:49,697] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-29558575/tmp7415o9tw [2023-01-27 03:13:49,809] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:49,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:49,812] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:49,812] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:49,812] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:49,812] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:49,812] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:49,865] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-01-27 03:13:52,244] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_undetermined_fastqc.html [2023-01-27 03:13:52,246] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_undetermined_fastqc.html [2023-01-27 03:13:52,285] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_OCb_fastqc.html [2023-01-27 03:13:52,287] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_OCb_fastqc.html [2023-01-27 03:13:52,326] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WCb_fastqc.html [2023-01-27 03:13:52,328] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WCb_fastqc.html [2023-01-27 03:13:52,369] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WDa_fastqc.html [2023-01-27 03:13:52,371] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WDa_fastqc.html [2023-01-27 03:13:52,411] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WDb_fastqc.html [2023-01-27 03:13:52,413] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WDb_fastqc.html [2023-01-27 03:13:52,453] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_OCa_fastqc.html [2023-01-27 03:13:52,455] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_OCa_fastqc.html [2023-01-27 03:13:52,495] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WCa_fastqc.html [2023-01-27 03:13:52,497] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_WCa_fastqc.html [2023-01-27 03:13:52,537] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_ODa_fastqc.html [2023-01-27 03:13:52,539] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_ODa_fastqc.html [2023-01-27 03:13:52,582] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTFTDRX2_n01_ODb_fastqc.html [2023-01-27 03:13:52,584] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTFTDRX2_n01_ODb_fastqc.html [2023-01-27 03:13:52,958] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-01-27 03:13:52,960] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-01-27 03:13:52,969] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-01-27 03:13:52,974] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2023-01-27 03:13:52,984] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-01-27 03:13:52,992] multiqc [DEBUG ] No samples found: conpair [2023-01-27 03:13:52,999] multiqc [DEBUG ] No samples found: peddy [2023-01-27 03:13:53,006] multiqc [DEBUG ] No samples found: somalier [2023-01-27 03:13:53,014] multiqc [DEBUG ] No samples found: methylQA [2023-01-27 03:13:53,027] multiqc [DEBUG ] No samples found: mosdepth [2023-01-27 03:13:53,033] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-01-27 03:13:53,037] multiqc [DEBUG ] No samples found: qualimap [2023-01-27 03:13:53,044] multiqc [DEBUG ] No samples found: preseq [2023-01-27 03:13:53,049] multiqc [DEBUG ] No samples found: quast [2023-01-27 03:13:53,054] multiqc [DEBUG ] No samples found: qorts [2023-01-27 03:13:53,061] multiqc [DEBUG ] No samples found: rna_seqc [2023-01-27 03:13:53,067] multiqc [DEBUG ] No samples found: rockhopper [2023-01-27 03:13:53,074] multiqc [DEBUG ] No samples found: rsem [2023-01-27 03:13:53,092] multiqc [DEBUG ] No samples found: rseqc [2023-01-27 03:13:53,096] multiqc [DEBUG ] No samples found: busco [2023-01-27 03:13:53,103] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-01-27 03:13:53,108] multiqc [DEBUG ] No samples found: disambiguate [2023-01-27 03:13:53,115] multiqc [DEBUG ] No samples found: supernova [2023-01-27 03:13:53,132] multiqc [DEBUG ] No samples found: deeptools [2023-01-27 03:13:53,139] multiqc [DEBUG ] No samples found: sargasso [2023-01-27 03:13:53,143] multiqc [DEBUG ] No samples found: verifybamid [2023-01-27 03:13:53,150] multiqc [DEBUG ] No samples found: mirtrace [2023-01-27 03:13:53,156] multiqc [DEBUG ] No samples found: happy [2023-01-27 03:13:53,161] multiqc [DEBUG ] No samples found: mirtop [2023-01-27 03:13:53,167] multiqc [DEBUG ] No samples found: homer [2023-01-27 03:13:53,173] multiqc [DEBUG ] No samples found: macs2 [2023-01-27 03:13:53,180] multiqc [DEBUG ] No samples found: theta2 [2023-01-27 03:13:53,187] multiqc [DEBUG ] No samples found: snpeff [2023-01-27 03:13:53,197] multiqc [DEBUG ] No samples found: gatk [2023-01-27 03:13:53,202] multiqc [DEBUG ] No samples found: htseq [2023-01-27 03:13:53,211] multiqc [DEBUG ] No samples found: bcftools [2023-01-27 03:13:53,217] multiqc [DEBUG ] No samples found: featureCounts [2023-01-27 03:13:53,224] multiqc [DEBUG ] No samples found: fgbio [2023-01-27 03:13:53,246] multiqc [DEBUG ] No samples found: dragen [2023-01-27 03:13:53,253] multiqc [DEBUG ] No samples found: dedup [2023-01-27 03:13:53,258] multiqc [DEBUG ] No samples found: damageprofiler [2023-01-27 03:13:53,291] multiqc [DEBUG ] No samples found: biobambam2 [2023-01-27 03:13:53,296] multiqc [DEBUG ] No samples found: mtnucratio [2023-01-27 03:13:53,298] multiqc [DEBUG ] No samples found: picard [2023-01-27 03:13:53,305] multiqc [DEBUG ] No samples found: prokka [2023-01-27 03:13:53,310] multiqc [DEBUG ] No samples found: samblaster [2023-01-27 03:13:53,322] multiqc [DEBUG ] No samples found: samtools [2023-01-27 03:13:53,329] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-01-27 03:13:53,336] multiqc [DEBUG ] No samples found: bamtools [2023-01-27 03:13:53,342] multiqc [DEBUG ] No samples found: jellyfish [2023-01-27 03:13:53,352] multiqc [DEBUG ] No samples found: vcftools [2023-01-27 03:13:53,358] multiqc [DEBUG ] No samples found: longranger [2023-01-27 03:13:53,363] multiqc [DEBUG ] No samples found: stacks [2023-01-27 03:13:53,368] multiqc [DEBUG ] No samples found: varscan2 [2023-01-27 03:13:53,389] multiqc [DEBUG ] No samples found: bbmap [2023-01-27 03:13:53,397] multiqc [DEBUG ] No samples found: bismark [2023-01-27 03:13:53,403] multiqc [DEBUG ] No samples found: biscuit [2023-01-27 03:13:53,409] multiqc [DEBUG ] No samples found: hicexplorer [2023-01-27 03:13:53,417] multiqc [DEBUG ] No samples found: hicup [2023-01-27 03:13:53,423] multiqc [DEBUG ] No samples found: hicpro [2023-01-27 03:13:53,427] multiqc [DEBUG ] No samples found: salmon [2023-01-27 03:13:53,433] multiqc [DEBUG ] No samples found: kallisto [2023-01-27 03:13:53,438] multiqc [DEBUG ] No samples found: slamdunk [2023-01-27 03:13:53,444] multiqc [DEBUG ] No samples found: star [2023-01-27 03:13:53,451] multiqc [DEBUG ] No samples found: hisat2 [2023-01-27 03:13:53,456] multiqc [DEBUG ] No samples found: tophat [2023-01-27 03:13:53,461] multiqc [DEBUG ] No samples found: bowtie2 [2023-01-27 03:13:53,467] multiqc [DEBUG ] No samples found: bowtie1 [2023-01-27 03:13:53,473] multiqc [DEBUG ] No samples found: snpsplit [2023-01-27 03:13:53,477] multiqc [DEBUG ] No samples found: kat [2023-01-27 03:13:53,483] multiqc [DEBUG ] No samples found: leehom [2023-01-27 03:13:53,490] multiqc [DEBUG ] No samples found: adapterRemoval [2023-01-27 03:13:53,495] multiqc [DEBUG ] No samples found: clipandmerge [2023-01-27 03:13:53,502] multiqc [DEBUG ] No samples found: cutadapt [2023-01-27 03:13:53,506] multiqc [DEBUG ] No samples found: flexbar [2023-01-27 03:13:53,513] multiqc [DEBUG ] No samples found: kaiju [2023-01-27 03:13:53,517] multiqc [DEBUG ] No samples found: kraken [2023-01-27 03:13:53,522] multiqc [DEBUG ] No samples found: malt [2023-01-27 03:13:53,530] multiqc [DEBUG ] No samples found: trimmomatic [2023-01-27 03:13:53,538] multiqc [DEBUG ] No samples found: sickle [2023-01-27 03:13:53,543] multiqc [DEBUG ] No samples found: skewer [2023-01-27 03:13:53,551] multiqc [DEBUG ] No samples found: sortmerna [2023-01-27 03:13:53,558] multiqc [DEBUG ] No samples found: biobloomtools [2023-01-27 03:13:53,567] multiqc [DEBUG ] No samples found: fastq_screen [2023-01-27 03:13:53,573] multiqc [DEBUG ] No samples found: afterqc [2023-01-27 03:13:53,579] multiqc [DEBUG ] No samples found: fastp [2023-01-27 03:13:53,911] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports [2023-01-27 03:13:54,052] multiqc [DEBUG ] No samples found: pycoqc [2023-01-27 03:13:54,059] multiqc [DEBUG ] No samples found: minionqc [2023-01-27 03:13:54,064] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-01-27 03:13:54,071] multiqc [DEBUG ] No samples found: clusterflow [2023-01-27 03:13:54,078] multiqc [DEBUG ] No samples found: bcl2fastq [2023-01-27 03:13:54,084] multiqc [DEBUG ] No samples found: interop [2023-01-27 03:13:54,091] multiqc [DEBUG ] No samples found: ivar [2023-01-27 03:13:54,123] multiqc [DEBUG ] No samples found: flash [2023-01-27 03:13:54,129] multiqc [DEBUG ] No samples found: seqyclean [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-01-27 03:13:54,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-01-27 03:13:54,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-01-27 03:13:54,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-01-27 03:13:54,130] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-01-27 03:13:54,130] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-01-27 03:13:54,130] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-01-27 03:13:54,142] multiqc [INFO ] Compressing plot data [2023-01-27 03:13:54,323] multiqc [INFO ] Report : multiqc_report.html [2023-01-27 03:13:54,323] multiqc [INFO ] Data : multiqc_data [2023-01-27 03:13:54,323] multiqc [DEBUG ] Moving data file from '/state/partition1/job-29558575/tmp7415o9tw/multiqc_data' to '/scratch/gencore/logs/html/HKTFTDRX2/merged/multiqc_data' [2023-01-27 03:13:54,453] multiqc [INFO ] MultiQC complete