[2023-06-21 04:31:25,575] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-06-21 04:31:25,575] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-06-21 04:31:25,575] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-21 04:31:25,578] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-06-21 04:31:25,578] 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}} [2023-06-21 04:31:25,578] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCMTGBGXT/merged [2023-06-21 04:31:25,789] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-06-21 04:31:25,789] multiqc [INFO ] This is MultiQC v1.9 [2023-06-21 04:31:25,789] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCMTGBGXT/merged [2023-06-21 04:31:25,789] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HCMTGBGXT/merged [2023-06-21 04:31:25,789] multiqc [INFO ] Template : default [2023-06-21 04:31:25,789] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-06-21 04:31:25,789] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HCMTGBGXT/merged [2023-06-21 04:31:25,790] 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 [2023-06-21 04:31:25,790] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-34758401/tmpo6nhjdue [2023-06-21 04:31:25,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTGBGXT_n01_pIXHALO_pegCvi-B_ab2_fastqc.html [2023-06-21 04:31:25,902] multiqc [DEBUG ] File ignored by longranger/invocation because it 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longranger/invocation because it exceeded search pattern filesize limit: HCMTGBGXT_n01_DEL2_pegCvi-B_ab2_fastqc.html [2023-06-21 04:31:27,932] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTGBGXT_n01_daplib_pegCvi-input_ab3_fastqc.html [2023-06-21 04:31:27,934] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTGBGXT_n01_daplib_pegCvi-input_ab3_fastqc.html [2023-06-21 04:31:27,978] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTGBGXT_n01_daplib_pegCol-input_ab2_fastqc.html [2023-06-21 04:31:27,980] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTGBGXT_n01_daplib_pegCol-input_ab2_fastqc.html [2023-06-21 04:31:28,021] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTGBGXT_n01_DEL2_pegCol-B_ab2_fastqc.html [2023-06-21 04:31:28,023] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTGBGXT_n01_DEL2_pegCol-B_ab2_fastqc.html [2023-06-21 04:31:28,063] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTGBGXT_n01_DEL2_pegF1CV-B_ab3_fastqc.html [2023-06-21 04:31:28,065] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTGBGXT_n01_DEL2_pegF1CV-B_ab3_fastqc.html [2023-06-21 04:31:28,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTGBGXT_n01_pIXHALO_pegF1CV-B_ab3_fastqc.html [2023-06-21 04:31:28,108] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTGBGXT_n01_pIXHALO_pegF1CV-B_ab3_fastqc.html [2023-06-21 04:31:28,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTGBGXT_n01_pIXHALO_pegF1CV-B_ab1_fastqc.html [2023-06-21 04:31:28,153] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTGBGXT_n01_pIXHALO_pegF1CV-B_ab1_fastqc.html [2023-06-21 04:31:28,601] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-21 04:31:28,602] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-21 04:31:28,634] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 53 samples (table) [2023-06-21 04:31:28,635] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-06-21 04:31:28,645] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-06-21 04:31:28,650] multiqc [DEBUG ] No samples found: conpair [2023-06-21 04:31:28,656] multiqc [DEBUG ] No samples found: peddy [2023-06-21 04:31:28,661] multiqc [DEBUG ] No samples found: somalier [2023-06-21 04:31:28,667] multiqc [DEBUG ] No samples found: methylQA [2023-06-21 04:31:28,676] multiqc [DEBUG ] No samples found: mosdepth [2023-06-21 04:31:28,681] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-21 04:31:28,684] multiqc [DEBUG ] No samples found: qualimap [2023-06-21 04:31:28,690] multiqc [DEBUG ] No samples found: preseq [2023-06-21 04:31:28,695] multiqc [DEBUG ] No samples found: quast [2023-06-21 04:31:28,700] multiqc [DEBUG ] No samples found: qorts [2023-06-21 04:31:28,704] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-21 04:31:28,709] multiqc [DEBUG ] No samples found: rockhopper [2023-06-21 04:31:28,714] multiqc [DEBUG ] No samples found: rsem [2023-06-21 04:31:28,726] multiqc [DEBUG ] No samples found: rseqc [2023-06-21 04:31:28,731] multiqc [DEBUG ] No samples found: busco [2023-06-21 04:31:28,736] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-21 04:31:28,741] multiqc [DEBUG ] No samples found: disambiguate [2023-06-21 04:31:28,746] multiqc [DEBUG ] No samples found: supernova [2023-06-21 04:31:28,759] multiqc [DEBUG ] No samples found: deeptools [2023-06-21 04:31:28,763] multiqc [DEBUG ] No samples found: sargasso [2023-06-21 04:31:28,768] multiqc [DEBUG ] No samples found: verifybamid [2023-06-21 04:31:28,773] multiqc [DEBUG ] No samples found: mirtrace [2023-06-21 04:31:28,778] multiqc [DEBUG ] No samples found: happy [2023-06-21 04:31:28,783] multiqc [DEBUG ] No samples found: mirtop [2023-06-21 04:31:28,790] multiqc [DEBUG ] No samples found: homer [2023-06-21 04:31:28,795] multiqc [DEBUG ] No samples found: macs2 [2023-06-21 04:31:28,799] multiqc [DEBUG ] No samples found: theta2 [2023-06-21 04:31:28,804] multiqc [DEBUG ] No samples found: snpeff [2023-06-21 04:31:28,811] multiqc [DEBUG ] No samples found: gatk [2023-06-21 04:31:28,816] multiqc [DEBUG ] No samples found: htseq [2023-06-21 04:31:28,823] multiqc [DEBUG ] No samples found: bcftools [2023-06-21 04:31:28,828] multiqc [DEBUG ] No samples found: featureCounts [2023-06-21 04:31:28,835] multiqc [DEBUG ] No samples found: fgbio [2023-06-21 04:31:28,847] multiqc [DEBUG ] No samples found: dragen [2023-06-21 04:31:28,852] multiqc [DEBUG ] No samples found: dedup [2023-06-21 04:31:28,857] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-21 04:31:28,880] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-21 04:31:28,885] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-21 04:31:28,888] multiqc [DEBUG ] No samples found: picard [2023-06-21 04:31:28,892] multiqc [DEBUG ] No samples found: prokka [2023-06-21 04:31:28,897] multiqc [DEBUG ] No samples found: samblaster [2023-06-21 04:31:28,905] multiqc [DEBUG ] No samples found: samtools [2023-06-21 04:31:28,910] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-21 04:31:28,916] multiqc [DEBUG ] No samples found: bamtools [2023-06-21 04:31:28,920] multiqc [DEBUG ] No samples found: jellyfish [2023-06-21 04:31:28,927] multiqc [DEBUG ] No samples found: vcftools [2023-06-21 04:31:28,933] multiqc [DEBUG ] No samples found: longranger [2023-06-21 04:31:28,938] multiqc [DEBUG ] No samples found: stacks [2023-06-21 04:31:28,943] multiqc [DEBUG ] No samples found: varscan2 [2023-06-21 04:31:28,956] multiqc [DEBUG ] No samples found: bbmap [2023-06-21 04:31:28,962] multiqc [DEBUG ] No samples found: bismark [2023-06-21 04:31:28,967] multiqc [DEBUG ] No samples found: biscuit [2023-06-21 04:31:28,973] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-21 04:31:28,977] multiqc [DEBUG ] No samples found: hicup [2023-06-21 04:31:28,982] multiqc [DEBUG ] No samples found: hicpro [2023-06-21 04:31:28,987] multiqc [DEBUG ] No samples found: salmon [2023-06-21 04:31:28,991] multiqc [DEBUG ] No samples found: kallisto [2023-06-21 04:31:28,996] multiqc [DEBUG ] No samples found: slamdunk [2023-06-21 04:31:29,002] multiqc [DEBUG ] No samples found: star [2023-06-21 04:31:29,007] multiqc [DEBUG ] No samples found: hisat2 [2023-06-21 04:31:29,012] multiqc [DEBUG ] No samples found: tophat [2023-06-21 04:31:29,016] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-21 04:31:29,021] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-21 04:31:29,026] multiqc [DEBUG ] No samples found: snpsplit [2023-06-21 04:31:29,030] multiqc [DEBUG ] No samples found: kat [2023-06-21 04:31:29,034] multiqc [DEBUG ] No samples found: leehom [2023-06-21 04:31:29,039] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-21 04:31:29,044] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-21 04:31:29,048] multiqc [DEBUG ] No samples found: cutadapt [2023-06-21 04:31:29,053] multiqc [DEBUG ] No samples found: flexbar [2023-06-21 04:31:29,058] multiqc [DEBUG ] No samples found: kaiju [2023-06-21 04:31:29,063] multiqc [DEBUG ] No samples found: kraken [2023-06-21 04:31:29,068] multiqc [DEBUG ] No samples found: malt [2023-06-21 04:31:29,073] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-21 04:31:29,077] multiqc [DEBUG ] No samples found: sickle [2023-06-21 04:31:29,082] multiqc [DEBUG ] No samples found: skewer [2023-06-21 04:31:29,086] multiqc [DEBUG ] No samples found: sortmerna [2023-06-21 04:31:29,091] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-21 04:31:29,096] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-21 04:31:29,100] multiqc [DEBUG ] No samples found: afterqc [2023-06-21 04:31:29,106] multiqc [DEBUG ] No samples found: fastp [2023-06-21 04:31:32,580] multiqc.modules.fastqc.fastqc [INFO ] Found 53 reports [2023-06-21 04:31:32,582] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HCMTGBGXT_n01_DEL2_8AmpPoolIHm-IDTp-B_ab2' [2023-06-21 04:31:33,586] multiqc [DEBUG ] No samples found: pycoqc [2023-06-21 04:31:33,591] multiqc [DEBUG ] No samples found: minionqc [2023-06-21 04:31:33,596] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-06-21 04:31:33,601] multiqc [DEBUG ] No samples found: clusterflow [2023-06-21 04:31:33,606] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-21 04:31:33,612] multiqc [DEBUG ] No samples found: interop [2023-06-21 04:31:33,616] multiqc [DEBUG ] No samples found: ivar [2023-06-21 04:31:33,621] multiqc [DEBUG ] No samples found: flash [2023-06-21 04:31:33,626] multiqc [DEBUG ] No samples found: seqyclean [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-06-21 04:31:33,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-06-21 04:31:33,627] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-06-21 04:31:33,694] multiqc [INFO ] Compressing plot data [2023-06-21 04:31:34,623] multiqc [INFO ] Report : multiqc_report.html [2023-06-21 04:31:34,623] multiqc [INFO ] Data : multiqc_data [2023-06-21 04:31:34,623] multiqc [DEBUG ] Moving data file from '/state/partition1/job-34758401/tmpo6nhjdue/multiqc_data' to '/scratch/gencore/logs/html/HCMTGBGXT/merged/multiqc_data' [2023-06-21 04:31:34,754] multiqc [INFO ] MultiQC complete