[2024-08-15 03:52:27,526] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-15 03:52:27,527] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-15 03:52:27,527] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-15 03:52:27,530] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-15 03:52:27,530] 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}} [2024-08-15 03:52:27,530] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-15 03:52:27,552] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-15 03:52:27,552] multiqc [INFO ] This is MultiQC v1.9 [2024-08-15 03:52:27,552] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-15 03:52:27,552] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/f8/79ad01c7dfcc2204bd41b588b38d95/1 [2024-08-15 03:52:27,552] multiqc [INFO ] Template : default [2024-08-15 03:52:27,552] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-15 03:52:27,552] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/f8/79ad01c7dfcc2204bd41b588b38d95/1 [2024-08-15 03:52:27,553] 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 [2024-08-15 03:52:27,553] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49936029/tmptpqpehjz [2024-08-15 03:52:27,646] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT033_fastqc.html [2024-08-15 03:52:27,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT033_fastqc.html [2024-08-15 03:52:27,699] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HFC3LDRX5_l01_n02_AT035_fastqc.html [2024-08-15 03:52:30,293] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT035_fastqc.html [2024-08-15 03:52:30,340] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT101_fastqc.html [2024-08-15 03:52:30,342] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT101_fastqc.html [2024-08-15 03:52:30,390] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n01_AT102_fastqc.html [2024-08-15 03:52:30,392] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n01_AT102_fastqc.html [2024-08-15 03:52:30,439] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n01_AT027C_fastqc.html [2024-08-15 03:52:30,441] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n01_AT027C_fastqc.html [2024-08-15 03:52:30,488] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT044_fastqc.html [2024-08-15 03:52:30,490] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT044_fastqc.html [2024-08-15 03:52:30,535] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n01_AT068_fastqc.html [2024-08-15 03:52:30,537] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n01_AT068_fastqc.html [2024-08-15 03:52:30,583] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT022.2_fastqc.html [2024-08-15 03:52:30,585] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFC3LDRX5_l01_n02_AT022.2_fastqc.html [2024-08-15 03:52:30,883] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-15 03:52:30,884] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-15 03:52:30,902] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-08-15 03:52:30,904] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-15 03:52:30,914] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-15 03:52:30,917] multiqc [DEBUG ] No samples found: conpair [2024-08-15 03:52:30,920] multiqc [DEBUG ] No samples found: peddy [2024-08-15 03:52:30,923] multiqc [DEBUG ] No samples found: somalier [2024-08-15 03:52:30,925] multiqc [DEBUG ] No samples found: methylQA [2024-08-15 03:52:30,929] multiqc [DEBUG ] No samples found: mosdepth [2024-08-15 03:52:30,932] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-15 03:52:30,934] multiqc [DEBUG ] No samples found: qualimap [2024-08-15 03:52:30,937] multiqc [DEBUG ] No samples found: preseq [2024-08-15 03:52:30,940] multiqc [DEBUG ] No samples found: quast [2024-08-15 03:52:30,943] multiqc [DEBUG ] No samples found: qorts [2024-08-15 03:52:30,945] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-15 03:52:30,948] multiqc [DEBUG ] No samples found: rockhopper [2024-08-15 03:52:30,951] multiqc [DEBUG ] No samples found: rsem [2024-08-15 03:52:30,956] multiqc [DEBUG ] No samples found: rseqc [2024-08-15 03:52:30,958] multiqc [DEBUG ] No samples found: busco [2024-08-15 03:52:30,961] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-15 03:52:30,964] multiqc [DEBUG ] No samples found: disambiguate [2024-08-15 03:52:30,967] multiqc [DEBUG ] No samples found: supernova [2024-08-15 03:52:30,971] multiqc [DEBUG ] No samples found: deeptools [2024-08-15 03:52:30,974] multiqc [DEBUG ] No samples found: sargasso [2024-08-15 03:52:30,977] multiqc [DEBUG ] No samples found: verifybamid [2024-08-15 03:52:30,980] multiqc [DEBUG ] No samples found: mirtrace [2024-08-15 03:52:30,982] multiqc [DEBUG ] No samples found: happy [2024-08-15 03:52:30,985] multiqc [DEBUG ] No samples found: mirtop [2024-08-15 03:52:30,989] multiqc [DEBUG ] No samples found: homer [2024-08-15 03:52:30,993] multiqc [DEBUG ] No samples found: macs2 [2024-08-15 03:52:30,995] multiqc [DEBUG ] No samples found: theta2 [2024-08-15 03:52:30,998] multiqc [DEBUG ] No samples found: snpeff [2024-08-15 03:52:31,002] multiqc [DEBUG ] No samples found: gatk [2024-08-15 03:52:31,005] multiqc [DEBUG ] No samples found: htseq [2024-08-15 03:52:31,008] multiqc [DEBUG ] No samples found: bcftools [2024-08-15 03:52:31,011] multiqc [DEBUG ] No samples found: featureCounts [2024-08-15 03:52:31,016] multiqc [DEBUG ] No samples found: fgbio [2024-08-15 03:52:31,021] multiqc [DEBUG ] No samples found: dragen [2024-08-15 03:52:31,024] multiqc [DEBUG ] No samples found: dedup [2024-08-15 03:52:31,027] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-15 03:52:31,034] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-15 03:52:31,037] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-15 03:52:31,039] multiqc [DEBUG ] No samples found: picard [2024-08-15 03:52:31,042] multiqc [DEBUG ] No samples found: prokka [2024-08-15 03:52:31,045] multiqc [DEBUG ] No samples found: samblaster [2024-08-15 03:52:31,048] multiqc [DEBUG ] No samples found: samtools [2024-08-15 03:52:31,051] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-15 03:52:31,054] multiqc [DEBUG ] No samples found: bamtools [2024-08-15 03:52:31,057] multiqc [DEBUG ] No samples found: jellyfish [2024-08-15 03:52:31,060] multiqc [DEBUG ] No samples found: vcftools [2024-08-15 03:52:31,063] multiqc [DEBUG ] No samples found: longranger [2024-08-15 03:52:31,066] multiqc [DEBUG ] No samples found: stacks [2024-08-15 03:52:31,069] multiqc [DEBUG ] No samples found: varscan2 [2024-08-15 03:52:31,074] multiqc [DEBUG ] No samples found: bbmap [2024-08-15 03:52:31,077] multiqc [DEBUG ] No samples found: bismark [2024-08-15 03:52:31,080] multiqc [DEBUG ] No samples found: biscuit [2024-08-15 03:52:31,083] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-15 03:52:31,085] multiqc [DEBUG ] No samples found: hicup [2024-08-15 03:52:31,088] multiqc [DEBUG ] No samples found: hicpro [2024-08-15 03:52:31,091] multiqc [DEBUG ] No samples found: salmon [2024-08-15 03:52:31,094] multiqc [DEBUG ] No samples found: kallisto [2024-08-15 03:52:31,096] multiqc [DEBUG ] No samples found: slamdunk [2024-08-15 03:52:31,099] multiqc [DEBUG ] No samples found: star [2024-08-15 03:52:31,102] multiqc [DEBUG ] No samples found: hisat2 [2024-08-15 03:52:31,104] multiqc [DEBUG ] No samples found: tophat [2024-08-15 03:52:31,107] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-15 03:52:31,110] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-15 03:52:31,113] multiqc [DEBUG ] No samples found: snpsplit [2024-08-15 03:52:31,115] multiqc [DEBUG ] No samples found: kat [2024-08-15 03:52:31,118] multiqc [DEBUG ] No samples found: leehom [2024-08-15 03:52:31,121] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-15 03:52:31,123] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-15 03:52:31,126] multiqc [DEBUG ] No samples found: cutadapt [2024-08-15 03:52:31,129] multiqc [DEBUG ] No samples found: flexbar [2024-08-15 03:52:31,132] multiqc [DEBUG ] No samples found: kaiju [2024-08-15 03:52:31,134] multiqc [DEBUG ] No samples found: kraken [2024-08-15 03:52:31,137] multiqc [DEBUG ] No samples found: malt [2024-08-15 03:52:31,140] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-15 03:52:31,142] multiqc [DEBUG ] No samples found: sickle [2024-08-15 03:52:31,145] multiqc [DEBUG ] No samples found: skewer [2024-08-15 03:52:31,148] multiqc [DEBUG ] No samples found: sortmerna [2024-08-15 03:52:31,151] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-15 03:52:31,153] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-15 03:52:31,156] multiqc [DEBUG ] No samples found: afterqc [2024-08-15 03:52:31,159] multiqc [DEBUG ] No samples found: fastp [2024-08-15 03:52:34,422] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2024-08-15 03:52:35,102] multiqc [DEBUG ] No samples found: pycoqc [2024-08-15 03:52:35,105] multiqc [DEBUG ] No samples found: minionqc [2024-08-15 03:52:35,108] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-15 03:52:35,111] multiqc [DEBUG ] No samples found: clusterflow [2024-08-15 03:52:35,113] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-15 03:52:35,120] multiqc [DEBUG ] No samples found: interop [2024-08-15 03:52:35,123] multiqc [DEBUG ] No samples found: ivar [2024-08-15 03:52:35,126] multiqc [DEBUG ] No samples found: flash [2024-08-15 03:52:35,128] multiqc [DEBUG ] No samples found: seqyclean [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-15 03:52:35,129] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-15 03:52:35,190] multiqc [INFO ] Compressing plot data [2024-08-15 03:52:36,123] multiqc [INFO ] Report : multiqc_report.html [2024-08-15 03:52:36,123] multiqc [INFO ] Data : multiqc_data [2024-08-15 03:52:36,123] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49936029/tmptpqpehjz/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/f8/79ad01c7dfcc2204bd41b588b38d95/1/multiqc_data' [2024-08-15 03:52:36,237] multiqc [INFO ] MultiQC complete