[2024-08-28 23:40:36,438] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-28 23:40:36,438] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-28 23:40:36,439] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-28 23:40:36,441] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-28 23:40:36,441] 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}} [2024-08-28 23:40:36,442] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-28 23:40:36,480] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-28 23:40:36,480] multiqc [INFO ] This is MultiQC v1.9 [2024-08-28 23:40:36,480] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-28 23:40:36,480] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/d2/b35511d82d7257f4dcc63d8c3b12fa/merged [2024-08-28 23:40:36,480] multiqc [INFO ] Template : default [2024-08-28 23:40:36,480] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-28 23:40:36,480] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/d2/b35511d82d7257f4dcc63d8c3b12fa/merged [2024-08-28 23:40:36,480] 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 [2024-08-28 23:40:36,481] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-50417774/tmpmeo1w73v [2024-08-28 23:40:36,591] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_H_O_A_z_fastqc.html [2024-08-28 23:40:36,594] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_H_O_A_z_fastqc.html [2024-08-28 23:40:36,644] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-08-28 23:40:37,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_H_W_A_x_fastqc.html [2024-08-28 23:40:37,724] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_H_W_A_x_fastqc.html [2024-08-28 23:40:37,771] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_O_B_x_fastqc.html [2024-08-28 23:40:37,773] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_O_B_x_fastqc.html [2024-08-28 23:40:37,820] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_W_B_Z_fastqc.html [2024-08-28 23:40:37,822] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_W_B_Z_fastqc.html [2024-08-28 23:40:37,869] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_D_O_B_z_fastqc.html [2024-08-28 23:40:37,871] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_D_O_B_z_fastqc.html [2024-08-28 23:40:37,918] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_D_W_A_z_fastqc.html [2024-08-28 23:40:37,919] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_D_W_A_z_fastqc.html [2024-08-28 23:40:37,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_D_W_B_z_fastqc.html [2024-08-28 23:40:37,968] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_D_W_B_z_fastqc.html [2024-08-28 23:40:38,015] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_H_O_A_x_fastqc.html [2024-08-28 23:40:38,017] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_H_O_A_x_fastqc.html [2024-08-28 23:40:38,065] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_W_B_x_fastqc.html [2024-08-28 23:40:38,067] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_W_B_x_fastqc.html [2024-08-28 23:40:38,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_O_B_z_fastqc.html [2024-08-28 23:40:38,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_C_O_B_z_fastqc.html [2024-08-28 23:40:38,162] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTCNDMXY_n01_E_W_A_x_fastqc.html [2024-08-28 23:40:38,164] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTCNDMXY_n01_E_W_A_x_fastqc.html [2024-08-28 23:40:38,685] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-28 23:40:38,686] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-28 23:40:38,711] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 33 samples (table) [2024-08-28 23:40:38,721] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-28 23:40:38,722] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-28 23:40:38,728] multiqc [DEBUG ] No samples found: conpair [2024-08-28 23:40:38,733] multiqc [DEBUG ] No samples found: peddy [2024-08-28 23:40:38,738] multiqc [DEBUG ] No samples found: somalier [2024-08-28 23:40:38,744] multiqc [DEBUG ] No samples found: methylQA [2024-08-28 23:40:38,752] multiqc [DEBUG ] No samples found: mosdepth [2024-08-28 23:40:38,756] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-28 23:40:38,760] multiqc [DEBUG ] No samples found: qualimap [2024-08-28 23:40:38,765] multiqc [DEBUG ] No samples found: preseq [2024-08-28 23:40:38,770] multiqc [DEBUG ] No samples found: quast [2024-08-28 23:40:38,775] multiqc [DEBUG ] No samples found: qorts [2024-08-28 23:40:38,780] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-28 23:40:38,784] multiqc [DEBUG ] No samples found: rockhopper [2024-08-28 23:40:38,789] multiqc [DEBUG ] No samples found: rsem [2024-08-28 23:40:38,801] multiqc [DEBUG ] No samples found: rseqc [2024-08-28 23:40:38,805] multiqc [DEBUG ] No samples found: busco [2024-08-28 23:40:38,811] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-28 23:40:38,815] multiqc [DEBUG ] No samples found: disambiguate [2024-08-28 23:40:38,821] multiqc [DEBUG ] No samples found: supernova [2024-08-28 23:40:38,836] multiqc [DEBUG ] No samples found: deeptools [2024-08-28 23:40:38,841] multiqc [DEBUG ] No samples found: sargasso [2024-08-28 23:40:38,847] multiqc [DEBUG ] No samples found: verifybamid [2024-08-28 23:40:38,851] multiqc [DEBUG ] No samples found: mirtrace [2024-08-28 23:40:38,856] multiqc [DEBUG ] No samples found: happy [2024-08-28 23:40:38,861] multiqc [DEBUG ] No samples found: mirtop [2024-08-28 23:40:38,868] multiqc [DEBUG ] No samples found: homer [2024-08-28 23:40:38,873] multiqc [DEBUG ] No samples found: macs2 [2024-08-28 23:40:38,877] multiqc [DEBUG ] No samples found: theta2 [2024-08-28 23:40:38,883] multiqc [DEBUG ] No samples found: snpeff [2024-08-28 23:40:38,890] multiqc [DEBUG ] No samples found: gatk [2024-08-28 23:40:38,895] multiqc [DEBUG ] No samples found: htseq [2024-08-28 23:40:38,905] multiqc [DEBUG ] No samples found: bcftools [2024-08-28 23:40:38,910] multiqc [DEBUG ] No samples found: featureCounts [2024-08-28 23:40:38,918] multiqc [DEBUG ] No samples found: fgbio [2024-08-28 23:40:38,933] multiqc [DEBUG ] No samples found: dragen [2024-08-28 23:40:38,939] multiqc [DEBUG ] No samples found: dedup [2024-08-28 23:40:38,944] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-28 23:40:38,971] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-28 23:40:38,977] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-28 23:40:38,980] multiqc [DEBUG ] No samples found: picard [2024-08-28 23:40:38,985] multiqc [DEBUG ] No samples found: prokka [2024-08-28 23:40:38,989] multiqc [DEBUG ] No samples found: samblaster [2024-08-28 23:40:38,999] multiqc [DEBUG ] No samples found: samtools [2024-08-28 23:40:39,004] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-28 23:40:39,010] multiqc [DEBUG ] No samples found: bamtools [2024-08-28 23:40:39,014] multiqc [DEBUG ] No samples found: jellyfish [2024-08-28 23:40:39,022] multiqc [DEBUG ] No samples found: vcftools [2024-08-28 23:40:39,027] multiqc [DEBUG ] No samples found: longranger [2024-08-28 23:40:39,032] multiqc [DEBUG ] No samples found: stacks [2024-08-28 23:40:39,036] multiqc [DEBUG ] No samples found: varscan2 [2024-08-28 23:40:39,053] multiqc [DEBUG ] No samples found: bbmap [2024-08-28 23:40:39,058] multiqc [DEBUG ] No samples found: bismark [2024-08-28 23:40:39,064] multiqc [DEBUG ] No samples found: biscuit [2024-08-28 23:40:39,069] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-28 23:40:39,074] multiqc [DEBUG ] No samples found: hicup [2024-08-28 23:40:39,082] multiqc [DEBUG ] No samples found: hicpro [2024-08-28 23:40:39,087] multiqc [DEBUG ] No samples found: salmon [2024-08-28 23:40:39,092] multiqc [DEBUG ] No samples found: kallisto [2024-08-28 23:40:39,097] multiqc [DEBUG ] No samples found: slamdunk [2024-08-28 23:40:39,102] multiqc [DEBUG ] No samples found: star [2024-08-28 23:40:39,107] multiqc [DEBUG ] No samples found: hisat2 [2024-08-28 23:40:39,112] multiqc [DEBUG ] No samples found: tophat [2024-08-28 23:40:39,117] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-28 23:40:39,122] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-28 23:40:39,128] multiqc [DEBUG ] No samples found: snpsplit [2024-08-28 23:40:39,134] multiqc [DEBUG ] No samples found: kat [2024-08-28 23:40:39,139] multiqc [DEBUG ] No samples found: leehom [2024-08-28 23:40:39,144] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-28 23:40:39,149] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-28 23:40:39,154] multiqc [DEBUG ] No samples found: cutadapt [2024-08-28 23:40:39,159] multiqc [DEBUG ] No samples found: flexbar [2024-08-28 23:40:39,164] multiqc [DEBUG ] No samples found: kaiju [2024-08-28 23:40:39,169] multiqc [DEBUG ] No samples found: kraken [2024-08-28 23:40:39,174] multiqc [DEBUG ] No samples found: malt [2024-08-28 23:40:39,179] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-28 23:40:39,185] multiqc [DEBUG ] No samples found: sickle [2024-08-28 23:40:39,190] multiqc [DEBUG ] No samples found: skewer [2024-08-28 23:40:39,196] multiqc [DEBUG ] No samples found: sortmerna [2024-08-28 23:40:39,200] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-28 23:40:39,205] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-28 23:40:39,211] multiqc [DEBUG ] No samples found: afterqc [2024-08-28 23:40:39,216] multiqc [DEBUG ] No samples found: fastp [2024-08-28 23:40:44,037] multiqc.modules.fastqc.fastqc [INFO ] Found 33 reports [2024-08-28 23:40:44,545] multiqc [DEBUG ] No samples found: pycoqc [2024-08-28 23:40:44,551] multiqc [DEBUG ] No samples found: minionqc [2024-08-28 23:40:44,556] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-28 23:40:44,561] multiqc [DEBUG ] No samples found: clusterflow [2024-08-28 23:40:44,566] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-28 23:40:44,571] multiqc [DEBUG ] No samples found: interop [2024-08-28 23:40:44,575] multiqc [DEBUG ] No samples found: ivar [2024-08-28 23:40:44,580] multiqc [DEBUG ] No samples found: flash [2024-08-28 23:40:44,585] multiqc [DEBUG ] No samples found: seqyclean [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-28 23:40:44,585] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-28 23:40:44,586] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-28 23:40:44,586] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-28 23:40:44,626] multiqc [INFO ] Compressing plot data [2024-08-28 23:40:45,268] multiqc [INFO ] Report : multiqc_report.html [2024-08-28 23:40:45,268] multiqc [INFO ] Data : multiqc_data [2024-08-28 23:40:45,269] multiqc [DEBUG ] Moving data file from '/state/partition1/job-50417774/tmpmeo1w73v/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/d2/b35511d82d7257f4dcc63d8c3b12fa/merged/multiqc_data' [2024-08-28 23:40:45,412] multiqc [INFO ] MultiQC complete