[2024-10-16 18:27:58,791] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-10-16 18:27:58,792] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-10-16 18:27:58,792] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-10-16 18:27:58,794] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-10-16 18:27:58,794] 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}} [2024-10-16 18:27:58,795] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-16 18:27:58,832] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-10-16 18:27:58,832] multiqc [INFO ] This is MultiQC v1.9 [2024-10-16 18:27:58,832] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-16 18:27:58,832] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/4d/9f651e523e74cfd5dcb817395e55d2/4 [2024-10-16 18:27:58,832] multiqc [INFO ] Template : default [2024-10-16 18:27:58,832] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-10-16 18:27:58,832] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/4d/9f651e523e74cfd5dcb817395e55d2/4 [2024-10-16 18:27:58,833] 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 [2024-10-16 18:27:58,833] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-52279820/tmp8vkxwpmw [2024-10-16 18:27:58,930] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Et_3_fastqc.html [2024-10-16 18:27:58,933] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Et_3_fastqc.html [2024-10-16 18:27:58,983] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HNJLWDSXC_l04_n01_P0Cp_3_fastqc.html [2024-10-16 18:28:01,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Cp_3_fastqc.html [2024-10-16 18:28:01,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Bp_3_fastqc.html [2024-10-16 18:28:01,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Bp_3_fastqc.html [2024-10-16 18:28:01,737] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_horvitzi_L2_3_fastqc.html [2024-10-16 18:28:01,739] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_horvitzi_L2_3_fastqc.html [2024-10-16 18:28:01,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_Sp_30_E_3_fastqc.html [2024-10-16 18:28:01,787] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_Sp_30_E_3_fastqc.html [2024-10-16 18:28:01,833] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Ap_3_fastqc.html [2024-10-16 18:28:01,835] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Ap_3_fastqc.html [2024-10-16 18:28:01,881] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n02_P0Ep_3_fastqc.html [2024-10-16 18:28:01,883] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n02_P0Ep_3_fastqc.html [2024-10-16 18:28:01,928] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n02_F1B_3_fastqc.html [2024-10-16 18:28:01,930] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n02_F1B_3_fastqc.html [2024-10-16 18:28:01,977] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n02_F2A_3_fastqc.html [2024-10-16 18:28:01,979] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n02_F2A_3_fastqc.html [2024-10-16 18:28:02,026] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Ep_3_fastqc.html [2024-10-16 18:28:02,028] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Ep_3_fastqc.html [2024-10-16 18:28:02,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_horvitzi_L3_3_fastqc.html [2024-10-16 18:28:02,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_horvitzi_L3_3_fastqc.html [2024-10-16 18:28:02,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Ct_3_fastqc.html [2024-10-16 18:28:02,125] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l04_n01_P0Ct_3_fastqc.html [2024-10-16 18:28:02,459] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-16 18:28:02,460] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-16 18:28:02,482] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 33 samples (table) [2024-10-16 18:28:02,492] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-10-16 18:28:02,494] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-10-16 18:28:02,497] multiqc [DEBUG ] No samples found: conpair [2024-10-16 18:28:02,500] multiqc [DEBUG ] No samples found: peddy [2024-10-16 18:28:02,504] multiqc [DEBUG ] No samples found: somalier [2024-10-16 18:28:02,507] multiqc [DEBUG ] No samples found: methylQA [2024-10-16 18:28:02,511] multiqc [DEBUG ] No samples found: mosdepth [2024-10-16 18:28:02,514] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-10-16 18:28:02,516] multiqc [DEBUG ] No samples found: qualimap [2024-10-16 18:28:02,519] multiqc [DEBUG ] No samples found: preseq [2024-10-16 18:28:02,522] multiqc [DEBUG ] No samples found: quast [2024-10-16 18:28:02,525] multiqc [DEBUG ] No samples found: qorts [2024-10-16 18:28:02,528] multiqc [DEBUG ] No samples found: rna_seqc [2024-10-16 18:28:02,531] multiqc [DEBUG ] No samples found: rockhopper [2024-10-16 18:28:02,534] multiqc [DEBUG ] No samples found: rsem [2024-10-16 18:28:02,539] multiqc [DEBUG ] No samples found: rseqc [2024-10-16 18:28:02,542] multiqc [DEBUG ] No samples found: busco [2024-10-16 18:28:02,545] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-10-16 18:28:02,548] multiqc [DEBUG ] No samples found: disambiguate [2024-10-16 18:28:02,551] multiqc [DEBUG ] No samples found: supernova [2024-10-16 18:28:02,556] multiqc [DEBUG ] No samples found: deeptools [2024-10-16 18:28:02,559] multiqc [DEBUG ] No samples found: sargasso [2024-10-16 18:28:02,562] multiqc [DEBUG ] No samples found: verifybamid [2024-10-16 18:28:02,565] multiqc [DEBUG ] No samples found: mirtrace [2024-10-16 18:28:02,568] multiqc [DEBUG ] No samples found: happy [2024-10-16 18:28:02,571] multiqc [DEBUG ] No samples found: mirtop [2024-10-16 18:28:02,574] multiqc [DEBUG ] No samples found: homer [2024-10-16 18:28:02,577] multiqc [DEBUG ] No samples found: macs2 [2024-10-16 18:28:02,580] multiqc [DEBUG ] No samples found: theta2 [2024-10-16 18:28:02,583] multiqc [DEBUG ] No samples found: snpeff [2024-10-16 18:28:02,587] multiqc [DEBUG ] No samples found: gatk [2024-10-16 18:28:02,590] multiqc [DEBUG ] No samples found: htseq [2024-10-16 18:28:02,593] multiqc [DEBUG ] No samples found: bcftools [2024-10-16 18:28:02,596] multiqc [DEBUG ] No samples found: featureCounts [2024-10-16 18:28:02,599] multiqc [DEBUG ] No samples found: fgbio [2024-10-16 18:28:02,605] multiqc [DEBUG ] No samples found: dragen [2024-10-16 18:28:02,608] multiqc [DEBUG ] No samples found: dedup [2024-10-16 18:28:02,611] multiqc [DEBUG ] No samples found: damageprofiler [2024-10-16 18:28:02,619] multiqc [DEBUG ] No samples found: biobambam2 [2024-10-16 18:28:02,622] multiqc [DEBUG ] No samples found: mtnucratio [2024-10-16 18:28:02,625] multiqc [DEBUG ] No samples found: picard [2024-10-16 18:28:02,628] multiqc [DEBUG ] No samples found: prokka [2024-10-16 18:28:02,631] multiqc [DEBUG ] No samples found: samblaster [2024-10-16 18:28:02,634] multiqc [DEBUG ] No samples found: samtools [2024-10-16 18:28:02,637] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-10-16 18:28:02,641] multiqc [DEBUG ] No samples found: bamtools [2024-10-16 18:28:02,643] multiqc [DEBUG ] No samples found: jellyfish [2024-10-16 18:28:02,647] multiqc [DEBUG ] No samples found: vcftools [2024-10-16 18:28:02,650] multiqc [DEBUG ] No samples found: longranger [2024-10-16 18:28:02,653] multiqc [DEBUG ] No samples found: stacks [2024-10-16 18:28:02,656] multiqc [DEBUG ] No samples found: varscan2 [2024-10-16 18:28:02,661] multiqc [DEBUG ] No samples found: bbmap [2024-10-16 18:28:02,664] multiqc [DEBUG ] No samples found: bismark [2024-10-16 18:28:02,668] multiqc [DEBUG ] No samples found: biscuit [2024-10-16 18:28:02,671] multiqc [DEBUG ] No samples found: hicexplorer [2024-10-16 18:28:02,674] multiqc [DEBUG ] No samples found: hicup [2024-10-16 18:28:02,677] multiqc [DEBUG ] No samples found: hicpro [2024-10-16 18:28:02,680] multiqc [DEBUG ] No samples found: salmon [2024-10-16 18:28:02,683] multiqc [DEBUG ] No samples found: kallisto [2024-10-16 18:28:02,686] multiqc [DEBUG ] No samples found: slamdunk [2024-10-16 18:28:02,689] multiqc [DEBUG ] No samples found: star [2024-10-16 18:28:02,692] multiqc [DEBUG ] No samples found: hisat2 [2024-10-16 18:28:02,695] multiqc [DEBUG ] No samples found: tophat [2024-10-16 18:28:02,698] multiqc [DEBUG ] No samples found: bowtie2 [2024-10-16 18:28:02,701] multiqc [DEBUG ] No samples found: bowtie1 [2024-10-16 18:28:02,704] multiqc [DEBUG ] No samples found: snpsplit [2024-10-16 18:28:02,707] multiqc [DEBUG ] No samples found: kat [2024-10-16 18:28:02,710] multiqc [DEBUG ] No samples found: leehom [2024-10-16 18:28:02,713] multiqc [DEBUG ] No samples found: adapterRemoval [2024-10-16 18:28:02,716] multiqc [DEBUG ] No samples found: clipandmerge [2024-10-16 18:28:02,719] multiqc [DEBUG ] No samples found: cutadapt [2024-10-16 18:28:02,721] multiqc [DEBUG ] No samples found: flexbar [2024-10-16 18:28:02,724] multiqc [DEBUG ] No samples found: kaiju [2024-10-16 18:28:02,727] multiqc [DEBUG ] No samples found: kraken [2024-10-16 18:28:02,730] multiqc [DEBUG ] No samples found: malt [2024-10-16 18:28:02,733] multiqc [DEBUG ] No samples found: trimmomatic [2024-10-16 18:28:02,736] multiqc [DEBUG ] No samples found: sickle [2024-10-16 18:28:02,739] multiqc [DEBUG ] No samples found: skewer [2024-10-16 18:28:02,742] multiqc [DEBUG ] No samples found: sortmerna [2024-10-16 18:28:02,745] multiqc [DEBUG ] No samples found: biobloomtools [2024-10-16 18:28:02,748] multiqc [DEBUG ] No samples found: fastq_screen [2024-10-16 18:28:02,751] multiqc [DEBUG ] No samples found: afterqc [2024-10-16 18:28:02,754] multiqc [DEBUG ] No samples found: fastp [2024-10-16 18:28:11,194] multiqc.modules.fastqc.fastqc [INFO ] Found 66 reports [2024-10-16 18:28:11,679] multiqc [DEBUG ] No samples found: pycoqc [2024-10-16 18:28:11,682] multiqc [DEBUG ] No samples found: minionqc [2024-10-16 18:28:11,685] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-10-16 18:28:11,688] multiqc [DEBUG ] No samples found: clusterflow [2024-10-16 18:28:11,788] multiqc [DEBUG ] No samples found: bcl2fastq [2024-10-16 18:28:11,791] multiqc [DEBUG ] No samples found: interop [2024-10-16 18:28:11,794] multiqc [DEBUG ] No samples found: ivar [2024-10-16 18:28:11,797] multiqc [DEBUG ] No samples found: flash [2024-10-16 18:28:11,800] multiqc [DEBUG ] No samples found: seqyclean [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-10-16 18:28:11,801] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-10-16 18:28:11,880] multiqc [INFO ] Compressing plot data [2024-10-16 18:28:13,043] multiqc [INFO ] Report : multiqc_report.html [2024-10-16 18:28:13,043] multiqc [INFO ] Data : multiqc_data [2024-10-16 18:28:13,043] multiqc [DEBUG ] Moving data file from '/state/partition1/job-52279820/tmp8vkxwpmw/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/4d/9f651e523e74cfd5dcb817395e55d2/4/multiqc_data' [2024-10-16 18:28:13,149] multiqc [INFO ] MultiQC complete