[2024-12-23 23:25:05,105] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-23 23:25:05,105] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-23 23:25:05,105] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-23 23:25:05,108] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-23 23:25:05,108] 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}} [2024-12-23 23:25:05,108] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-23 23:25:05,139] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-23 23:25:05,139] multiqc [INFO ] This is MultiQC v1.9 [2024-12-23 23:25:05,139] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-23 23:25:05,139] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/99/1822056b0706ecfad683fb842e57b8/merged [2024-12-23 23:25:05,139] multiqc [INFO ] Template : default [2024-12-23 23:25:05,139] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-23 23:25:05,139] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/99/1822056b0706ecfad683fb842e57b8/merged [2024-12-23 23:25:05,140] 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 [2024-12-23 23:25:05,140] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55336784/tmppx5_85q2 [2024-12-23 23:25:05,250] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Oak1_H_Bb_fastqc.html [2024-12-23 23:25:05,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Oak1_H_Bb_fastqc.html [2024-12-23 23:25:05,304] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H2LKCDMX2_n01_Wine1_D_Ar_fastqc.html [2024-12-23 23:25:12,398] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_D_Ar_fastqc.html [2024-12-23 23:25:12,445] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Oak1_P_Br_fastqc.html [2024-12-23 23:25:12,447] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Oak1_P_Br_fastqc.html [2024-12-23 23:25:12,494] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_D_Bbl_fastqc.html [2024-12-23 23:25:12,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_D_Bbl_fastqc.html [2024-12-23 23:25:12,543] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_H_Ar_fastqc.html [2024-12-23 23:25:12,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_H_Ar_fastqc.html [2024-12-23 23:25:12,596] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_P_Ab_fastqc.html [2024-12-23 23:25:12,598] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_P_Ab_fastqc.html [2024-12-23 23:25:12,646] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Oak1_D_Bb_fastqc.html [2024-12-23 23:25:12,648] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Oak1_D_Bb_fastqc.html [2024-12-23 23:25:12,697] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_P_Br_fastqc.html [2024-12-23 23:25:12,699] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2LKCDMX2_n01_Wine1_P_Br_fastqc.html [2024-12-23 23:25:13,150] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-23 23:25:13,152] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-23 23:25:13,178] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 37 samples (table) [2024-12-23 23:25:13,179] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-23 23:25:13,189] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-23 23:25:13,195] multiqc [DEBUG ] No samples found: conpair [2024-12-23 23:25:13,200] multiqc [DEBUG ] No samples found: peddy [2024-12-23 23:25:13,206] multiqc [DEBUG ] No samples found: somalier [2024-12-23 23:25:13,211] multiqc [DEBUG ] No samples found: methylQA [2024-12-23 23:25:13,220] multiqc [DEBUG ] No samples found: mosdepth [2024-12-23 23:25:13,224] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-23 23:25:13,228] multiqc [DEBUG ] No samples found: qualimap [2024-12-23 23:25:13,233] multiqc [DEBUG ] No samples found: preseq [2024-12-23 23:25:13,238] multiqc [DEBUG ] No samples found: quast [2024-12-23 23:25:13,244] multiqc [DEBUG ] No samples found: qorts [2024-12-23 23:25:13,249] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-23 23:25:13,254] multiqc [DEBUG ] No samples found: rockhopper [2024-12-23 23:25:13,259] multiqc [DEBUG ] No samples found: rsem [2024-12-23 23:25:13,273] multiqc [DEBUG ] No samples found: rseqc [2024-12-23 23:25:13,278] multiqc [DEBUG ] No samples found: busco [2024-12-23 23:25:13,283] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-23 23:25:13,288] multiqc [DEBUG ] No samples found: disambiguate [2024-12-23 23:25:13,294] multiqc [DEBUG ] No samples found: supernova [2024-12-23 23:25:13,309] multiqc [DEBUG ] No samples found: deeptools [2024-12-23 23:25:13,314] multiqc [DEBUG ] No samples found: sargasso [2024-12-23 23:25:13,319] multiqc [DEBUG ] No samples found: verifybamid [2024-12-23 23:25:13,325] multiqc [DEBUG ] No samples found: mirtrace [2024-12-23 23:25:13,330] multiqc [DEBUG ] No samples found: happy [2024-12-23 23:25:13,335] multiqc [DEBUG ] No samples found: mirtop [2024-12-23 23:25:13,343] multiqc [DEBUG ] No samples found: homer [2024-12-23 23:25:13,348] multiqc [DEBUG ] No samples found: macs2 [2024-12-23 23:25:13,353] multiqc [DEBUG ] No samples found: theta2 [2024-12-23 23:25:13,358] multiqc [DEBUG ] No samples found: snpeff [2024-12-23 23:25:13,365] multiqc [DEBUG ] No samples found: gatk [2024-12-23 23:25:13,370] multiqc [DEBUG ] No samples found: htseq [2024-12-23 23:25:13,376] multiqc [DEBUG ] No samples found: bcftools [2024-12-23 23:25:13,381] multiqc [DEBUG ] No samples found: featureCounts [2024-12-23 23:25:13,388] multiqc [DEBUG ] No samples found: fgbio [2024-12-23 23:25:13,403] multiqc [DEBUG ] No samples found: dragen [2024-12-23 23:25:13,408] multiqc [DEBUG ] No samples found: dedup [2024-12-23 23:25:13,413] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-23 23:25:13,440] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-23 23:25:13,445] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-23 23:25:13,447] multiqc [DEBUG ] No samples found: picard [2024-12-23 23:25:13,453] multiqc [DEBUG ] No samples found: prokka [2024-12-23 23:25:13,457] multiqc [DEBUG ] No samples found: samblaster [2024-12-23 23:25:13,467] multiqc [DEBUG ] No samples found: samtools [2024-12-23 23:25:13,472] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-23 23:25:13,479] multiqc [DEBUG ] No samples found: bamtools [2024-12-23 23:25:13,484] multiqc [DEBUG ] No samples found: jellyfish [2024-12-23 23:25:13,492] multiqc [DEBUG ] No samples found: vcftools [2024-12-23 23:25:13,498] multiqc [DEBUG ] No samples found: longranger [2024-12-23 23:25:13,503] multiqc [DEBUG ] No samples found: stacks [2024-12-23 23:25:13,508] multiqc [DEBUG ] No samples found: varscan2 [2024-12-23 23:25:13,525] multiqc [DEBUG ] No samples found: bbmap [2024-12-23 23:25:13,531] multiqc [DEBUG ] No samples found: bismark [2024-12-23 23:25:13,536] multiqc [DEBUG ] No samples found: biscuit [2024-12-23 23:25:13,542] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-23 23:25:13,547] multiqc [DEBUG ] No samples found: hicup [2024-12-23 23:25:13,552] multiqc [DEBUG ] No samples found: hicpro [2024-12-23 23:25:13,557] multiqc [DEBUG ] No samples found: salmon [2024-12-23 23:25:13,562] multiqc [DEBUG ] No samples found: kallisto [2024-12-23 23:25:13,567] multiqc [DEBUG ] No samples found: slamdunk [2024-12-23 23:25:13,572] multiqc [DEBUG ] No samples found: star [2024-12-23 23:25:13,577] multiqc [DEBUG ] No samples found: hisat2 [2024-12-23 23:25:13,582] multiqc [DEBUG ] No samples found: tophat [2024-12-23 23:25:13,587] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-23 23:25:13,592] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-23 23:25:13,597] multiqc [DEBUG ] No samples found: snpsplit [2024-12-23 23:25:13,602] multiqc [DEBUG ] No samples found: kat [2024-12-23 23:25:13,606] multiqc [DEBUG ] No samples found: leehom [2024-12-23 23:25:13,611] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-23 23:25:13,616] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-23 23:25:13,621] multiqc [DEBUG ] No samples found: cutadapt [2024-12-23 23:25:13,626] multiqc [DEBUG ] No samples found: flexbar [2024-12-23 23:25:13,631] multiqc [DEBUG ] No samples found: kaiju [2024-12-23 23:25:13,636] multiqc [DEBUG ] No samples found: kraken [2024-12-23 23:25:13,641] multiqc [DEBUG ] No samples found: malt [2024-12-23 23:25:13,646] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-23 23:25:13,651] multiqc [DEBUG ] No samples found: sickle [2024-12-23 23:25:13,656] multiqc [DEBUG ] No samples found: skewer [2024-12-23 23:25:13,661] multiqc [DEBUG ] No samples found: sortmerna [2024-12-23 23:25:13,666] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-23 23:25:13,671] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-23 23:25:13,677] multiqc [DEBUG ] No samples found: afterqc [2024-12-23 23:25:13,682] multiqc [DEBUG ] No samples found: fastp [2024-12-23 23:25:19,163] multiqc.modules.fastqc.fastqc [INFO ] Found 37 reports [2024-12-23 23:25:19,714] multiqc [DEBUG ] No samples found: pycoqc [2024-12-23 23:25:19,720] multiqc [DEBUG ] No samples found: minionqc [2024-12-23 23:25:19,725] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-23 23:25:19,731] multiqc [DEBUG ] No samples found: clusterflow [2024-12-23 23:25:19,736] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-23 23:25:19,741] multiqc [DEBUG ] No samples found: interop [2024-12-23 23:25:19,746] multiqc [DEBUG ] No samples found: ivar [2024-12-23 23:25:19,751] multiqc [DEBUG ] No samples found: flash [2024-12-23 23:25:19,757] multiqc [DEBUG ] No samples found: seqyclean [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-23 23:25:19,757] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-23 23:25:19,758] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-23 23:25:19,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-23 23:25:19,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-23 23:25:19,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-23 23:25:19,758] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-23 23:25:19,758] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-23 23:25:19,758] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-23 23:25:19,802] multiqc [INFO ] Compressing plot data [2024-12-23 23:25:20,539] multiqc [INFO ] Report : multiqc_report.html [2024-12-23 23:25:20,540] multiqc [INFO ] Data : multiqc_data [2024-12-23 23:25:20,540] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55336784/tmppx5_85q2/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/99/1822056b0706ecfad683fb842e57b8/merged/multiqc_data' [2024-12-23 23:25:20,670] multiqc [INFO ] MultiQC complete