[2024-12-06 22:17:40,984] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-06 22:17:40,984] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-06 22:17:40,984] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-06 22:17:40,987] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-06 22:17:40,987] 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}} [2024-12-06 22:17:40,987] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-06 22:17:41,016] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-06 22:17:41,017] multiqc [INFO ] This is MultiQC v1.9 [2024-12-06 22:17:41,017] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-06 22:17:41,017] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/dc/bf2a12f900c63e7d3c1b6bf00fc65a/2 [2024-12-06 22:17:41,017] multiqc [INFO ] Template : default [2024-12-06 22:17:41,017] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-06 22:17:41,017] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/dc/bf2a12f900c63e7d3c1b6bf00fc65a/2 [2024-12-06 22:17:41,017] 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 [2024-12-06 22:17:41,017] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-54428480/tmpidl3dn4l [2024-12-06 22:17:41,129] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_33-B_fastqc.html [2024-12-06 22:17:41,132] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_33-B_fastqc.html [2024-12-06 22:17:41,180] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HLF5YDRX5_l02_n02_15-B_fastqc.html [2024-12-06 22:17:45,531] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n02_AT038-1_fastqc.html [2024-12-06 22:17:45,533] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n02_AT038-1_fastqc.html [2024-12-06 22:17:45,577] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_17-B_fastqc.html [2024-12-06 22:17:45,579] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_17-B_fastqc.html [2024-12-06 22:17:45,623] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_AT038-1_fastqc.html [2024-12-06 22:17:45,625] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_AT038-1_fastqc.html [2024-12-06 22:17:45,670] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_29-B_fastqc.html [2024-12-06 22:17:45,672] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n01_29-B_fastqc.html [2024-12-06 22:17:45,717] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n02_10-B_fastqc.html [2024-12-06 22:17:45,719] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLF5YDRX5_l02_n02_10-B_fastqc.html [2024-12-06 22:17:46,262] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-06 22:17:46,264] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-06 22:17:46,272] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-06 22:17:46,282] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-06 22:17:46,303] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 45 samples (table) [2024-12-06 22:17:46,309] multiqc [DEBUG ] No samples found: conpair [2024-12-06 22:17:46,315] multiqc [DEBUG ] No samples found: peddy [2024-12-06 22:17:46,321] multiqc [DEBUG ] No samples found: somalier [2024-12-06 22:17:46,326] multiqc [DEBUG ] No samples found: methylQA [2024-12-06 22:17:46,337] multiqc [DEBUG ] No samples found: mosdepth [2024-12-06 22:17:46,341] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-06 22:17:46,345] multiqc [DEBUG ] No samples found: qualimap [2024-12-06 22:17:46,351] multiqc [DEBUG ] No samples found: preseq [2024-12-06 22:17:46,356] multiqc [DEBUG ] No samples found: quast [2024-12-06 22:17:46,362] multiqc [DEBUG ] No samples found: qorts [2024-12-06 22:17:46,368] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-06 22:17:46,373] multiqc [DEBUG ] No samples found: rockhopper [2024-12-06 22:17:46,379] multiqc [DEBUG ] No samples found: rsem [2024-12-06 22:17:46,393] multiqc [DEBUG ] No samples found: rseqc [2024-12-06 22:17:46,399] multiqc [DEBUG ] No samples found: busco [2024-12-06 22:17:46,405] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-06 22:17:46,410] multiqc [DEBUG ] No samples found: disambiguate [2024-12-06 22:17:46,415] multiqc [DEBUG ] No samples found: supernova [2024-12-06 22:17:46,433] multiqc [DEBUG ] No samples found: deeptools [2024-12-06 22:17:46,438] multiqc [DEBUG ] No samples found: sargasso [2024-12-06 22:17:46,444] multiqc [DEBUG ] No samples found: verifybamid [2024-12-06 22:17:46,450] multiqc [DEBUG ] No samples found: mirtrace [2024-12-06 22:17:46,455] multiqc [DEBUG ] No samples found: happy [2024-12-06 22:17:46,460] multiqc [DEBUG ] No samples found: mirtop [2024-12-06 22:17:46,468] multiqc [DEBUG ] No samples found: homer [2024-12-06 22:17:46,473] multiqc [DEBUG ] No samples found: macs2 [2024-12-06 22:17:46,479] multiqc [DEBUG ] No samples found: theta2 [2024-12-06 22:17:46,484] multiqc [DEBUG ] No samples found: snpeff [2024-12-06 22:17:46,492] multiqc [DEBUG ] No samples found: gatk [2024-12-06 22:17:46,497] multiqc [DEBUG ] No samples found: htseq [2024-12-06 22:17:46,504] multiqc [DEBUG ] No samples found: bcftools [2024-12-06 22:17:46,509] multiqc [DEBUG ] No samples found: featureCounts [2024-12-06 22:17:46,517] multiqc [DEBUG ] No samples found: fgbio [2024-12-06 22:17:46,532] multiqc [DEBUG ] No samples found: dragen [2024-12-06 22:17:46,539] multiqc [DEBUG ] No samples found: dedup [2024-12-06 22:17:46,547] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-06 22:17:46,578] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-06 22:17:46,583] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-06 22:17:46,585] multiqc [DEBUG ] No samples found: picard [2024-12-06 22:17:46,591] multiqc [DEBUG ] No samples found: prokka [2024-12-06 22:17:46,596] multiqc [DEBUG ] No samples found: samblaster [2024-12-06 22:17:46,608] multiqc [DEBUG ] No samples found: samtools [2024-12-06 22:17:46,613] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-06 22:17:46,620] multiqc [DEBUG ] No samples found: bamtools [2024-12-06 22:17:46,625] multiqc [DEBUG ] No samples found: jellyfish [2024-12-06 22:17:46,636] multiqc [DEBUG ] No samples found: vcftools [2024-12-06 22:17:46,642] multiqc [DEBUG ] No samples found: longranger [2024-12-06 22:17:46,647] multiqc [DEBUG ] No samples found: stacks [2024-12-06 22:17:46,653] multiqc [DEBUG ] No samples found: varscan2 [2024-12-06 22:17:46,669] multiqc [DEBUG ] No samples found: bbmap [2024-12-06 22:17:46,675] multiqc [DEBUG ] No samples found: bismark [2024-12-06 22:17:46,680] multiqc [DEBUG ] No samples found: biscuit [2024-12-06 22:17:46,686] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-06 22:17:46,691] multiqc [DEBUG ] No samples found: hicup [2024-12-06 22:17:46,696] multiqc [DEBUG ] No samples found: hicpro [2024-12-06 22:17:46,701] multiqc [DEBUG ] No samples found: salmon [2024-12-06 22:17:46,706] multiqc [DEBUG ] No samples found: kallisto [2024-12-06 22:17:46,712] multiqc [DEBUG ] No samples found: slamdunk [2024-12-06 22:17:46,717] multiqc [DEBUG ] No samples found: star [2024-12-06 22:17:46,723] multiqc [DEBUG ] No samples found: hisat2 [2024-12-06 22:17:46,728] multiqc [DEBUG ] No samples found: tophat [2024-12-06 22:17:46,733] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-06 22:17:46,738] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-06 22:17:46,743] multiqc [DEBUG ] No samples found: snpsplit [2024-12-06 22:17:46,748] multiqc [DEBUG ] No samples found: kat [2024-12-06 22:17:46,753] multiqc [DEBUG ] No samples found: leehom [2024-12-06 22:17:46,762] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-06 22:17:46,767] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-06 22:17:46,772] multiqc [DEBUG ] No samples found: cutadapt [2024-12-06 22:17:46,777] multiqc [DEBUG ] No samples found: flexbar [2024-12-06 22:17:46,782] multiqc [DEBUG ] No samples found: kaiju [2024-12-06 22:17:46,787] multiqc [DEBUG ] No samples found: kraken [2024-12-06 22:17:46,792] multiqc [DEBUG ] No samples found: malt [2024-12-06 22:17:46,797] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-06 22:17:46,803] multiqc [DEBUG ] No samples found: sickle [2024-12-06 22:17:46,808] multiqc [DEBUG ] No samples found: skewer [2024-12-06 22:17:46,813] multiqc [DEBUG ] No samples found: sortmerna [2024-12-06 22:17:46,818] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-06 22:17:46,824] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-06 22:17:46,829] multiqc [DEBUG ] No samples found: afterqc [2024-12-06 22:17:46,834] multiqc [DEBUG ] No samples found: fastp [2024-12-06 22:17:52,873] multiqc.modules.fastqc.fastqc [INFO ] Found 90 reports [2024-12-06 22:17:54,074] multiqc [DEBUG ] No samples found: pycoqc [2024-12-06 22:17:54,080] multiqc [DEBUG ] No samples found: minionqc [2024-12-06 22:17:54,084] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-06 22:17:54,090] multiqc [DEBUG ] No samples found: clusterflow [2024-12-06 22:17:54,096] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-06 22:17:54,102] multiqc [DEBUG ] No samples found: interop [2024-12-06 22:17:54,106] multiqc [DEBUG ] No samples found: ivar [2024-12-06 22:17:54,111] multiqc [DEBUG ] No samples found: flash [2024-12-06 22:17:54,117] multiqc [DEBUG ] No samples found: seqyclean [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:17:54,117] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-06 22:17:54,118] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-06 22:17:54,223] multiqc [INFO ] Compressing plot data [2024-12-06 22:17:55,876] multiqc [INFO ] Report : multiqc_report.html [2024-12-06 22:17:55,876] multiqc [INFO ] Data : multiqc_data [2024-12-06 22:17:55,876] multiqc [DEBUG ] Moving data file from '/state/partition1/job-54428480/tmpidl3dn4l/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/dc/bf2a12f900c63e7d3c1b6bf00fc65a/2/multiqc_data' [2024-12-06 22:17:56,022] multiqc [INFO ] MultiQC complete