[2024-08-16 03:35:37,688] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-16 03:35:37,688] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-16 03:35:37,689] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-16 03:35:37,691] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-16 03:35:37,691] 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}} [2024-08-16 03:35:37,691] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-16 03:35:37,738] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-16 03:35:37,738] multiqc [INFO ] This is MultiQC v1.9 [2024-08-16 03:35:37,738] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-16 03:35:37,739] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/d9/94afccc42f63c5eee2c03ec86a5d89/merged [2024-08-16 03:35:37,739] multiqc [INFO ] Template : default [2024-08-16 03:35:37,739] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-16 03:35:37,739] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/d9/94afccc42f63c5eee2c03ec86a5d89/merged [2024-08-16 03:35:37,739] 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 [2024-08-16 03:35:37,739] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49979406/tmpp1s8vdyr [2024-08-16 03:35:37,857] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_E_W_A_p_fastqc.html [2024-08-16 03:35:37,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_E_W_A_p_fastqc.html [2024-08-16 03:35:37,913] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-08-16 03:35:38,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_O_A_q_fastqc.html [2024-08-16 03:35:38,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_O_A_q_fastqc.html [2024-08-16 03:35:38,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_H_O_B_q_fastqc.html [2024-08-16 03:35:38,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_H_O_B_q_fastqc.html [2024-08-16 03:35:38,905] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_W_A_p_fastqc.html [2024-08-16 03:35:38,907] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_W_A_p_fastqc.html [2024-08-16 03:35:38,953] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_W_B_p_fastqc.html [2024-08-16 03:35:38,955] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_W_B_p_fastqc.html [2024-08-16 03:35:39,000] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_E_W_B_p_fastqc.html [2024-08-16 03:35:39,002] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_E_W_B_p_fastqc.html [2024-08-16 03:35:39,047] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_W_B_r_fastqc.html [2024-08-16 03:35:39,049] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_W_B_r_fastqc.html [2024-08-16 03:35:39,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_H_W_A_q_fastqc.html [2024-08-16 03:35:39,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_H_W_A_q_fastqc.html [2024-08-16 03:35:39,142] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_O_B_p_fastqc.html [2024-08-16 03:35:39,143] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_D_O_B_p_fastqc.html [2024-08-16 03:35:39,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMMFDMXY_n01_C_O_A_r_fastqc.html [2024-08-16 03:35:39,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMMFDMXY_n01_C_O_A_r_fastqc.html [2024-08-16 03:35:39,778] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-16 03:35:39,781] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-16 03:35:39,791] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-16 03:35:39,801] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-16 03:35:39,814] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2024-08-16 03:35:39,822] multiqc [DEBUG ] No samples found: conpair [2024-08-16 03:35:39,829] multiqc [DEBUG ] No samples found: peddy [2024-08-16 03:35:39,837] multiqc [DEBUG ] No samples found: somalier [2024-08-16 03:35:39,844] multiqc [DEBUG ] No samples found: methylQA [2024-08-16 03:35:39,856] multiqc [DEBUG ] No samples found: mosdepth [2024-08-16 03:35:39,862] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-16 03:35:39,866] multiqc [DEBUG ] No samples found: qualimap [2024-08-16 03:35:39,874] multiqc [DEBUG ] No samples found: preseq [2024-08-16 03:35:39,881] multiqc [DEBUG ] No samples found: quast [2024-08-16 03:35:39,888] multiqc [DEBUG ] No samples found: qorts [2024-08-16 03:35:39,894] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-16 03:35:39,900] multiqc [DEBUG ] No samples found: rockhopper [2024-08-16 03:35:39,907] multiqc [DEBUG ] No samples found: rsem [2024-08-16 03:35:39,922] multiqc [DEBUG ] No samples found: rseqc [2024-08-16 03:35:39,928] multiqc [DEBUG ] No samples found: busco [2024-08-16 03:35:39,935] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-16 03:35:39,941] multiqc [DEBUG ] No samples found: disambiguate [2024-08-16 03:35:39,947] multiqc [DEBUG ] No samples found: supernova [2024-08-16 03:35:39,965] multiqc [DEBUG ] No samples found: deeptools [2024-08-16 03:35:39,970] multiqc [DEBUG ] No samples found: sargasso [2024-08-16 03:35:39,977] multiqc [DEBUG ] No samples found: verifybamid [2024-08-16 03:35:39,983] multiqc [DEBUG ] No samples found: mirtrace [2024-08-16 03:35:39,990] multiqc [DEBUG ] No samples found: happy [2024-08-16 03:35:39,996] multiqc [DEBUG ] No samples found: mirtop [2024-08-16 03:35:40,005] multiqc [DEBUG ] No samples found: homer [2024-08-16 03:35:40,011] multiqc [DEBUG ] No samples found: macs2 [2024-08-16 03:35:40,018] multiqc [DEBUG ] No samples found: theta2 [2024-08-16 03:35:40,025] multiqc [DEBUG ] No samples found: snpeff [2024-08-16 03:35:40,034] multiqc [DEBUG ] No samples found: gatk [2024-08-16 03:35:40,041] multiqc [DEBUG ] No samples found: htseq [2024-08-16 03:35:40,049] multiqc [DEBUG ] No samples found: bcftools [2024-08-16 03:35:40,057] multiqc [DEBUG ] No samples found: featureCounts [2024-08-16 03:35:40,066] multiqc [DEBUG ] No samples found: fgbio [2024-08-16 03:35:40,085] multiqc [DEBUG ] No samples found: dragen [2024-08-16 03:35:40,092] multiqc [DEBUG ] No samples found: dedup [2024-08-16 03:35:40,099] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-16 03:35:40,136] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-16 03:35:40,142] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-16 03:35:40,144] multiqc [DEBUG ] No samples found: picard [2024-08-16 03:35:40,152] multiqc [DEBUG ] No samples found: prokka [2024-08-16 03:35:40,159] multiqc [DEBUG ] No samples found: samblaster [2024-08-16 03:35:40,172] multiqc [DEBUG ] No samples found: samtools [2024-08-16 03:35:40,179] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-16 03:35:40,186] multiqc [DEBUG ] No samples found: bamtools [2024-08-16 03:35:40,192] multiqc [DEBUG ] No samples found: jellyfish [2024-08-16 03:35:40,202] multiqc [DEBUG ] No samples found: vcftools [2024-08-16 03:35:40,209] multiqc [DEBUG ] No samples found: longranger [2024-08-16 03:35:40,216] multiqc [DEBUG ] No samples found: stacks [2024-08-16 03:35:40,222] multiqc [DEBUG ] No samples found: varscan2 [2024-08-16 03:35:40,242] multiqc [DEBUG ] No samples found: bbmap [2024-08-16 03:35:40,250] multiqc [DEBUG ] No samples found: bismark [2024-08-16 03:35:40,257] multiqc [DEBUG ] No samples found: biscuit [2024-08-16 03:35:40,264] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-16 03:35:40,271] multiqc [DEBUG ] No samples found: hicup [2024-08-16 03:35:40,279] multiqc [DEBUG ] No samples found: hicpro [2024-08-16 03:35:40,285] multiqc [DEBUG ] No samples found: salmon [2024-08-16 03:35:40,291] multiqc [DEBUG ] No samples found: kallisto [2024-08-16 03:35:40,299] multiqc [DEBUG ] No samples found: slamdunk [2024-08-16 03:35:40,310] multiqc [DEBUG ] No samples found: star [2024-08-16 03:35:40,317] multiqc [DEBUG ] No samples found: hisat2 [2024-08-16 03:35:40,324] multiqc [DEBUG ] No samples found: tophat [2024-08-16 03:35:40,331] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-16 03:35:40,338] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-16 03:35:40,345] multiqc [DEBUG ] No samples found: snpsplit [2024-08-16 03:35:40,351] multiqc [DEBUG ] No samples found: kat [2024-08-16 03:35:40,357] multiqc [DEBUG ] No samples found: leehom [2024-08-16 03:35:40,365] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-16 03:35:40,372] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-16 03:35:40,379] multiqc [DEBUG ] No samples found: cutadapt [2024-08-16 03:35:40,384] multiqc [DEBUG ] No samples found: flexbar [2024-08-16 03:35:40,391] multiqc [DEBUG ] No samples found: kaiju [2024-08-16 03:35:40,398] multiqc [DEBUG ] No samples found: kraken [2024-08-16 03:35:40,405] multiqc [DEBUG ] No samples found: malt [2024-08-16 03:35:40,412] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-16 03:35:40,418] multiqc [DEBUG ] No samples found: sickle [2024-08-16 03:35:40,424] multiqc [DEBUG ] No samples found: skewer [2024-08-16 03:35:40,430] multiqc [DEBUG ] No samples found: sortmerna [2024-08-16 03:35:40,437] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-16 03:35:40,444] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-16 03:35:40,451] multiqc [DEBUG ] No samples found: afterqc [2024-08-16 03:35:40,458] multiqc [DEBUG ] No samples found: fastp [2024-08-16 03:35:44,512] multiqc.modules.fastqc.fastqc [INFO ] Found 29 reports [2024-08-16 03:35:44,945] multiqc [DEBUG ] No samples found: pycoqc [2024-08-16 03:35:44,951] multiqc [DEBUG ] No samples found: minionqc [2024-08-16 03:35:44,958] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-16 03:35:44,966] multiqc [DEBUG ] No samples found: clusterflow [2024-08-16 03:35:44,972] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-16 03:35:44,980] multiqc [DEBUG ] No samples found: interop [2024-08-16 03:35:44,986] multiqc [DEBUG ] No samples found: ivar [2024-08-16 03:35:44,992] multiqc [DEBUG ] No samples found: flash [2024-08-16 03:35:44,999] multiqc [DEBUG ] No samples found: seqyclean [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 03:35:44,999] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-16 03:35:45,000] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-16 03:35:45,033] multiqc [INFO ] Compressing plot data [2024-08-16 03:35:45,584] multiqc [INFO ] Report : multiqc_report.html [2024-08-16 03:35:45,584] multiqc [INFO ] Data : multiqc_data [2024-08-16 03:35:45,584] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49979406/tmpp1s8vdyr/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/d9/94afccc42f63c5eee2c03ec86a5d89/merged/multiqc_data' [2024-08-16 03:35:45,745] multiqc [INFO ] MultiQC complete