[2024-06-30 06:39:10,168] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-30 06:39:10,168] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-30 06:39:10,168] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-30 06:39:10,171] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-30 06:39:10,171] 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}} [2024-06-30 06:39:10,171] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-30 06:39:10,209] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-30 06:39:10,209] multiqc [INFO ] This is MultiQC v1.9 [2024-06-30 06:39:10,209] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-30 06:39:10,209] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/bf/5b0bde794148033a8e274546773799/merged [2024-06-30 06:39:10,209] multiqc [INFO ] Template : default [2024-06-30 06:39:10,209] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-30 06:39:10,209] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/bf/5b0bde794148033a8e274546773799/merged [2024-06-30 06:39:10,209] 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 [2024-06-30 06:39:10,210] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-48077233/tmp0x1l0o97 [2024-06-30 06:39:10,344] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n01_DMS0_1_fastqc.html [2024-06-30 06:39:10,353] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n01_DMS0_1_fastqc.html [2024-06-30 06:39:10,423] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-06-30 06:39:12,765] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_IFN_2_fastqc.html [2024-06-30 06:39:12,834] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_IFN_3_fastqc.html [2024-06-30 06:39:12,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_IFN_3_fastqc.html [2024-06-30 06:39:12,909] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_IFN_4_fastqc.html [2024-06-30 06:39:12,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_IFN_4_fastqc.html [2024-06-30 06:39:12,982] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_IFN_5_fastqc.html [2024-06-30 06:39:12,988] multiqc [DEBUG ] 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[2024-06-30 06:39:13,751] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_3_fastqc.html [2024-06-30 06:39:13,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_3_fastqc.html [2024-06-30 06:39:13,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_4_fastqc.html [2024-06-30 06:39:13,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_4_fastqc.html [2024-06-30 06:39:13,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_5_fastqc.html [2024-06-30 06:39:13,906] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_5_fastqc.html [2024-06-30 06:39:13,971] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_6_fastqc.html [2024-06-30 06:39:13,978] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_SAHA_6_fastqc.html [2024-06-30 06:39:14,049] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_undetermined_fastqc.html [2024-06-30 06:39:14,055] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2JWDSXC_n02_undetermined_fastqc.html [2024-06-30 06:39:14,119] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:14,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:14,126] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:14,126] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:14,126] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:14,126] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:14,126] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:14,155] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-30 06:39:15,792] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-30 06:39:15,793] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-30 06:39:15,813] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-06-30 06:39:15,815] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-30 06:39:15,825] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-30 06:39:15,831] multiqc [DEBUG ] No samples found: conpair [2024-06-30 06:39:15,837] multiqc [DEBUG ] No samples found: peddy [2024-06-30 06:39:15,844] multiqc [DEBUG ] No samples found: somalier [2024-06-30 06:39:15,850] multiqc [DEBUG ] No samples found: methylQA [2024-06-30 06:39:15,861] multiqc [DEBUG ] No samples found: mosdepth [2024-06-30 06:39:15,865] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-30 06:39:15,869] multiqc [DEBUG ] No samples found: qualimap [2024-06-30 06:39:15,875] multiqc [DEBUG ] No samples found: preseq [2024-06-30 06:39:15,881] multiqc [DEBUG ] No samples found: quast [2024-06-30 06:39:15,887] multiqc [DEBUG ] No samples found: qorts [2024-06-30 06:39:15,893] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-30 06:39:15,898] multiqc [DEBUG ] No samples found: rockhopper [2024-06-30 06:39:15,904] multiqc [DEBUG ] No samples found: rsem [2024-06-30 06:39:15,919] multiqc [DEBUG ] No samples found: rseqc [2024-06-30 06:39:15,925] multiqc [DEBUG ] No samples found: busco [2024-06-30 06:39:15,930] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-30 06:39:15,936] multiqc [DEBUG ] No samples found: disambiguate [2024-06-30 06:39:15,942] multiqc [DEBUG ] No samples found: supernova [2024-06-30 06:39:15,961] multiqc [DEBUG ] No samples found: deeptools [2024-06-30 06:39:15,968] multiqc [DEBUG ] No samples found: sargasso [2024-06-30 06:39:15,973] multiqc [DEBUG ] No samples found: verifybamid [2024-06-30 06:39:15,979] multiqc [DEBUG ] No samples found: mirtrace [2024-06-30 06:39:15,984] multiqc [DEBUG ] No samples found: happy [2024-06-30 06:39:15,990] multiqc [DEBUG ] No samples found: mirtop [2024-06-30 06:39:15,998] multiqc [DEBUG ] No samples found: homer [2024-06-30 06:39:16,004] multiqc [DEBUG ] No samples found: macs2 [2024-06-30 06:39:16,009] multiqc [DEBUG ] No samples found: theta2 [2024-06-30 06:39:16,015] multiqc [DEBUG ] No samples found: snpeff [2024-06-30 06:39:16,024] multiqc [DEBUG ] No samples found: gatk [2024-06-30 06:39:16,029] multiqc [DEBUG ] No samples found: htseq [2024-06-30 06:39:16,036] multiqc [DEBUG ] No samples found: bcftools [2024-06-30 06:39:16,041] multiqc [DEBUG ] No samples found: featureCounts [2024-06-30 06:39:16,050] multiqc [DEBUG ] No samples found: fgbio [2024-06-30 06:39:16,064] multiqc [DEBUG ] No samples found: dragen [2024-06-30 06:39:16,070] multiqc [DEBUG ] No samples found: dedup [2024-06-30 06:39:16,076] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-30 06:39:16,154] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-30 06:39:16,160] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-30 06:39:16,162] multiqc [DEBUG ] No samples found: picard [2024-06-30 06:39:16,167] multiqc [DEBUG ] No samples found: prokka [2024-06-30 06:39:16,173] multiqc [DEBUG ] No samples found: samblaster [2024-06-30 06:39:16,182] multiqc [DEBUG ] No samples found: samtools [2024-06-30 06:39:16,187] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-30 06:39:16,193] multiqc [DEBUG ] No samples found: bamtools [2024-06-30 06:39:16,198] multiqc [DEBUG ] No samples found: jellyfish [2024-06-30 06:39:16,208] multiqc [DEBUG ] No samples found: vcftools [2024-06-30 06:39:16,214] multiqc [DEBUG ] No samples found: longranger [2024-06-30 06:39:16,220] multiqc [DEBUG ] No samples found: stacks [2024-06-30 06:39:16,226] multiqc [DEBUG ] No samples found: varscan2 [2024-06-30 06:39:16,245] multiqc [DEBUG ] No samples found: bbmap [2024-06-30 06:39:16,251] multiqc [DEBUG ] No samples found: bismark [2024-06-30 06:39:16,257] multiqc [DEBUG ] No samples found: biscuit [2024-06-30 06:39:16,262] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-30 06:39:16,268] multiqc [DEBUG ] No samples found: hicup [2024-06-30 06:39:16,273] multiqc [DEBUG ] No samples found: hicpro [2024-06-30 06:39:16,278] multiqc [DEBUG ] No samples found: salmon [2024-06-30 06:39:16,284] multiqc [DEBUG ] No samples found: kallisto [2024-06-30 06:39:16,290] multiqc [DEBUG ] No samples found: slamdunk [2024-06-30 06:39:16,296] multiqc [DEBUG ] No samples found: star [2024-06-30 06:39:16,301] multiqc [DEBUG ] No samples found: hisat2 [2024-06-30 06:39:16,306] multiqc [DEBUG ] No samples found: tophat [2024-06-30 06:39:16,312] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-30 06:39:16,317] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-30 06:39:16,322] multiqc [DEBUG ] No samples found: snpsplit [2024-06-30 06:39:16,328] multiqc [DEBUG ] No samples found: kat [2024-06-30 06:39:16,333] multiqc [DEBUG ] No samples found: leehom [2024-06-30 06:39:16,338] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-30 06:39:16,343] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-30 06:39:16,349] multiqc [DEBUG ] No samples found: cutadapt [2024-06-30 06:39:16,354] multiqc [DEBUG ] No samples found: flexbar [2024-06-30 06:39:16,359] multiqc [DEBUG ] No samples found: kaiju [2024-06-30 06:39:16,364] multiqc [DEBUG ] No samples found: kraken [2024-06-30 06:39:16,370] multiqc [DEBUG ] No samples found: malt [2024-06-30 06:39:16,375] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-30 06:39:16,380] multiqc [DEBUG ] No samples found: sickle [2024-06-30 06:39:16,385] multiqc [DEBUG ] No samples found: skewer [2024-06-30 06:39:16,390] multiqc [DEBUG ] No samples found: sortmerna [2024-06-30 06:39:16,395] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-30 06:39:16,401] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-30 06:39:16,406] multiqc [DEBUG ] No samples found: afterqc [2024-06-30 06:39:16,412] multiqc [DEBUG ] No samples found: fastp [2024-06-30 06:39:23,052] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2024-06-30 06:39:23,495] multiqc [DEBUG ] No samples found: pycoqc [2024-06-30 06:39:23,501] multiqc [DEBUG ] No samples found: minionqc [2024-06-30 06:39:23,506] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-30 06:39:23,512] multiqc [DEBUG ] No samples found: clusterflow [2024-06-30 06:39:23,517] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-30 06:39:23,523] multiqc [DEBUG ] No samples found: interop [2024-06-30 06:39:23,528] multiqc [DEBUG ] No samples found: ivar [2024-06-30 06:39:23,534] multiqc [DEBUG ] No samples found: flash [2024-06-30 06:39:23,539] multiqc [DEBUG ] No samples found: seqyclean [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-30 06:39:23,539] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-30 06:39:23,540] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-30 06:39:23,599] multiqc [INFO ] Compressing plot data [2024-06-30 06:39:24,457] multiqc [INFO ] Report : multiqc_report.html [2024-06-30 06:39:24,457] multiqc [INFO ] Data : multiqc_data [2024-06-30 06:39:24,457] multiqc [DEBUG ] Moving data file from '/state/partition1/job-48077233/tmp0x1l0o97/multiqc_data' to '/vast/gencore/GENEFLOW/work/bf/5b0bde794148033a8e274546773799/merged/multiqc_data' [2024-06-30 06:39:24,631] multiqc [INFO ] MultiQC complete