[2024-05-29 06:25:39,628] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-05-29 06:25:39,628] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-05-29 06:25:39,629] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-05-29 06:25:39,631] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-05-29 06:25:39,631] 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}} [2024-05-29 06:25:39,631] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-29 06:25:39,667] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-05-29 06:25:39,667] multiqc [INFO ] This is MultiQC v1.9 [2024-05-29 06:25:39,667] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-29 06:25:39,667] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/be/2bc827eff224986bf4ab6189b28721/2 [2024-05-29 06:25:39,667] multiqc [INFO ] Template : default [2024-05-29 06:25:39,667] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-05-29 06:25:39,667] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/be/2bc827eff224986bf4ab6189b28721/2 [2024-05-29 06:25:39,668] 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 [2024-05-29 06:25:39,668] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47073692/tmpryhz06hm [2024-05-29 06:25:39,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYMY5DRX3_l02_n01_ah_01_fastqc.html [2024-05-29 06:25:39,807] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYMY5DRX3_l02_n01_ah_01_fastqc.html [2024-05-29 06:25:39,878] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HYMY5DRX3_l02_n01_jh_8_fastqc.html [2024-05-29 06:25:42,832] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYMY5DRX3_l02_n01_jh_8_fastqc.html [2024-05-29 06:25:42,899] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYMY5DRX3_l02_n01_jh_9_fastqc.html [2024-05-29 06:25:42,906] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYMY5DRX3_l02_n01_jh_9_fastqc.html [2024-05-29 06:25:42,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYMY5DRX3_l02_n01_undetermined_fastqc.html [2024-05-29 06:25:42,981] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYMY5DRX3_l02_n01_undetermined_fastqc.html [2024-05-29 06:25:43,045] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-29 06:25:43,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-29 06:25:43,648] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-29 06:25:43,650] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-29 06:25:43,677] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 40 samples (table) [2024-05-29 06:25:43,679] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-05-29 06:25:43,688] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-05-29 06:25:43,694] multiqc [DEBUG ] No samples found: conpair [2024-05-29 06:25:43,700] multiqc [DEBUG ] No samples found: peddy [2024-05-29 06:25:43,707] multiqc [DEBUG ] No samples found: somalier [2024-05-29 06:25:43,713] multiqc [DEBUG ] No samples found: methylQA [2024-05-29 06:25:43,724] multiqc [DEBUG ] No samples found: mosdepth [2024-05-29 06:25:43,729] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-05-29 06:25:43,733] multiqc [DEBUG ] No samples found: qualimap [2024-05-29 06:25:43,738] multiqc [DEBUG ] No samples found: preseq [2024-05-29 06:25:43,745] multiqc [DEBUG ] No samples found: quast [2024-05-29 06:25:43,751] multiqc [DEBUG ] No samples found: qorts [2024-05-29 06:25:43,756] multiqc [DEBUG ] No samples found: rna_seqc [2024-05-29 06:25:43,762] multiqc [DEBUG ] No samples found: rockhopper [2024-05-29 06:25:43,767] multiqc [DEBUG ] No samples found: rsem [2024-05-29 06:25:43,782] multiqc [DEBUG ] No samples found: rseqc [2024-05-29 06:25:43,787] multiqc [DEBUG ] No samples found: busco [2024-05-29 06:25:43,793] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-05-29 06:25:43,799] multiqc [DEBUG ] No samples found: disambiguate [2024-05-29 06:25:43,805] multiqc [DEBUG ] No samples found: supernova [2024-05-29 06:25:43,822] multiqc [DEBUG ] No samples found: deeptools [2024-05-29 06:25:43,827] multiqc [DEBUG ] No samples found: sargasso [2024-05-29 06:25:43,833] multiqc [DEBUG ] No samples found: verifybamid [2024-05-29 06:25:43,839] multiqc [DEBUG ] No samples found: mirtrace [2024-05-29 06:25:43,845] multiqc [DEBUG ] No samples found: happy [2024-05-29 06:25:43,850] multiqc [DEBUG ] No samples found: mirtop [2024-05-29 06:25:43,858] multiqc [DEBUG ] No samples found: homer [2024-05-29 06:25:43,864] multiqc [DEBUG ] No samples found: macs2 [2024-05-29 06:25:43,870] multiqc [DEBUG ] No samples found: theta2 [2024-05-29 06:25:43,876] multiqc [DEBUG ] No samples found: snpeff [2024-05-29 06:25:43,884] multiqc [DEBUG ] No samples found: gatk [2024-05-29 06:25:43,890] multiqc [DEBUG ] No samples found: htseq [2024-05-29 06:25:43,896] multiqc [DEBUG ] No samples found: bcftools [2024-05-29 06:25:43,902] multiqc [DEBUG ] No samples found: featureCounts [2024-05-29 06:25:43,910] multiqc [DEBUG ] No samples found: fgbio [2024-05-29 06:25:43,926] multiqc [DEBUG ] No samples found: dragen [2024-05-29 06:25:43,932] multiqc [DEBUG ] No samples found: dedup [2024-05-29 06:25:43,938] multiqc [DEBUG ] No samples found: damageprofiler [2024-05-29 06:25:43,968] multiqc [DEBUG ] No samples found: biobambam2 [2024-05-29 06:25:43,973] multiqc [DEBUG ] No samples found: mtnucratio [2024-05-29 06:25:43,975] multiqc [DEBUG ] No samples found: picard [2024-05-29 06:25:43,981] multiqc [DEBUG ] No samples found: prokka [2024-05-29 06:25:43,986] multiqc [DEBUG ] No samples found: samblaster [2024-05-29 06:25:43,996] multiqc [DEBUG ] No samples found: samtools [2024-05-29 06:25:44,002] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-05-29 06:25:44,008] multiqc [DEBUG ] No samples found: bamtools [2024-05-29 06:25:44,014] multiqc [DEBUG ] No samples found: jellyfish [2024-05-29 06:25:44,023] multiqc [DEBUG ] No samples found: vcftools [2024-05-29 06:25:44,029] multiqc [DEBUG ] No samples found: longranger [2024-05-29 06:25:44,034] multiqc [DEBUG ] No samples found: stacks [2024-05-29 06:25:44,040] multiqc [DEBUG ] No samples found: varscan2 [2024-05-29 06:25:44,059] multiqc [DEBUG ] No samples found: bbmap [2024-05-29 06:25:44,065] multiqc [DEBUG ] No samples found: bismark [2024-05-29 06:25:44,071] multiqc [DEBUG ] No samples found: biscuit [2024-05-29 06:25:44,076] multiqc [DEBUG ] No samples found: hicexplorer [2024-05-29 06:25:44,082] multiqc [DEBUG ] No samples found: hicup [2024-05-29 06:25:44,088] multiqc [DEBUG ] No samples found: hicpro [2024-05-29 06:25:44,093] multiqc [DEBUG ] No samples found: salmon [2024-05-29 06:25:44,099] multiqc [DEBUG ] No samples found: kallisto [2024-05-29 06:25:44,105] multiqc [DEBUG ] No samples found: slamdunk [2024-05-29 06:25:44,111] multiqc [DEBUG ] No samples found: star [2024-05-29 06:25:44,116] multiqc [DEBUG ] No samples found: hisat2 [2024-05-29 06:25:44,122] multiqc [DEBUG ] No samples found: tophat [2024-05-29 06:25:44,127] multiqc [DEBUG ] No samples found: bowtie2 [2024-05-29 06:25:44,133] multiqc [DEBUG ] No samples found: bowtie1 [2024-05-29 06:25:44,139] multiqc [DEBUG ] No samples found: snpsplit [2024-05-29 06:25:44,144] multiqc [DEBUG ] No samples found: kat [2024-05-29 06:25:44,149] multiqc [DEBUG ] No samples found: leehom [2024-05-29 06:25:44,155] multiqc [DEBUG ] No samples found: adapterRemoval [2024-05-29 06:25:44,160] multiqc [DEBUG ] No samples found: clipandmerge [2024-05-29 06:25:44,166] multiqc [DEBUG ] No samples found: cutadapt [2024-05-29 06:25:44,171] multiqc [DEBUG ] No samples found: flexbar [2024-05-29 06:25:44,177] multiqc [DEBUG ] No samples found: kaiju [2024-05-29 06:25:44,182] multiqc [DEBUG ] No samples found: kraken [2024-05-29 06:25:44,188] multiqc [DEBUG ] No samples found: malt [2024-05-29 06:25:44,193] multiqc [DEBUG ] No samples found: trimmomatic [2024-05-29 06:25:44,198] multiqc [DEBUG ] No samples found: sickle [2024-05-29 06:25:44,204] multiqc [DEBUG ] No samples found: skewer [2024-05-29 06:25:44,209] multiqc [DEBUG ] No samples found: sortmerna [2024-05-29 06:25:44,214] multiqc [DEBUG ] No samples found: biobloomtools [2024-05-29 06:25:44,220] multiqc [DEBUG ] No samples found: fastq_screen [2024-05-29 06:25:44,227] multiqc [DEBUG ] No samples found: afterqc [2024-05-29 06:25:44,232] multiqc [DEBUG ] No samples found: fastp [2024-05-29 06:25:45,595] multiqc.modules.fastqc.fastqc [INFO ] Found 40 reports [2024-05-29 06:25:46,156] multiqc [DEBUG ] No samples found: pycoqc [2024-05-29 06:25:46,162] multiqc [DEBUG ] No samples found: minionqc [2024-05-29 06:25:46,168] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-05-29 06:25:46,173] multiqc [DEBUG ] No samples found: clusterflow [2024-05-29 06:25:46,179] multiqc [DEBUG ] No samples found: bcl2fastq [2024-05-29 06:25:46,185] multiqc [DEBUG ] No samples found: interop [2024-05-29 06:25:46,191] multiqc [DEBUG ] No samples found: ivar [2024-05-29 06:25:46,196] multiqc [DEBUG ] No samples found: flash [2024-05-29 06:25:46,201] multiqc [DEBUG ] No samples found: seqyclean [2024-05-29 06:25:46,201] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-05-29 06:25:46,202] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-05-29 06:25:46,250] multiqc [INFO ] Compressing plot data [2024-05-29 06:25:46,983] multiqc [INFO ] Report : multiqc_report.html [2024-05-29 06:25:46,984] multiqc [INFO ] Data : multiqc_data [2024-05-29 06:25:46,984] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47073692/tmpryhz06hm/multiqc_data' to '/vast/gencore/GENEFLOW/work/be/2bc827eff224986bf4ab6189b28721/2/multiqc_data' [2024-05-29 06:25:47,176] multiqc [INFO ] MultiQC complete