[2023-11-30 02:23:06,807] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-11-30 02:23:06,808] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-11-30 02:23:06,808] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-11-30 02:23:06,811] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-11-30 02:23:06,811] 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}} [2023-11-30 02:23:06,811] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-11-30 02:23:06,984] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-11-30 02:23:06,985] multiqc [INFO ] This is MultiQC v1.9 [2023-11-30 02:23:06,985] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-11-30 02:23:06,985] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/94/8fa0854c5b200267759d206fd6d0ab/merged [2023-11-30 02:23:06,985] multiqc [INFO ] Template : default [2023-11-30 02:23:06,985] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-11-30 02:23:06,985] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/94/8fa0854c5b200267759d206fd6d0ab/merged [2023-11-30 02:23:06,986] 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 [2023-11-30 02:23:06,986] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40452046/tmpgq0_my_g [2023-11-30 02:23:07,158] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWVKNBGXT_1_fastqc.html [2023-11-30 02:23:07,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWVKNBGXT_1_fastqc.html [2023-11-30 02:23:07,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWVKNBGXT_2_fastqc.html [2023-11-30 02:23:07,257] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWVKNBGXT_2_fastqc.html [2023-11-30 02:23:07,617] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-30 02:23:07,619] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-30 02:23:07,624] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-11-30 02:23:07,629] multiqc [DEBUG ] No samples found: conpair [2023-11-30 02:23:07,634] multiqc [DEBUG ] No samples found: peddy [2023-11-30 02:23:07,639] multiqc [DEBUG ] No samples found: somalier [2023-11-30 02:23:07,644] multiqc [DEBUG ] No samples found: methylQA [2023-11-30 02:23:07,653] multiqc [DEBUG ] No samples found: mosdepth [2023-11-30 02:23:07,658] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-11-30 02:23:07,661] multiqc [DEBUG ] No samples found: qualimap [2023-11-30 02:23:07,670] multiqc [DEBUG ] No samples found: preseq [2023-11-30 02:23:07,675] multiqc [DEBUG ] No samples found: quast [2023-11-30 02:23:07,680] multiqc [DEBUG ] No samples found: qorts [2023-11-30 02:23:07,686] multiqc [DEBUG ] No samples found: rna_seqc [2023-11-30 02:23:07,691] multiqc [DEBUG ] No samples found: rockhopper [2023-11-30 02:23:07,696] multiqc [DEBUG ] No samples found: rsem [2023-11-30 02:23:07,707] multiqc [DEBUG ] No samples found: rseqc [2023-11-30 02:23:07,712] multiqc [DEBUG ] No samples found: busco [2023-11-30 02:23:07,717] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-11-30 02:23:07,722] multiqc [DEBUG ] No samples found: disambiguate [2023-11-30 02:23:07,727] multiqc [DEBUG ] No samples found: supernova [2023-11-30 02:23:07,740] multiqc [DEBUG ] No samples found: deeptools [2023-11-30 02:23:07,745] multiqc [DEBUG ] No samples found: sargasso [2023-11-30 02:23:07,750] multiqc [DEBUG ] No samples found: verifybamid [2023-11-30 02:23:07,755] multiqc [DEBUG ] No samples found: mirtrace [2023-11-30 02:23:07,761] multiqc [DEBUG ] No samples found: happy [2023-11-30 02:23:07,766] multiqc [DEBUG ] No samples found: mirtop [2023-11-30 02:23:07,772] multiqc [DEBUG ] No samples found: homer [2023-11-30 02:23:07,777] multiqc [DEBUG ] No samples found: macs2 [2023-11-30 02:23:07,782] multiqc [DEBUG ] No samples found: theta2 [2023-11-30 02:23:07,787] multiqc [DEBUG ] No samples found: snpeff [2023-11-30 02:23:07,794] multiqc [DEBUG ] No samples found: gatk [2023-11-30 02:23:07,798] multiqc [DEBUG ] No samples found: htseq [2023-11-30 02:23:07,804] multiqc [DEBUG ] No samples found: bcftools [2023-11-30 02:23:07,809] multiqc [DEBUG ] No samples found: featureCounts [2023-11-30 02:23:07,816] multiqc [DEBUG ] No samples found: fgbio [2023-11-30 02:23:07,829] multiqc [DEBUG ] No samples found: dragen [2023-11-30 02:23:07,834] multiqc [DEBUG ] No samples found: dedup [2023-11-30 02:23:07,839] multiqc [DEBUG ] No samples found: damageprofiler [2023-11-30 02:23:07,863] multiqc [DEBUG ] No samples found: biobambam2 [2023-11-30 02:23:07,869] multiqc [DEBUG ] No samples found: mtnucratio [2023-11-30 02:23:07,872] multiqc [DEBUG ] No samples found: picard [2023-11-30 02:23:07,879] multiqc [DEBUG ] No samples found: prokka [2023-11-30 02:23:07,884] multiqc [DEBUG ] No samples found: samblaster [2023-11-30 02:23:07,892] multiqc [DEBUG ] No samples found: samtools [2023-11-30 02:23:07,898] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-11-30 02:23:07,903] multiqc [DEBUG ] No samples found: bamtools [2023-11-30 02:23:07,907] multiqc [DEBUG ] No samples found: jellyfish [2023-11-30 02:23:07,915] multiqc [DEBUG ] No samples found: vcftools [2023-11-30 02:23:07,920] multiqc [DEBUG ] No samples found: longranger [2023-11-30 02:23:07,925] multiqc [DEBUG ] No samples found: stacks [2023-11-30 02:23:07,930] multiqc [DEBUG ] No samples found: varscan2 [2023-11-30 02:23:07,944] multiqc [DEBUG ] No samples found: bbmap [2023-11-30 02:23:07,949] multiqc [DEBUG ] No samples found: bismark [2023-11-30 02:23:07,954] multiqc [DEBUG ] No samples found: biscuit [2023-11-30 02:23:07,959] multiqc [DEBUG ] No samples found: hicexplorer [2023-11-30 02:23:07,964] multiqc [DEBUG ] No samples found: hicup [2023-11-30 02:23:07,970] multiqc [DEBUG ] No samples found: hicpro [2023-11-30 02:23:07,974] multiqc [DEBUG ] No samples found: salmon [2023-11-30 02:23:07,979] multiqc [DEBUG ] No samples found: kallisto [2023-11-30 02:23:07,984] multiqc [DEBUG ] No samples found: slamdunk [2023-11-30 02:23:07,989] multiqc [DEBUG ] No samples found: star [2023-11-30 02:23:07,994] multiqc [DEBUG ] No samples found: hisat2 [2023-11-30 02:23:07,999] multiqc [DEBUG ] No samples found: tophat [2023-11-30 02:23:08,004] multiqc [DEBUG ] No samples found: bowtie2 [2023-11-30 02:23:08,009] multiqc [DEBUG ] No samples found: bowtie1 [2023-11-30 02:23:08,014] multiqc [DEBUG ] No samples found: snpsplit [2023-11-30 02:23:08,019] multiqc [DEBUG ] No samples found: kat [2023-11-30 02:23:08,024] multiqc [DEBUG ] No samples found: leehom [2023-11-30 02:23:08,029] multiqc [DEBUG ] No samples found: adapterRemoval [2023-11-30 02:23:08,033] multiqc [DEBUG ] No samples found: clipandmerge [2023-11-30 02:23:08,038] multiqc [DEBUG ] No samples found: cutadapt [2023-11-30 02:23:08,043] multiqc [DEBUG ] No samples found: flexbar [2023-11-30 02:23:08,048] multiqc [DEBUG ] No samples found: kaiju [2023-11-30 02:23:08,053] multiqc [DEBUG ] No samples found: kraken [2023-11-30 02:23:08,058] multiqc [DEBUG ] No samples found: malt [2023-11-30 02:23:08,063] multiqc [DEBUG ] No samples found: trimmomatic [2023-11-30 02:23:08,068] multiqc [DEBUG ] No samples found: sickle [2023-11-30 02:23:08,073] multiqc [DEBUG ] No samples found: skewer [2023-11-30 02:23:08,077] multiqc [DEBUG ] No samples found: sortmerna [2023-11-30 02:23:08,081] multiqc [DEBUG ] No samples found: biobloomtools [2023-11-30 02:23:08,087] multiqc [DEBUG ] No samples found: fastq_screen [2023-11-30 02:23:08,092] multiqc [DEBUG ] No samples found: afterqc [2023-11-30 02:23:08,097] multiqc [DEBUG ] No samples found: fastp [2023-11-30 02:23:08,182] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2023-11-30 02:23:08,232] multiqc [DEBUG ] No samples found: pycoqc [2023-11-30 02:23:08,237] multiqc [DEBUG ] No samples found: minionqc [2023-11-30 02:23:08,242] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-11-30 02:23:08,247] multiqc [DEBUG ] No samples found: clusterflow [2023-11-30 02:23:08,252] multiqc [DEBUG ] No samples found: bcl2fastq [2023-11-30 02:23:08,257] multiqc [DEBUG ] No samples found: interop [2023-11-30 02:23:08,263] multiqc [DEBUG ] No samples found: ivar [2023-11-30 02:23:08,268] multiqc [DEBUG ] No samples found: flash [2023-11-30 02:23:08,273] multiqc [DEBUG ] No samples found: seqyclean [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-11-30 02:23:08,273] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-11-30 02:23:08,276] multiqc [INFO ] Compressing plot data [2023-11-30 02:23:08,315] multiqc [INFO ] Report : multiqc_report.html [2023-11-30 02:23:08,315] multiqc [INFO ] Data : multiqc_data [2023-11-30 02:23:08,315] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40452046/tmpgq0_my_g/multiqc_data' to '/vast/gencore/GENEFLOW/work/94/8fa0854c5b200267759d206fd6d0ab/merged/multiqc_data' [2023-11-30 02:23:08,484] multiqc [INFO ] MultiQC complete