[2023-08-09 04:48:36,683] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-08-09 04:48:36,683] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-08-09 04:48:36,684] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-08-09 04:48:36,686] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-08-09 04:48:36,686] 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}} [2023-08-09 04:48:36,687] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-08-09 04:48:36,862] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-08-09 04:48:36,862] multiqc [INFO ] This is MultiQC v1.9 [2023-08-09 04:48:36,862] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-08-09 04:48:36,863] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/12/83e076487cc8dec33fc0cb5bf573f6/merged [2023-08-09 04:48:36,863] multiqc [INFO ] Template : default [2023-08-09 04:48:36,863] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-08-09 04:48:36,863] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/12/83e076487cc8dec33fc0cb5bf573f6/merged [2023-08-09 04:48:36,863] 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 [2023-08-09 04:48:36,863] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-36278635/tmpjl9xa3yy [2023-08-09 04:48:37,585] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-09 04:48:37,587] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-09 04:48:37,607] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 27 samples (table) [2023-08-09 04:48:37,609] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-08-09 04:48:37,616] multiqc [DEBUG ] No samples found: conpair [2023-08-09 04:48:37,623] multiqc [DEBUG ] No samples found: peddy [2023-08-09 04:48:37,630] multiqc [DEBUG ] No samples found: somalier [2023-08-09 04:48:37,637] multiqc [DEBUG ] No samples found: methylQA [2023-08-09 04:48:37,650] multiqc [DEBUG ] No samples found: mosdepth [2023-08-09 04:48:37,657] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-08-09 04:48:37,661] multiqc [DEBUG ] No samples found: qualimap [2023-08-09 04:48:37,668] multiqc [DEBUG ] No samples found: preseq [2023-08-09 04:48:37,675] multiqc [DEBUG ] No samples found: quast [2023-08-09 04:48:37,682] multiqc [DEBUG ] No samples found: qorts [2023-08-09 04:48:37,689] multiqc [DEBUG ] No samples found: rna_seqc [2023-08-09 04:48:37,696] multiqc [DEBUG ] No samples found: rockhopper [2023-08-09 04:48:37,703] multiqc [DEBUG ] No samples found: rsem [2023-08-09 04:48:37,722] multiqc [DEBUG ] No samples found: rseqc [2023-08-09 04:48:37,728] multiqc [DEBUG ] No samples found: busco [2023-08-09 04:48:37,736] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-08-09 04:48:37,742] multiqc [DEBUG ] No samples found: disambiguate [2023-08-09 04:48:37,750] multiqc [DEBUG ] No samples found: supernova [2023-08-09 04:48:37,771] multiqc [DEBUG ] No samples found: deeptools [2023-08-09 04:48:37,778] multiqc [DEBUG ] No samples found: sargasso [2023-08-09 04:48:37,785] multiqc [DEBUG ] No samples found: verifybamid [2023-08-09 04:48:37,792] multiqc [DEBUG ] No samples found: mirtrace [2023-08-09 04:48:37,799] multiqc [DEBUG ] No samples found: happy [2023-08-09 04:48:37,806] multiqc [DEBUG ] No samples found: mirtop [2023-08-09 04:48:37,816] multiqc [DEBUG ] No samples found: homer [2023-08-09 04:48:37,823] multiqc [DEBUG ] No samples found: macs2 [2023-08-09 04:48:37,829] multiqc [DEBUG ] No samples found: theta2 [2023-08-09 04:48:37,836] multiqc [DEBUG ] No samples found: snpeff [2023-08-09 04:48:37,847] multiqc [DEBUG ] No samples found: gatk [2023-08-09 04:48:37,853] multiqc [DEBUG ] No samples found: htseq [2023-08-09 04:48:37,861] multiqc [DEBUG ] No samples found: bcftools [2023-08-09 04:48:37,868] multiqc [DEBUG ] No samples found: featureCounts [2023-08-09 04:48:37,878] multiqc [DEBUG ] No samples found: fgbio [2023-08-09 04:48:37,897] multiqc [DEBUG ] No samples found: dragen [2023-08-09 04:48:37,904] multiqc [DEBUG ] No samples found: dedup [2023-08-09 04:48:37,911] multiqc [DEBUG ] No samples found: damageprofiler [2023-08-09 04:48:37,944] multiqc [DEBUG ] No samples found: biobambam2 [2023-08-09 04:48:37,951] multiqc [DEBUG ] No samples found: mtnucratio [2023-08-09 04:48:37,954] multiqc [DEBUG ] No samples found: picard [2023-08-09 04:48:37,960] multiqc [DEBUG ] No samples found: prokka [2023-08-09 04:48:37,967] multiqc [DEBUG ] No samples found: samblaster [2023-08-09 04:48:37,979] multiqc [DEBUG ] No samples found: samtools [2023-08-09 04:48:37,986] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-08-09 04:48:37,993] multiqc [DEBUG ] No samples found: bamtools [2023-08-09 04:48:37,999] multiqc [DEBUG ] No samples found: jellyfish [2023-08-09 04:48:38,011] multiqc [DEBUG ] No samples found: vcftools [2023-08-09 04:48:38,018] multiqc [DEBUG ] No samples found: longranger [2023-08-09 04:48:38,024] multiqc [DEBUG ] No samples found: stacks [2023-08-09 04:48:38,031] multiqc [DEBUG ] No samples found: varscan2 [2023-08-09 04:48:38,052] multiqc [DEBUG ] No samples found: bbmap [2023-08-09 04:48:38,059] multiqc [DEBUG ] No samples found: bismark [2023-08-09 04:48:38,067] multiqc [DEBUG ] No samples found: biscuit [2023-08-09 04:48:38,073] multiqc [DEBUG ] No samples found: hicexplorer [2023-08-09 04:48:38,081] multiqc [DEBUG ] No samples found: hicup [2023-08-09 04:48:38,088] multiqc [DEBUG ] No samples found: hicpro [2023-08-09 04:48:38,094] multiqc [DEBUG ] No samples found: salmon [2023-08-09 04:48:38,101] multiqc [DEBUG ] No samples found: kallisto [2023-08-09 04:48:38,107] multiqc [DEBUG ] No samples found: slamdunk [2023-08-09 04:48:38,114] multiqc [DEBUG ] No samples found: star [2023-08-09 04:48:38,120] multiqc [DEBUG ] No samples found: hisat2 [2023-08-09 04:48:38,127] multiqc [DEBUG ] No samples found: tophat [2023-08-09 04:48:38,133] multiqc [DEBUG ] No samples found: bowtie2 [2023-08-09 04:48:38,140] multiqc [DEBUG ] No samples found: bowtie1 [2023-08-09 04:48:38,146] multiqc [DEBUG ] No samples found: snpsplit [2023-08-09 04:48:38,153] multiqc [DEBUG ] No samples found: kat [2023-08-09 04:48:38,159] multiqc [DEBUG ] No samples found: leehom [2023-08-09 04:48:38,166] multiqc [DEBUG ] No samples found: adapterRemoval [2023-08-09 04:48:38,172] multiqc [DEBUG ] No samples found: clipandmerge [2023-08-09 04:48:38,186] multiqc [DEBUG ] No samples found: cutadapt [2023-08-09 04:48:38,192] multiqc [DEBUG ] No samples found: flexbar [2023-08-09 04:48:38,199] multiqc [DEBUG ] No samples found: kaiju [2023-08-09 04:48:38,206] multiqc [DEBUG ] No samples found: kraken [2023-08-09 04:48:38,213] multiqc [DEBUG ] No samples found: malt [2023-08-09 04:48:38,219] multiqc [DEBUG ] No samples found: trimmomatic [2023-08-09 04:48:38,226] multiqc [DEBUG ] No samples found: sickle [2023-08-09 04:48:38,233] multiqc [DEBUG ] No samples found: skewer [2023-08-09 04:48:38,240] multiqc [DEBUG ] No samples found: sortmerna [2023-08-09 04:48:38,246] multiqc [DEBUG ] No samples found: biobloomtools [2023-08-09 04:48:38,253] multiqc [DEBUG ] No samples found: fastq_screen [2023-08-09 04:48:38,260] multiqc [DEBUG ] No samples found: afterqc [2023-08-09 04:48:38,267] multiqc [DEBUG ] No samples found: fastp [2023-08-09 04:48:38,274] multiqc [DEBUG ] No samples found: fastqc [2023-08-09 04:48:38,281] multiqc [DEBUG ] No samples found: pycoqc [2023-08-09 04:48:38,287] multiqc [DEBUG ] No samples found: minionqc [2023-08-09 04:48:38,294] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-08-09 04:48:38,301] multiqc [DEBUG ] No samples found: clusterflow [2023-08-09 04:48:38,308] multiqc [DEBUG ] No samples found: bcl2fastq [2023-08-09 04:48:38,315] multiqc [DEBUG ] No samples found: interop [2023-08-09 04:48:38,322] multiqc [DEBUG ] No samples found: ivar [2023-08-09 04:48:38,328] multiqc [DEBUG ] No samples found: flash [2023-08-09 04:48:38,335] multiqc [DEBUG ] No samples found: seqyclean [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-08-09 04:48:38,335] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-08-09 04:48:38,335] multiqc [INFO ] Compressing plot data [2023-08-09 04:48:38,337] multiqc [INFO ] Report : multiqc_report.html [2023-08-09 04:48:38,337] multiqc [INFO ] Data : multiqc_data [2023-08-09 04:48:38,337] multiqc [DEBUG ] Moving data file from '/state/partition1/job-36278635/tmpjl9xa3yy/multiqc_data' to '/vast/gencore/GENEFLOW/work/12/83e076487cc8dec33fc0cb5bf573f6/merged/multiqc_data' [2023-08-09 04:48:38,515] multiqc [INFO ] MultiQC complete