[2022-04-08 09:15:13,257] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-08 09:15:13,257] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-08 09:15:13,257] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-08 09:15:13,258] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-08 09:15:13,258] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-08 09:15:13,258] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJLKNBGXL/merged [2022-04-08 09:15:13,809] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-08 09:15:13,809] multiqc [INFO ] This is MultiQC v1.9 [2022-04-08 09:15:13,809] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJLKNBGXL/merged [2022-04-08 09:15:13,809] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJLKNBGXL/merged [2022-04-08 09:15:13,809] multiqc [INFO ] Template : default [2022-04-08 09:15:13,809] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-08 09:15:13,809] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJLKNBGXL/merged [2022-04-08 09:15:13,809] 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 [2022-04-08 09:15:13,810] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-17457068/tmpjr6045d0 [2022-04-08 09:15:13,906] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n02_undetermined_fastqc.html [2022-04-08 09:15:13,909] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n02_undetermined_fastqc.html [2022-04-08 09:15:13,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n02_Optix_Lib1_March_31_2022_fastqc.html [2022-04-08 09:15:13,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n02_Optix_Lib1_March_31_2022_fastqc.html [2022-04-08 09:15:13,992] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:13,993] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:13,993] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:13,993] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:13,993] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:13,993] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:13,994] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:14,062] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 09:15:17,083] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n01_Optix_Lib1_March_31_2022_fastqc.html [2022-04-08 09:15:17,086] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n01_Optix_Lib1_March_31_2022_fastqc.html [2022-04-08 09:15:17,126] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n02_Optix_Lib2_March_31_2022_fastqc.html [2022-04-08 09:15:17,128] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n02_Optix_Lib2_March_31_2022_fastqc.html [2022-04-08 09:15:17,171] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n01_undetermined_fastqc.html [2022-04-08 09:15:17,173] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n01_undetermined_fastqc.html [2022-04-08 09:15:17,214] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n02_Optix_Lib3_March_31_2022_fastqc.html [2022-04-08 09:15:17,216] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n02_Optix_Lib3_March_31_2022_fastqc.html [2022-04-08 09:15:17,258] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n01_Optix_Lib2_March_31_2022_fastqc.html [2022-04-08 09:15:17,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n01_Optix_Lib2_March_31_2022_fastqc.html [2022-04-08 09:15:17,301] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLKNBGXL_n01_Optix_Lib3_March_31_2022_fastqc.html [2022-04-08 09:15:17,303] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLKNBGXL_n01_Optix_Lib3_March_31_2022_fastqc.html [2022-04-08 09:15:17,617] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-08 09:15:17,617] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-08 09:15:17,624] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-08 09:15:17,626] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 4 samples (table) [2022-04-08 09:15:17,636] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-08 09:15:17,639] multiqc [DEBUG ] No samples found: conpair [2022-04-08 09:15:17,642] multiqc [DEBUG ] No samples found: peddy [2022-04-08 09:15:17,646] multiqc [DEBUG ] No samples found: somalier [2022-04-08 09:15:17,649] multiqc [DEBUG ] No samples found: methylQA [2022-04-08 09:15:17,653] multiqc [DEBUG ] No samples found: mosdepth [2022-04-08 09:15:17,657] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-08 09:15:17,659] multiqc [DEBUG ] No samples found: qualimap [2022-04-08 09:15:17,662] multiqc [DEBUG ] No samples found: preseq [2022-04-08 09:15:17,665] multiqc [DEBUG ] No samples found: quast [2022-04-08 09:15:17,669] multiqc [DEBUG ] No samples found: qorts [2022-04-08 09:15:17,672] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-08 09:15:17,675] multiqc [DEBUG ] No samples found: rockhopper [2022-04-08 09:15:17,678] multiqc [DEBUG ] No samples found: rsem [2022-04-08 09:15:17,685] multiqc [DEBUG ] No samples found: rseqc [2022-04-08 09:15:17,688] multiqc [DEBUG ] No samples found: busco [2022-04-08 09:15:17,691] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-08 09:15:17,694] multiqc [DEBUG ] No samples found: disambiguate [2022-04-08 09:15:17,698] multiqc [DEBUG ] No samples found: supernova [2022-04-08 09:15:17,704] multiqc [DEBUG ] No samples found: deeptools [2022-04-08 09:15:17,707] multiqc [DEBUG ] No samples found: sargasso [2022-04-08 09:15:17,710] multiqc [DEBUG ] No samples found: verifybamid [2022-04-08 09:15:17,713] multiqc [DEBUG ] No samples found: mirtrace [2022-04-08 09:15:17,717] multiqc [DEBUG ] No samples found: happy [2022-04-08 09:15:17,720] multiqc [DEBUG ] No samples found: mirtop [2022-04-08 09:15:17,724] multiqc [DEBUG ] No samples found: homer [2022-04-08 09:15:17,727] multiqc [DEBUG ] No samples found: macs2 [2022-04-08 09:15:17,730] multiqc [DEBUG ] No samples found: theta2 [2022-04-08 09:15:17,733] multiqc [DEBUG ] No samples found: snpeff [2022-04-08 09:15:17,737] multiqc [DEBUG ] No samples found: gatk [2022-04-08 09:15:17,741] multiqc [DEBUG ] No samples found: htseq [2022-04-08 09:15:17,744] multiqc [DEBUG ] No samples found: bcftools [2022-04-08 09:15:17,747] multiqc [DEBUG ] No samples found: featureCounts [2022-04-08 09:15:17,751] multiqc [DEBUG ] No samples found: fgbio [2022-04-08 09:15:17,757] multiqc [DEBUG ] No samples found: dragen [2022-04-08 09:15:17,761] multiqc [DEBUG ] No samples found: dedup [2022-04-08 09:15:17,764] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-08 09:15:17,774] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-08 09:15:17,778] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-08 09:15:17,780] multiqc [DEBUG ] No samples found: picard [2022-04-08 09:15:17,784] multiqc [DEBUG ] No samples found: prokka [2022-04-08 09:15:17,787] multiqc [DEBUG ] No samples found: samblaster [2022-04-08 09:15:17,792] multiqc [DEBUG ] No samples found: samtools [2022-04-08 09:15:17,795] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-08 09:15:17,798] multiqc [DEBUG ] No samples found: bamtools [2022-04-08 09:15:17,802] multiqc [DEBUG ] No samples found: jellyfish [2022-04-08 09:15:17,806] multiqc [DEBUG ] No samples found: vcftools [2022-04-08 09:15:17,809] multiqc [DEBUG ] No samples found: longranger [2022-04-08 09:15:17,812] multiqc [DEBUG ] No samples found: stacks [2022-04-08 09:15:17,816] multiqc [DEBUG ] No samples found: varscan2 [2022-04-08 09:15:17,823] multiqc [DEBUG ] No samples found: bbmap [2022-04-08 09:15:17,826] multiqc [DEBUG ] No samples found: bismark [2022-04-08 09:15:17,829] multiqc [DEBUG ] No samples found: biscuit [2022-04-08 09:15:17,833] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-08 09:15:17,836] multiqc [DEBUG ] No samples found: hicup [2022-04-08 09:15:17,839] multiqc [DEBUG ] No samples found: hicpro [2022-04-08 09:15:17,842] multiqc [DEBUG ] No samples found: salmon [2022-04-08 09:15:17,845] multiqc [DEBUG ] No samples found: kallisto [2022-04-08 09:15:17,849] multiqc [DEBUG ] No samples found: slamdunk [2022-04-08 09:15:17,852] multiqc [DEBUG ] No samples found: star [2022-04-08 09:15:17,855] multiqc [DEBUG ] No samples found: hisat2 [2022-04-08 09:15:17,858] multiqc [DEBUG ] No samples found: tophat [2022-04-08 09:15:17,861] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-08 09:15:17,864] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-08 09:15:17,867] multiqc [DEBUG ] No samples found: snpsplit [2022-04-08 09:15:17,870] multiqc [DEBUG ] No samples found: kat [2022-04-08 09:15:17,874] multiqc [DEBUG ] No samples found: leehom [2022-04-08 09:15:17,877] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-08 09:15:17,880] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-08 09:15:17,883] multiqc [DEBUG ] No samples found: cutadapt [2022-04-08 09:15:17,886] multiqc [DEBUG ] No samples found: flexbar [2022-04-08 09:15:17,889] multiqc [DEBUG ] No samples found: kaiju [2022-04-08 09:15:17,893] multiqc [DEBUG ] No samples found: kraken [2022-04-08 09:15:17,896] multiqc [DEBUG ] No samples found: malt [2022-04-08 09:15:17,899] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-08 09:15:17,902] multiqc [DEBUG ] No samples found: sickle [2022-04-08 09:15:17,905] multiqc [DEBUG ] No samples found: skewer [2022-04-08 09:15:17,908] multiqc [DEBUG ] No samples found: sortmerna [2022-04-08 09:15:17,911] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-08 09:15:17,914] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-08 09:15:17,918] multiqc [DEBUG ] No samples found: afterqc [2022-04-08 09:15:17,921] multiqc [DEBUG ] No samples found: fastp [2022-04-08 09:15:18,394] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-04-08 09:15:18,470] multiqc [DEBUG ] No samples found: pycoqc [2022-04-08 09:15:18,473] multiqc [DEBUG ] No samples found: minionqc [2022-04-08 09:15:18,476] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-08 09:15:18,479] multiqc [DEBUG ] No samples found: clusterflow [2022-04-08 09:15:18,482] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-08 09:15:18,486] multiqc [DEBUG ] No samples found: interop [2022-04-08 09:15:18,489] multiqc [DEBUG ] No samples found: ivar [2022-04-08 09:15:18,492] multiqc [DEBUG ] No samples found: flash [2022-04-08 09:15:18,495] multiqc [DEBUG ] No samples found: seqyclean [2022-04-08 09:15:18,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-08 09:15:18,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-08 09:15:18,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-08 09:15:18,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-08 09:15:18,506] multiqc [INFO ] Compressing plot data [2022-04-08 09:15:18,642] multiqc [INFO ] Report : multiqc_report.html [2022-04-08 09:15:18,642] multiqc [INFO ] Data : multiqc_data [2022-04-08 09:15:18,642] multiqc [DEBUG ] Moving data file from '/state/partition1/job-17457068/tmpjr6045d0/multiqc_data' to '/scratch/gencore/logs/html/HJLKNBGXL/merged/multiqc_data' [2022-04-08 09:15:18,746] multiqc [INFO ] MultiQC complete