[2022-09-15 09:37:02,579] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-09-15 09:37:02,579] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-09-15 09:37:02,579] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-15 09:37:02,581] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-09-15 09:37:02,581] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-09-15 09:37:02,581] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNYWNBGXM/merged [2022-09-15 09:37:03,107] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-09-15 09:37:03,107] multiqc [INFO ] This is MultiQC v1.9 [2022-09-15 09:37:03,107] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNYWNBGXM/merged [2022-09-15 09:37:03,107] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNYWNBGXM/merged [2022-09-15 09:37:03,107] multiqc [INFO ] Template : default [2022-09-15 09:37:03,108] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-09-15 09:37:03,108] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNYWNBGXM/merged [2022-09-15 09:37:03,109] 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 [2022-09-15 09:37:03,109] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-24908974/tmp69diujg_ [2022-09-15 09:37:03,275] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYWNBGXM_n01_dpp_Lib2_Aug_31_2022_fastqc.html [2022-09-15 09:37:03,278] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYWNBGXM_n01_dpp_Lib2_Aug_31_2022_fastqc.html [2022-09-15 09:37:03,318] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:03,319] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:03,320] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:03,320] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:03,320] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:03,320] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:03,320] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:03,357] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-15 09:37:04,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYWNBGXM_n02_dpp_Lib2_Aug_31_2022_fastqc.html [2022-09-15 09:37:04,977] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYWNBGXM_n02_dpp_Lib2_Aug_31_2022_fastqc.html [2022-09-15 09:37:05,016] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYWNBGXM_n02_undetermined_fastqc.html [2022-09-15 09:37:05,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYWNBGXM_n02_undetermined_fastqc.html [2022-09-15 09:37:05,058] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYWNBGXM_n01_dpp_Lib1_Aug_31_2022_fastqc.html [2022-09-15 09:37:05,060] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYWNBGXM_n01_dpp_Lib1_Aug_31_2022_fastqc.html [2022-09-15 09:37:05,097] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYWNBGXM_n01_undetermined_fastqc.html [2022-09-15 09:37:05,099] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYWNBGXM_n01_undetermined_fastqc.html [2022-09-15 09:37:05,138] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYWNBGXM_n02_dpp_Lib1_Aug_31_2022_fastqc.html [2022-09-15 09:37:05,140] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYWNBGXM_n02_dpp_Lib1_Aug_31_2022_fastqc.html [2022-09-15 09:37:05,642] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-15 09:37:05,649] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-15 09:37:05,662] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-09-15 09:37:05,673] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-09-15 09:37:05,675] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2022-09-15 09:37:05,685] multiqc [DEBUG ] No samples found: conpair [2022-09-15 09:37:05,696] multiqc [DEBUG ] No samples found: peddy [2022-09-15 09:37:05,705] multiqc [DEBUG ] No samples found: somalier [2022-09-15 09:37:05,715] multiqc [DEBUG ] No samples found: methylQA [2022-09-15 09:37:05,742] multiqc [DEBUG ] No samples found: mosdepth [2022-09-15 09:37:05,753] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-15 09:37:05,762] multiqc [DEBUG ] No samples found: qualimap [2022-09-15 09:37:05,774] multiqc [DEBUG ] No samples found: preseq [2022-09-15 09:37:05,788] multiqc [DEBUG ] No samples found: quast [2022-09-15 09:37:05,802] multiqc [DEBUG ] No samples found: qorts [2022-09-15 09:37:05,814] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-15 09:37:05,826] multiqc [DEBUG ] No samples found: rockhopper [2022-09-15 09:37:05,838] multiqc [DEBUG ] No samples found: rsem [2022-09-15 09:37:05,875] multiqc [DEBUG ] No samples found: rseqc [2022-09-15 09:37:05,887] multiqc [DEBUG ] No samples found: busco [2022-09-15 09:37:05,899] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-15 09:37:05,910] multiqc [DEBUG ] No samples found: disambiguate [2022-09-15 09:37:05,921] multiqc [DEBUG ] No samples found: supernova [2022-09-15 09:37:05,972] multiqc [DEBUG ] No samples found: deeptools [2022-09-15 09:37:05,989] multiqc [DEBUG ] No samples found: sargasso [2022-09-15 09:37:06,001] multiqc [DEBUG ] No samples found: verifybamid [2022-09-15 09:37:06,021] multiqc [DEBUG ] No samples found: mirtrace [2022-09-15 09:37:06,035] multiqc [DEBUG ] No samples found: happy [2022-09-15 09:37:06,048] multiqc [DEBUG ] No samples found: mirtop [2022-09-15 09:37:06,069] multiqc [DEBUG ] No samples found: homer [2022-09-15 09:37:06,081] multiqc [DEBUG ] No samples found: macs2 [2022-09-15 09:37:06,092] multiqc [DEBUG ] No samples found: theta2 [2022-09-15 09:37:06,109] multiqc [DEBUG ] No samples found: snpeff [2022-09-15 09:37:06,130] multiqc [DEBUG ] No samples found: gatk [2022-09-15 09:37:06,143] multiqc [DEBUG ] No samples found: htseq [2022-09-15 09:37:06,159] multiqc [DEBUG ] No samples found: bcftools [2022-09-15 09:37:06,172] multiqc [DEBUG ] No samples found: featureCounts [2022-09-15 09:37:06,192] multiqc [DEBUG ] No samples found: fgbio [2022-09-15 09:37:06,243] multiqc [DEBUG ] No samples found: dragen [2022-09-15 09:37:06,259] multiqc [DEBUG ] No samples found: dedup [2022-09-15 09:37:06,270] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-15 09:37:06,365] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-15 09:37:06,378] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-15 09:37:06,382] multiqc [DEBUG ] No samples found: picard [2022-09-15 09:37:06,394] multiqc [DEBUG ] No samples found: prokka [2022-09-15 09:37:06,403] multiqc [DEBUG ] No samples found: samblaster [2022-09-15 09:37:06,427] multiqc [DEBUG ] No samples found: samtools [2022-09-15 09:37:06,437] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-15 09:37:06,449] multiqc [DEBUG ] No samples found: bamtools [2022-09-15 09:37:06,458] multiqc [DEBUG ] No samples found: jellyfish [2022-09-15 09:37:06,475] multiqc [DEBUG ] No samples found: vcftools [2022-09-15 09:37:06,486] multiqc [DEBUG ] No samples found: longranger [2022-09-15 09:37:06,497] multiqc [DEBUG ] No samples found: stacks [2022-09-15 09:37:06,509] multiqc [DEBUG ] No samples found: varscan2 [2022-09-15 09:37:06,555] multiqc [DEBUG ] No samples found: bbmap [2022-09-15 09:37:06,570] multiqc [DEBUG ] No samples found: bismark [2022-09-15 09:37:06,584] multiqc [DEBUG ] No samples found: biscuit [2022-09-15 09:37:06,595] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-15 09:37:06,606] multiqc [DEBUG ] No samples found: hicup [2022-09-15 09:37:06,616] multiqc [DEBUG ] No samples found: hicpro [2022-09-15 09:37:06,625] multiqc [DEBUG ] No samples found: salmon [2022-09-15 09:37:06,637] multiqc [DEBUG ] No samples found: kallisto [2022-09-15 09:37:06,649] multiqc [DEBUG ] No samples found: slamdunk [2022-09-15 09:37:06,660] multiqc [DEBUG ] No samples found: star [2022-09-15 09:37:06,673] multiqc [DEBUG ] No samples found: hisat2 [2022-09-15 09:37:06,687] multiqc [DEBUG ] No samples found: tophat [2022-09-15 09:37:06,703] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-15 09:37:06,716] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-15 09:37:06,732] multiqc [DEBUG ] No samples found: snpsplit [2022-09-15 09:37:06,742] multiqc [DEBUG ] No samples found: kat [2022-09-15 09:37:06,754] multiqc [DEBUG ] No samples found: leehom [2022-09-15 09:37:06,772] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-15 09:37:06,783] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-15 09:37:06,797] multiqc [DEBUG ] No samples found: cutadapt [2022-09-15 09:37:06,807] multiqc [DEBUG ] No samples found: flexbar [2022-09-15 09:37:06,817] multiqc [DEBUG ] No samples found: kaiju [2022-09-15 09:37:06,827] multiqc [DEBUG ] No samples found: kraken [2022-09-15 09:37:06,836] multiqc [DEBUG ] No samples found: malt [2022-09-15 09:37:06,846] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-15 09:37:06,854] multiqc [DEBUG ] No samples found: sickle [2022-09-15 09:37:06,864] multiqc [DEBUG ] No samples found: skewer [2022-09-15 09:37:06,869] multiqc [DEBUG ] No samples found: sortmerna [2022-09-15 09:37:06,877] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-15 09:37:06,888] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-15 09:37:06,898] multiqc [DEBUG ] No samples found: afterqc [2022-09-15 09:37:06,910] multiqc [DEBUG ] No samples found: fastp [2022-09-15 09:37:07,300] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2022-09-15 09:37:07,371] multiqc [DEBUG ] No samples found: pycoqc [2022-09-15 09:37:07,383] multiqc [DEBUG ] No samples found: minionqc [2022-09-15 09:37:07,400] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-09-15 09:37:07,416] multiqc [DEBUG ] No samples found: clusterflow [2022-09-15 09:37:07,432] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-15 09:37:07,444] multiqc [DEBUG ] No samples found: interop [2022-09-15 09:37:07,460] multiqc [DEBUG ] No samples found: ivar [2022-09-15 09:37:07,479] multiqc [DEBUG ] No samples found: flash [2022-09-15 09:37:07,495] multiqc [DEBUG ] No samples found: seqyclean [2022-09-15 09:37:07,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-09-15 09:37:07,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-09-15 09:37:07,495] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-09-15 09:37:07,496] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-09-15 09:37:07,507] multiqc [INFO ] Compressing plot data [2022-09-15 09:37:07,620] multiqc [INFO ] Report : multiqc_report.html [2022-09-15 09:37:07,620] multiqc [INFO ] Data : multiqc_data [2022-09-15 09:37:07,620] multiqc [DEBUG ] Moving data file from '/state/partition1/job-24908974/tmp69diujg_/multiqc_data' to '/scratch/gencore/logs/html/HNYWNBGXM/merged/multiqc_data' [2022-09-15 09:37:07,931] multiqc [INFO ] MultiQC complete