[2021-12-22 06:33:58,801] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-22 06:33:58,802] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-22 06:33:58,802] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-22 06:33:58,802] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-22 06:33:58,803] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-22 06:33:58,803] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNGLVDRXY/merged [2021-12-22 06:34:00,247] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-22 06:34:00,247] multiqc [INFO ] This is MultiQC v1.9 [2021-12-22 06:34:00,248] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNGLVDRXY/merged [2021-12-22 06:34:00,248] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNGLVDRXY/merged [2021-12-22 06:34:00,248] multiqc [INFO ] Template : default [2021-12-22 06:34:00,248] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-22 06:34:00,248] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNGLVDRXY/merged [2021-12-22 06:34:00,248] 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 [2021-12-22 06:34:00,248] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13249431/tmpttt9_k9g [2021-12-22 06:34:00,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:00,348] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:00,348] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:00,348] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:00,348] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:00,348] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:00,349] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:00,368] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-22 06:34:01,197] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_UnselectedC_fastqc.html [2021-12-22 06:34:01,199] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_UnselectedC_fastqc.html [2021-12-22 06:34:01,240] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_UnselectedA_fastqc.html [2021-12-22 06:34:01,242] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_UnselectedA_fastqc.html [2021-12-22 06:34:01,283] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_SelectedC_fastqc.html [2021-12-22 06:34:01,284] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_SelectedC_fastqc.html [2021-12-22 06:34:01,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_SelectedA_fastqc.html [2021-12-22 06:34:01,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGLVDRXY_n01_CuSO4_CSSI_SelectedA_fastqc.html [2021-12-22 06:34:01,401] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGLVDRXY_n01_undetermined_fastqc.html [2021-12-22 06:34:01,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGLVDRXY_n01_undetermined_fastqc.html [2021-12-22 06:34:01,839] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-22 06:34:01,841] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-22 06:34:01,848] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-22 06:34:01,857] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-22 06:34:01,860] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2021-12-22 06:34:01,864] multiqc [DEBUG ] No samples found: conpair [2021-12-22 06:34:01,869] multiqc [DEBUG ] No samples found: peddy [2021-12-22 06:34:01,874] multiqc [DEBUG ] No samples found: somalier [2021-12-22 06:34:01,878] multiqc [DEBUG ] No samples found: methylQA [2021-12-22 06:34:01,884] multiqc [DEBUG ] No samples found: mosdepth [2021-12-22 06:34:01,888] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-22 06:34:01,891] multiqc [DEBUG ] No samples found: qualimap [2021-12-22 06:34:01,895] multiqc [DEBUG ] No samples found: preseq [2021-12-22 06:34:01,899] multiqc [DEBUG ] No samples found: quast [2021-12-22 06:34:01,903] multiqc [DEBUG ] No samples found: qorts [2021-12-22 06:34:01,907] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-22 06:34:01,911] multiqc [DEBUG ] No samples found: rockhopper [2021-12-22 06:34:01,915] multiqc [DEBUG ] No samples found: rsem [2021-12-22 06:34:01,923] multiqc [DEBUG ] No samples found: rseqc [2021-12-22 06:34:01,927] multiqc [DEBUG ] No samples found: busco [2021-12-22 06:34:01,931] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-22 06:34:01,935] multiqc [DEBUG ] No samples found: disambiguate [2021-12-22 06:34:01,939] multiqc [DEBUG ] No samples found: supernova [2021-12-22 06:34:01,949] multiqc [DEBUG ] No samples found: deeptools [2021-12-22 06:34:01,953] multiqc [DEBUG ] No samples found: sargasso [2021-12-22 06:34:01,957] multiqc [DEBUG ] No samples found: verifybamid [2021-12-22 06:34:01,961] multiqc [DEBUG ] No samples found: mirtrace [2021-12-22 06:34:01,965] multiqc [DEBUG ] No samples found: happy [2021-12-22 06:34:01,969] multiqc [DEBUG ] No samples found: mirtop [2021-12-22 06:34:01,974] multiqc [DEBUG ] No samples found: homer [2021-12-22 06:34:01,978] multiqc [DEBUG ] No samples found: macs2 [2021-12-22 06:34:01,981] multiqc [DEBUG ] No samples found: theta2 [2021-12-22 06:34:01,985] multiqc [DEBUG ] No samples found: snpeff [2021-12-22 06:34:01,991] multiqc [DEBUG ] No samples found: gatk [2021-12-22 06:34:01,995] multiqc [DEBUG ] No samples found: htseq [2021-12-22 06:34:01,999] multiqc [DEBUG ] No samples found: bcftools [2021-12-22 06:34:02,003] multiqc [DEBUG ] No samples found: featureCounts [2021-12-22 06:34:02,008] multiqc [DEBUG ] No samples found: fgbio [2021-12-22 06:34:02,018] multiqc [DEBUG ] No samples found: dragen [2021-12-22 06:34:02,022] multiqc [DEBUG ] No samples found: dedup [2021-12-22 06:34:02,026] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-22 06:34:02,043] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-22 06:34:02,047] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-22 06:34:02,049] multiqc [DEBUG ] No samples found: picard [2021-12-22 06:34:02,053] multiqc [DEBUG ] No samples found: prokka [2021-12-22 06:34:02,057] multiqc [DEBUG ] No samples found: samblaster [2021-12-22 06:34:02,064] multiqc [DEBUG ] No samples found: samtools [2021-12-22 06:34:02,068] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-22 06:34:02,072] multiqc [DEBUG ] No samples found: bamtools [2021-12-22 06:34:02,076] multiqc [DEBUG ] No samples found: jellyfish [2021-12-22 06:34:02,081] multiqc [DEBUG ] No samples found: vcftools [2021-12-22 06:34:02,085] multiqc [DEBUG ] No samples found: longranger [2021-12-22 06:34:02,089] multiqc [DEBUG ] No samples found: stacks [2021-12-22 06:34:02,093] multiqc [DEBUG ] No samples found: varscan2 [2021-12-22 06:34:02,104] multiqc [DEBUG ] No samples found: bbmap [2021-12-22 06:34:02,108] multiqc [DEBUG ] No samples found: bismark [2021-12-22 06:34:02,112] multiqc [DEBUG ] No samples found: biscuit [2021-12-22 06:34:02,116] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-22 06:34:02,120] multiqc [DEBUG ] No samples found: hicup [2021-12-22 06:34:02,124] multiqc [DEBUG ] No samples found: hicpro [2021-12-22 06:34:02,128] multiqc [DEBUG ] No samples found: salmon [2021-12-22 06:34:02,131] multiqc [DEBUG ] No samples found: kallisto [2021-12-22 06:34:02,136] multiqc [DEBUG ] No samples found: slamdunk [2021-12-22 06:34:02,140] multiqc [DEBUG ] No samples found: star [2021-12-22 06:34:02,143] multiqc [DEBUG ] No samples found: hisat2 [2021-12-22 06:34:02,147] multiqc [DEBUG ] No samples found: tophat [2021-12-22 06:34:02,151] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-22 06:34:02,155] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-22 06:34:02,159] multiqc [DEBUG ] No samples found: snpsplit [2021-12-22 06:34:02,162] multiqc [DEBUG ] No samples found: kat [2021-12-22 06:34:02,166] multiqc [DEBUG ] No samples found: leehom [2021-12-22 06:34:02,170] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-22 06:34:02,174] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-22 06:34:02,178] multiqc [DEBUG ] No samples found: cutadapt [2021-12-22 06:34:02,181] multiqc [DEBUG ] No samples found: flexbar [2021-12-22 06:34:02,185] multiqc [DEBUG ] No samples found: kaiju [2021-12-22 06:34:02,189] multiqc [DEBUG ] No samples found: kraken [2021-12-22 06:34:02,193] multiqc [DEBUG ] No samples found: malt [2021-12-22 06:34:02,197] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-22 06:34:02,201] multiqc [DEBUG ] No samples found: sickle [2021-12-22 06:34:02,205] multiqc [DEBUG ] No samples found: skewer [2021-12-22 06:34:02,208] multiqc [DEBUG ] No samples found: sortmerna [2021-12-22 06:34:02,212] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-22 06:34:02,216] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-22 06:34:02,219] multiqc [DEBUG ] No samples found: afterqc [2021-12-22 06:34:02,223] multiqc [DEBUG ] No samples found: fastp [2021-12-22 06:34:02,488] multiqc.modules.fastqc.fastqc [INFO ] Found 5 reports [2021-12-22 06:34:02,578] multiqc [DEBUG ] No samples found: pycoqc [2021-12-22 06:34:02,581] multiqc [DEBUG ] No samples found: minionqc [2021-12-22 06:34:02,585] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-22 06:34:02,589] multiqc [DEBUG ] No samples found: clusterflow [2021-12-22 06:34:02,593] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-22 06:34:02,597] multiqc [DEBUG ] No samples found: interop [2021-12-22 06:34:02,601] multiqc [DEBUG ] No samples found: ivar [2021-12-22 06:34:02,605] multiqc [DEBUG ] No samples found: flash [2021-12-22 06:34:02,609] multiqc [DEBUG ] No samples found: seqyclean [2021-12-22 06:34:02,609] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-22 06:34:02,609] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-22 06:34:02,609] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-22 06:34:02,609] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-22 06:34:02,616] multiqc [INFO ] Compressing plot data [2021-12-22 06:34:02,731] multiqc [INFO ] Report : multiqc_report.html [2021-12-22 06:34:02,731] multiqc [INFO ] Data : multiqc_data [2021-12-22 06:34:02,731] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13249431/tmpttt9_k9g/multiqc_data' to '/scratch/gencore/logs/html/HNGLVDRXY/merged/multiqc_data' [2021-12-22 06:34:02,846] multiqc [INFO ] MultiQC complete