[2020-01-31 19:47:03,409] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/20170330/intel/lib/python2.7/site-packages/multiqc-1.0.dev0-py2.7.egg/multiqc_config.yaml [2020-01-31 19:47:03,409] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2020-01-31 19:47:03,409] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-01-31 19:47:03,410] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-01-31 19:47:03,410] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-01-31 19:47:03,410] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-D6VGL/1 [2020-01-31 19:47:03,410] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-01-31 19:47:03,410] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-01-31 19:47:03,410] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-D6VGL/1 [2020-01-31 19:47:03,410] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/000000000-D6VGL/1 [2020-01-31 19:47:03,410] multiqc [INFO ] Template : default [2020-01-31 19:47:03,410] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-01-31 19:47:03,410] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/000000000-D6VGL/1' [2020-01-31 19:47:03,410] multiqc [DEBUG ] Analysing modules: rna_seqc, custom_content, peddy, methylQA, qualimap, preseq, quast, rseqc, busco, goleft_indexcov, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, bismark, hicup, salmon, kallisto, slamdunk, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc, clusterflow [2020-01-31 19:47:03,411] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7185246/tmpQ9LRSx [2020-01-31 19:47:03,417] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/000000000-D6VGL/1/multiqc_data [2020-01-31 19:47:03,627] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,641] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2020-01-31 19:47:03,643] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 2 samples (table) [2020-01-31 19:47:03,644] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-01-31 19:47:03,651] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,657] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,663] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-01-31 19:47:03,667] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,697] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,703] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,799] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,805] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,810] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,836] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,862] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,887] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,912] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:03,917] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,137] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,146] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,171] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,240] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,265] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,273] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,279] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,285] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,309] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,434] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-01-31 19:47:04,440] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,446] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,471] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,495] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,520] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,545] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,570] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,576] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,584] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-D6VGL_l01_n02_undetermined_fastqc.zip' - Bad zip file [2020-01-31 19:47:04,584] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-01-31 19:47:04,585] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-D6VGL_l01_n01_undetermined_fastqc.zip' - Bad zip file [2020-01-31 19:47:04,585] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-01-31 19:47:04,601] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2020-01-31 19:47:04,800] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-D6VGL/1',) [2020-01-31 19:47:04,803] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2020-01-31 19:47:04,804] multiqc [INFO ] Report : multiqc_report.html [2020-01-31 19:47:04,804] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2020-01-31 19:47:04,809] multiqc [INFO ] Data : multiqc_data [2020-01-31 19:47:04,809] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7185246/tmpQ9LRSx/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/000000000-D6VGL/1/multiqc_data' [2020-01-31 19:47:04,812] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7185246/tmpQ9LRSx/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/000000000-D6VGL/1/multiqc_data' [2020-01-31 19:47:04,816] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7185246/tmpQ9LRSx/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/000000000-D6VGL/1/multiqc_data' [2020-01-31 19:47:04,913] multiqc [INFO ] MultiQC complete