[2018-11-16 01:08:21,786] 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 [2018-11-16 01:08:21,806] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-11-16 01:08:21,806] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-11-16 01:08:21,808] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-11-16 01:08:21,808] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-11-16 01:08:21,808] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HFKN2BGX9/merged [2018-11-16 01:08:21,808] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-11-16 01:08:21,808] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-11-16 01:08:21,808] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HFKN2BGX9/merged [2018-11-16 01:08:21,808] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HFKN2BGX9/merged [2018-11-16 01:08:21,808] multiqc [INFO ] Template : default [2018-11-16 01:08:21,808] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-11-16 01:08:21,808] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HFKN2BGX9/merged' [2018-11-16 01:08:21,809] 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 [2018-11-16 01:08:21,809] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10135073/tmpQ_bApz [2018-11-16 01:08:22,227] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:22,282] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2018-11-16 01:08:22,284] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-11-16 01:08:22,305] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:22,315] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:22,324] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-11-16 01:08:22,347] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:23,251] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:23,261] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:23,746] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:23,756] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:23,770] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:23,893] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:24,030] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:24,149] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:24,311] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:24,321] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:25,492] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:25,505] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:25,625] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:25,980] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:26,103] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:26,128] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:26,139] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:26,153] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:26,278] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:26,990] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-11-16 01:08:27,005] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:27,016] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:27,136] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:27,258] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:27,380] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:27,501] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:27,621] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:27,632] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:40,313] multiqc.modules.fastqc.fastqc [INFO ] Found 29 reports [2018-11-16 01:08:43,454] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFKN2BGX9/merged',) [2018-11-16 01:08:43,498] multiqc [INFO ] Report : multiqc_report.html [2018-11-16 01:08:43,500] multiqc [INFO ] Data : multiqc_data [2018-11-16 01:08:43,500] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10135073/tmpQ_bApz/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HFKN2BGX9/merged/multiqc_data' [2018-11-16 01:08:43,503] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10135073/tmpQ_bApz/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HFKN2BGX9/merged/multiqc_data' [2018-11-16 01:08:43,505] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10135073/tmpQ_bApz/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HFKN2BGX9/merged/multiqc_data' [2018-11-16 01:08:43,652] multiqc [INFO ] MultiQC complete