[2018-10-09 00:04:10,655] 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 [2018-10-09 00:04:10,655] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-10-09 00:04:10,655] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-10-09 00:04:10,666] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-10-09 00:04:10,666] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-10-09 00:04:10,666] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HG5YYBGX7/merged [2018-10-09 00:04:10,666] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-10-09 00:04:10,667] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-10-09 00:04:10,667] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HG5YYBGX7/merged [2018-10-09 00:04:10,667] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HG5YYBGX7/merged [2018-10-09 00:04:10,667] multiqc [INFO ] Template : default [2018-10-09 00:04:10,667] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-10-09 00:04:10,667] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HG5YYBGX7/merged' [2018-10-09 00:04:10,667] 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 [2018-10-09 00:04:10,667] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9086588/tmp1Do8EV [2018-10-09 00:04:11,039] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,057] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2018-10-09 00:04:11,059] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-10-09 00:04:11,067] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,074] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,081] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-10-09 00:04:11,085] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,143] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,151] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,210] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,217] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,224] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,240] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,258] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,275] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,293] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,299] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,420] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,429] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,446] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,488] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,505] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,515] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,521] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,529] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,546] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,615] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-10-09 00:04:11,623] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,631] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,648] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,665] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,683] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,701] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,718] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,725] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:11,735] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HG5YYBGX7_n01_undetermined_fastqc.zip' - Bad zip file [2018-10-09 00:04:11,735] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2018-10-09 00:04:11,736] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HG5YYBGX7_n02_undetermined_fastqc.zip' - Bad zip file [2018-10-09 00:04:11,736] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2018-10-09 00:04:12,529] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2018-10-09 00:04:12,624] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HG5YYBGX7/merged',) [2018-10-09 00:04:12,629] multiqc [INFO ] Report : multiqc_report.html [2018-10-09 00:04:12,630] multiqc [INFO ] Data : multiqc_data [2018-10-09 00:04:12,630] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9086588/tmp1Do8EV/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HG5YYBGX7/merged/multiqc_data' [2018-10-09 00:04:12,633] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9086588/tmp1Do8EV/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HG5YYBGX7/merged/multiqc_data' [2018-10-09 00:04:12,637] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9086588/tmp1Do8EV/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HG5YYBGX7/merged/multiqc_data' [2018-10-09 00:04:12,765] multiqc [INFO ] MultiQC complete