[2018-05-26 07:28:33,982] 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 [2018-05-26 07:28:33,983] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-05-26 07:28:33,983] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-05-26 07:28:33,985] multiqc [DEBUG ] Loading config settings from: /beegfs/mk5636/scripts/mqc_config.yaml [2018-05-26 07:28:33,985] multiqc [DEBUG ] New config 'custom_content': {'order': ['run_stats', 'demux_report', 'demux_report-1', 'demux_report-2', 'demux_report-3', 'demux_report-4', 'demux_report-5', 'demux_report-6', 'demux_report-7', 'demux_report-8']} [2018-05-26 07:28:33,986] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /beegfs/mk5636/scripts/mqc_config.yaml /beegfs/mk5636/logs/html/HJ5Y2BCX2/1 [2018-05-26 07:28:33,986] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-05-26 07:28:33,986] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-05-26 07:28:33,986] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /beegfs/mk5636/scripts/mqc_config.yaml /beegfs/mk5636/logs/html/HJ5Y2BCX2/1 [2018-05-26 07:28:33,986] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HJ5Y2BCX2/1 [2018-05-26 07:28:33,986] multiqc [INFO ] Template : default [2018-05-26 07:28:33,986] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-05-26 07:28:33,986] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HJ5Y2BCX2/1' [2018-05-26 07:28:33,986] 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 [2018-05-26 07:28:33,986] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-6405894/tmpuvknMu [2018-05-26 07:28:34,262] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,276] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 2 samples (table) [2018-05-26 07:28:34,277] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-05-26 07:28:34,284] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,288] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,292] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-05-26 07:28:34,296] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,310] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,315] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,361] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,366] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,370] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,384] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,397] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,410] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,422] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,426] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,521] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,526] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,539] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,572] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,585] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,593] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,597] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,602] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,615] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,671] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-05-26 07:28:34,676] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,680] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,693] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,706] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,719] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,732] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,744] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,748] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,888] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HJ5Y2BCX2_l01_n02_undetermined_fastqc.zip' - Bad zip file [2018-05-26 07:28:34,888] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2018-05-26 07:28:34,889] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HJ5Y2BCX2_l01_n01_undetermined_fastqc.zip' - Bad zip file [2018-05-26 07:28:34,889] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2018-05-26 07:28:34,889] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2018-05-26 07:28:34,981] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/1',) [2018-05-26 07:28:34,985] multiqc [INFO ] Report : multiqc_report.html [2018-05-26 07:28:34,986] multiqc [INFO ] Data : multiqc_data [2018-05-26 07:28:34,986] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6405894/tmpuvknMu/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HJ5Y2BCX2/1/multiqc_data' [2018-05-26 07:28:34,989] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6405894/tmpuvknMu/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HJ5Y2BCX2/1/multiqc_data' [2018-05-26 07:28:34,991] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6405894/tmpuvknMu/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HJ5Y2BCX2/1/multiqc_data' [2018-05-26 07:28:35,111] multiqc [INFO ] MultiQC complete