[2020-02-11 08:20:15,772] 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 [2020-02-11 08:20:15,773] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-02-11 08:20:15,774] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-02-11 08:20:15,812] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-02-11 08:20:15,812] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-02-11 08:20:15,812] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H725TBGXF/merged [2020-02-11 08:20:15,812] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-02-11 08:20:15,812] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-02-11 08:20:15,812] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H725TBGXF/merged [2020-02-11 08:20:15,812] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/H725TBGXF/merged [2020-02-11 08:20:15,812] multiqc [INFO ] Template : default [2020-02-11 08:20:15,812] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-02-11 08:20:15,813] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/H725TBGXF/merged' [2020-02-11 08:20:15,813] 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 [2020-02-11 08:20:15,813] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7351320/tmpFDI_QX [2020-02-11 08:20:16,210] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,260] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2020-02-11 08:20:16,262] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2020-02-11 08:20:16,264] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-02-11 08:20:16,273] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,280] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,287] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-02-11 08:20:16,292] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,353] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,361] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,607] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,614] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,621] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,646] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,720] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,752] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,779] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,785] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,936] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,945] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:16,962] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,004] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,022] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,035] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,042] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,051] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,124] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,935] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-02-11 08:20:17,943] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,951] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,971] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:17,989] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:18,106] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:18,142] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:18,170] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:18,177] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:18,609] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H725TBGXF_n01_undetermined_fastqc.zip' - Bad zip file [2020-02-11 08:20:18,609] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-02-11 08:20:18,610] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H725TBGXF_n02_undetermined_fastqc.zip' - Bad zip file [2020-02-11 08:20:18,610] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-02-11 08:20:18,799] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2020-02-11 08:20:18,865] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H725TBGXF/merged',) [2020-02-11 08:20:18,875] multiqc [INFO ] Report : multiqc_report.html [2020-02-11 08:20:18,890] multiqc [INFO ] Data : multiqc_data [2020-02-11 08:20:18,890] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7351320/tmpFDI_QX/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/H725TBGXF/merged/multiqc_data' [2020-02-11 08:20:18,895] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7351320/tmpFDI_QX/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/H725TBGXF/merged/multiqc_data' [2020-02-11 08:20:18,899] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7351320/tmpFDI_QX/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/H725TBGXF/merged/multiqc_data' [2020-02-11 08:20:19,073] multiqc [INFO ] MultiQC complete