[2019-01-31 12:59:31,532] 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 [2019-01-31 12:59:31,532] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-01-31 12:59:31,533] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-01-31 12:59:31,541] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-01-31 12:59:31,541] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-01-31 12:59:31,542] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HH5VYBGX9/merged [2019-01-31 12:59:31,542] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-01-31 12:59:31,542] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-01-31 12:59:31,542] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HH5VYBGX9/merged [2019-01-31 12:59:31,542] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HH5VYBGX9/merged [2019-01-31 12:59:31,542] multiqc [INFO ] Template : default [2019-01-31 12:59:31,542] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-01-31 12:59:31,542] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HH5VYBGX9/merged' [2019-01-31 12:59:31,543] 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 [2019-01-31 12:59:31,543] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14889711/tmpxZpPGd [2019-01-31 12:59:31,931] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:31,954] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2019-01-31 12:59:31,967] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2019-01-31 12:59:31,969] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-01-31 12:59:31,988] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,000] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,011] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-01-31 12:59:32,027] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,057] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,069] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,190] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,201] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,214] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,245] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,276] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,307] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,338] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,349] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,591] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,605] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,636] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,717] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,748] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,770] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,781] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,795] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,826] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,967] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-01-31 12:59:32,982] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:32,994] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,025] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,056] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,086] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,116] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,146] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,157] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,170] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_Control_F_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,170] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,171] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_DI244_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,171] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,172] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_PBS_M2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,172] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,174] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_PBS_M2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,174] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,175] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_DI244_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,175] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,176] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_Control_F_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,176] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,177] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_PBS_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,177] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,179] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_Control_M_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,179] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,180] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_DI244_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,180] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,181] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_PBS_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,181] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,182] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_undetermined_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,182] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,184] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_Control_M_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,184] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,185] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_undetermined_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,185] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,186] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_PBS_M1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,186] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,187] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_DI244_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,187] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,189] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_DI244_M2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,189] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,190] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_PBS_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,190] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,191] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_DI244_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,191] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,192] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_DI244_M1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,192] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,194] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_PBS_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,194] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,195] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_Control_M_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,195] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,196] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_PBS_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,196] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,198] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_PBS_M1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,198] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,199] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_PBS_M1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,199] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,200] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_PBS_M2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,200] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,201] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_DI244_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,201] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,203] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_Control_F_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,203] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,204] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_DI244_M2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,204] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,205] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_Control_M_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,205] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,206] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_PBS_M2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,206] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,208] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_DI244_M1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,208] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,209] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_PBS_M1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,209] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,210] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_DI244_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,210] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,211] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_PBS_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,211] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,213] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_KO_PBS_F1_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,213] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,214] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n02_WT_PBS_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,214] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,215] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_KO_DI244_F2_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,215] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,216] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HH5VYBGX9_n01_WT_Control_F_fastqc.zip' - Bad zip file [2019-01-31 12:59:33,216] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-31 12:59:33,217] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,231] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HH5VYBGX9/merged',) [2019-01-31 12:59:33,232] multiqc [INFO ] Report : multiqc_report.html [2019-01-31 12:59:33,233] multiqc [INFO ] Data : multiqc_data [2019-01-31 12:59:33,233] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14889711/tmpxZpPGd/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HH5VYBGX9/merged/multiqc_data' [2019-01-31 12:59:33,373] multiqc [INFO ] MultiQC complete