[2020-01-31 04:28:25,545] 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 [2020-01-31 04:28:25,582] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-01-31 04:28:25,582] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-01-31 04:28:25,595] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-01-31 04:28:25,595] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-01-31 04:28:25,595] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H5CKCBGXF/merged [2020-01-31 04:28:25,596] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-01-31 04:28:25,596] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-01-31 04:28:25,596] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H5CKCBGXF/merged [2020-01-31 04:28:25,596] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/H5CKCBGXF/merged [2020-01-31 04:28:25,596] multiqc [INFO ] Template : default [2020-01-31 04:28:25,596] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-01-31 04:28:25,596] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/H5CKCBGXF/merged' [2020-01-31 04:28:25,597] 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 [2020-01-31 04:28:25,597] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7168199/tmpTK7DqL [2020-01-31 04:28:26,190] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,206] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2020-01-31 04:28:26,211] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2020-01-31 04:28:26,212] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-01-31 04:28:26,221] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,230] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,238] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-01-31 04:28:26,243] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,261] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,270] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,332] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,339] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,347] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,364] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,383] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,400] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,418] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,424] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,551] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,562] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,579] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,625] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,643] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,654] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,661] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,670] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,688] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,777] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-01-31 04:28:26,785] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,793] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,811] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,829] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,847] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,865] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,883] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,890] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:26,900] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H5CKCBGXF_n01_undetermined_fastqc.zip' - Bad zip file [2020-01-31 04:28:26,900] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-01-31 04:28:27,202] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H5CKCBGXF_n02_undetermined_fastqc.zip' - Bad zip file [2020-01-31 04:28:27,202] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-01-31 04:28:27,314] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2020-01-31 04:28:27,355] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5CKCBGXF/merged',) [2020-01-31 04:28:27,358] multiqc [INFO ] Report : multiqc_report.html [2020-01-31 04:28:27,359] multiqc [INFO ] Data : multiqc_data [2020-01-31 04:28:27,359] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7168199/tmpTK7DqL/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/H5CKCBGXF/merged/multiqc_data' [2020-01-31 04:28:27,362] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7168199/tmpTK7DqL/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/H5CKCBGXF/merged/multiqc_data' [2020-01-31 04:28:27,364] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7168199/tmpTK7DqL/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/H5CKCBGXF/merged/multiqc_data' [2020-01-31 04:28:27,534] multiqc [INFO ] MultiQC complete