[2019-01-28 19:06:34,776] 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 [2019-01-28 19:06:34,777] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-01-28 19:06:34,777] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-01-28 19:06:34,792] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-01-28 19:06:34,792] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-01-28 19:06:34,793] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HGYGMBGX9/merged [2019-01-28 19:06:34,793] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-01-28 19:06:34,793] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-01-28 19:06:34,793] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HGYGMBGX9/merged [2019-01-28 19:06:34,793] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HGYGMBGX9/merged [2019-01-28 19:06:34,793] multiqc [INFO ] Template : default [2019-01-28 19:06:34,793] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-01-28 19:06:34,793] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HGYGMBGX9/merged' [2019-01-28 19:06:34,793] 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 [2019-01-28 19:06:34,794] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14819558/tmpE89bTf [2019-01-28 19:06:34,833] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HGYGMBGX9/merged/multiqc_data [2019-01-28 19:06:34,895] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2019-01-28 19:06:35,288] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:35,339] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 22 samples (table) [2019-01-28 19:06:35,351] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-01-28 19:06:35,353] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-01-28 19:06:35,399] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:35,416] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:35,425] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-01-28 19:06:35,484] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:38,536] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:38,553] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:39,917] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:39,935] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:39,961] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:40,294] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:40,628] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:40,959] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:41,289] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:41,305] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:45,268] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:45,287] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:45,716] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:46,722] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:47,104] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:47,160] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:47,176] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:47,203] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:47,553] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:49,874] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-01-28 19:06:49,901] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:49,918] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:50,251] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:50,585] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:50,920] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:51,259] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:51,615] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:51,632] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:06:54,060] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HGYGMBGX9_n02_S_205_fastqc.zip' - Bad zip file [2019-01-28 19:06:54,060] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-28 19:06:58,802] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HGYGMBGX9_n01_S_205_fastqc.zip' - Bad zip file [2019-01-28 19:06:58,802] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-28 19:07:09,200] multiqc.modules.fastqc.fastqc [INFO ] Found 84 reports [2019-01-28 19:07:22,806] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HGYGMBGX9/merged',) [2019-01-28 19:07:22,929] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-01-28 19:07:22,931] multiqc [INFO ] Report : multiqc_report.html [2019-01-28 19:07:22,932] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-01-28 19:07:22,996] multiqc [INFO ] Data : multiqc_data [2019-01-28 19:07:22,997] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14819558/tmpE89bTf/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HGYGMBGX9/merged/multiqc_data' [2019-01-28 19:07:23,000] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14819558/tmpE89bTf/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HGYGMBGX9/merged/multiqc_data' [2019-01-28 19:07:23,003] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14819558/tmpE89bTf/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HGYGMBGX9/merged/multiqc_data' [2019-01-28 19:07:23,145] multiqc [INFO ] MultiQC complete