[2020-01-31 19:48:47,584] 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 19:48:47,584] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2020-01-31 19:48:47,584] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-01-31 19:48:47,586] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-01-31 19:48:47,586] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-01-31 19:48:47,587] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-CHT9C/1 [2020-01-31 19:48:47,587] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-01-31 19:48:47,587] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-01-31 19:48:47,587] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-CHT9C/1 [2020-01-31 19:48:47,587] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/000000000-CHT9C/1 [2020-01-31 19:48:47,587] multiqc [INFO ] Template : default [2020-01-31 19:48:47,588] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-01-31 19:48:47,588] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/000000000-CHT9C/1' [2020-01-31 19:48:47,588] 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 19:48:47,588] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7185247/tmp538Uvn [2020-01-31 19:48:47,662] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/000000000-CHT9C/1/multiqc_data [2020-01-31 19:48:48,152] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:48,218] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 47 samples (table) [2020-01-31 19:48:48,228] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-01-31 19:48:48,230] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-01-31 19:48:48,275] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:48,289] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:48,294] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-01-31 19:48:48,356] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:49,142] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:49,157] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:51,493] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:51,506] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:51,526] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:52,037] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:52,543] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:53,049] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:53,553] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:53,565] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:58,790] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:58,806] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:48:59,312] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:00,901] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:01,483] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:01,528] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:01,541] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:01,560] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:02,069] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:05,167] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-01-31 19:49:05,187] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:05,199] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:05,701] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:06,328] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:06,838] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:07,342] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:07,852] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:07,864] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:09,915] multiqc.modules.fastqc.fastqc [INFO ] Found 94 reports [2020-01-31 19:49:18,738] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-CHT9C/1',) [2020-01-31 19:49:18,844] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2020-01-31 19:49:18,845] multiqc [INFO ] Report : multiqc_report.html [2020-01-31 19:49:18,846] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2020-01-31 19:49:18,852] multiqc [INFO ] Data : multiqc_data [2020-01-31 19:49:18,852] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7185247/tmp538Uvn/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/000000000-CHT9C/1/multiqc_data' [2020-01-31 19:49:18,857] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7185247/tmp538Uvn/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/000000000-CHT9C/1/multiqc_data' [2020-01-31 19:49:18,861] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7185247/tmp538Uvn/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/000000000-CHT9C/1/multiqc_data' [2020-01-31 19:49:19,024] multiqc [INFO ] MultiQC complete