[2019-02-27 05:52:56,578] 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 [2019-02-27 05:52:56,578] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-02-27 05:52:56,578] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-02-27 05:52:56,580] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-02-27 05:52:56,580] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-02-27 05:52:56,580] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HWCLJBGX9/merged [2019-02-27 05:52:56,580] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-02-27 05:52:56,580] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-02-27 05:52:56,580] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HWCLJBGX9/merged [2019-02-27 05:52:56,580] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HWCLJBGX9/merged [2019-02-27 05:52:56,580] multiqc [INFO ] Template : default [2019-02-27 05:52:56,581] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-02-27 05:52:56,581] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HWCLJBGX9/merged' [2019-02-27 05:52:56,581] 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 [2019-02-27 05:52:56,581] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15749421/tmp5ojQdC [2019-02-27 05:52:56,847] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:56,872] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2019-02-27 05:52:56,884] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-02-27 05:52:56,886] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-02-27 05:52:56,899] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:56,905] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:56,909] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-02-27 05:52:56,924] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:57,629] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:57,635] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,130] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,137] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,145] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,269] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,393] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,516] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,632] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:52:58,640] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,059] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,068] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,179] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,543] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,657] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,672] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,678] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,687] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:00,802] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:01,516] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-02-27 05:53:01,526] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:01,532] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:01,646] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:01,760] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:01,874] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:01,989] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:02,103] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:02,109] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:08,294] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2019-02-27 05:53:08,716] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWCLJBGX9/merged',) [2019-02-27 05:53:08,743] multiqc [INFO ] Report : multiqc_report.html [2019-02-27 05:53:08,744] multiqc [INFO ] Data : multiqc_data [2019-02-27 05:53:08,744] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15749421/tmp5ojQdC/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HWCLJBGX9/merged/multiqc_data' [2019-02-27 05:53:08,747] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15749421/tmp5ojQdC/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HWCLJBGX9/merged/multiqc_data' [2019-02-27 05:53:08,749] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15749421/tmp5ojQdC/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HWCLJBGX9/merged/multiqc_data' [2019-02-27 05:53:08,870] multiqc [INFO ] MultiQC complete