[2018-10-12 22:00:54,401] 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 [2018-10-12 22:00:54,401] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-10-12 22:00:54,401] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-10-12 22:00:54,412] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-10-12 22:00:54,412] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-10-12 22:00:54,413] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMGMVBGX7/merged [2018-10-12 22:00:54,413] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-10-12 22:00:54,413] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-10-12 22:00:54,413] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMGMVBGX7/merged [2018-10-12 22:00:54,413] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HMGMVBGX7/merged [2018-10-12 22:00:54,413] multiqc [INFO ] Template : default [2018-10-12 22:00:54,413] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-10-12 22:00:54,413] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HMGMVBGX7/merged' [2018-10-12 22:00:54,413] 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 [2018-10-12 22:00:54,413] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9223461/tmpj7lunq [2018-10-12 22:00:54,711] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:54,746] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2018-10-12 22:00:54,748] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-10-12 22:00:54,765] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:54,773] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:54,780] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-10-12 22:00:54,799] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:55,888] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:55,905] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:56,551] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:56,561] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:56,574] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:56,726] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:56,878] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:57,023] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:57,156] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:57,164] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:58,449] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:58,460] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:58,570] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:58,971] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:59,098] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:59,119] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:59,127] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:59,139] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:59,249] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:00:59,992] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-10-12 22:01:00,004] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:00,013] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:00,124] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:00,236] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:00,347] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:00,460] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:00,584] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:00,592] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:11,019] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2018-10-12 22:01:12,408] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGMVBGX7/merged',) [2018-10-12 22:01:12,442] multiqc [INFO ] Report : multiqc_report.html [2018-10-12 22:01:12,443] multiqc [INFO ] Data : multiqc_data [2018-10-12 22:01:12,443] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9223461/tmpj7lunq/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HMGMVBGX7/merged/multiqc_data' [2018-10-12 22:01:12,445] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9223461/tmpj7lunq/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HMGMVBGX7/merged/multiqc_data' [2018-10-12 22:01:12,447] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9223461/tmpj7lunq/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HMGMVBGX7/merged/multiqc_data' [2018-10-12 22:01:12,548] multiqc [INFO ] MultiQC complete