[2019-03-09 19:41:33,209] 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 [2019-03-09 19:41:33,210] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-03-09 19:41:33,210] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-03-09 19:41:33,231] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-03-09 19:41:33,231] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-03-09 19:41:33,231] 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-BMH6J/1 [2019-03-09 19:41:33,231] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-03-09 19:41:33,231] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-03-09 19:41:33,231] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-BMH6J/1 [2019-03-09 19:41:33,231] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/000000000-BMH6J/1 [2019-03-09 19:41:33,232] multiqc [INFO ] Template : default [2019-03-09 19:41:33,232] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-03-09 19:41:33,232] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/000000000-BMH6J/1' [2019-03-09 19:41:33,232] 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 [2019-03-09 19:41:33,232] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15986307/tmpE0j5Sq [2019-03-09 19:41:33,442] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2019-03-09 19:41:33,983] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:34,214] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 221 samples (table) [2019-03-09 19:41:34,225] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-03-09 19:41:34,227] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-03-09 19:41:34,435] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:34,493] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:34,503] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-03-09 19:41:34,805] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:50,057] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:50,116] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:59,740] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:59,798] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:41:59,906] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:02,303] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:04,863] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:07,060] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:09,241] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:09,298] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:31,812] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:31,873] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:34,392] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:41,058] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:43,290] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:43,551] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:43,608] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:43,717] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:45,947] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:59,456] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-03-09 19:42:59,564] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:42:59,622] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:43:01,854] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:43:04,067] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:43:06,287] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:43:08,497] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:43:10,751] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:43:10,809] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:43:49,187] multiqc.modules.fastqc.fastqc [INFO ] Found 442 reports [2019-03-09 19:45:03,230] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BMH6J/1',) [2019-03-09 19:45:03,866] multiqc [INFO ] Report : multiqc_report.html [2019-03-09 19:45:03,867] multiqc [INFO ] Data : multiqc_data [2019-03-09 19:45:03,867] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,869] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,871] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,874] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,895] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,898] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,904] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,910] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,916] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,921] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:03,922] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15986307/tmpE0j5Sq/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/000000000-BMH6J/1/multiqc_data' [2019-03-09 19:45:04,153] multiqc [INFO ] MultiQC complete