[2018-12-18 09:40:25,913] 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 [2018-12-18 09:40:25,956] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-12-18 09:40:25,957] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-12-18 09:40:25,958] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-12-18 09:40:25,958] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-12-18 09:40:25,958] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H7HVFAFXY/merged [2018-12-18 09:40:25,958] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-12-18 09:40:25,959] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-12-18 09:40:25,959] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H7HVFAFXY/merged [2018-12-18 09:40:25,959] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/H7HVFAFXY/merged [2018-12-18 09:40:25,959] multiqc [INFO ] Template : default [2018-12-18 09:40:25,959] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-12-18 09:40:25,959] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/H7HVFAFXY/merged' [2018-12-18 09:40:25,959] 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 [2018-12-18 09:40:25,959] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11018709/tmpJb6GMH [2018-12-18 09:40:26,595] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:26,672] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 63 samples (table) [2018-12-18 09:40:26,673] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-12-18 09:40:26,737] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:26,756] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:26,761] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-12-18 09:40:26,849] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:31,642] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:31,662] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:35,380] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:35,399] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:35,433] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:36,427] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:37,304] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:38,257] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:39,144] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:39,163] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:48,186] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:48,209] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:49,064] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:51,843] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:52,739] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:52,818] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:52,837] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:52,871] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:53,721] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:59,014] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-12-18 09:40:59,049] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:59,068] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:40:59,981] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:41:00,878] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:41:01,817] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:41:02,671] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:41:03,583] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:41:03,602] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:41:21,437] multiqc.modules.fastqc.fastqc [INFO ] Found 126 reports [2018-12-18 09:41:41,094] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7HVFAFXY/merged',) [2018-12-18 09:41:41,279] multiqc [INFO ] Report : multiqc_report.html [2018-12-18 09:41:41,282] multiqc [INFO ] Data : multiqc_data [2018-12-18 09:41:41,282] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,297] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,308] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,321] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,331] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,341] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,353] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,404] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,418] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,437] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,453] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11018709/tmpJb6GMH/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/H7HVFAFXY/merged/multiqc_data' [2018-12-18 09:41:41,613] multiqc [INFO ] MultiQC complete