[2019-08-27 18:28:14,685] 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 [2019-08-27 18:28:14,685] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-08-27 18:28:14,685] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-08-27 18:28:14,687] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-08-27 18:28:14,687] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-08-27 18:28:14,687] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HNKYVAFXY/merged [2019-08-27 18:28:14,687] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-08-27 18:28:14,687] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-08-27 18:28:14,687] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HNKYVAFXY/merged [2019-08-27 18:28:14,687] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HNKYVAFXY/merged [2019-08-27 18:28:14,687] multiqc [INFO ] Template : default [2019-08-27 18:28:14,687] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-08-27 18:28:14,688] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HNKYVAFXY/merged' [2019-08-27 18:28:14,688] 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 [2019-08-27 18:28:14,688] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-2714143/tmpwlX7Az [2019-08-27 18:28:14,789] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2019-08-27 18:28:15,164] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:15,269] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 91 samples (table) [2019-08-27 18:28:15,280] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-08-27 18:28:15,282] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-08-27 18:28:15,374] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:15,402] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:15,410] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-08-27 18:28:15,537] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:21,248] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:21,277] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:24,517] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:24,546] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:24,594] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:25,328] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:26,033] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:26,857] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:27,470] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:27,497] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:35,155] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:35,186] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:35,914] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:37,865] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:38,478] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:38,592] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:38,619] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:38,668] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:39,401] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:43,644] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-08-27 18:28:43,694] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:43,722] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:44,419] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:45,034] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:45,647] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:46,268] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:46,875] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:28:46,904] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:29:11,344] multiqc.modules.fastqc.fastqc [INFO ] Found 182 reports [2019-08-27 18:29:49,003] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNKYVAFXY/merged',) [2019-08-27 18:29:49,266] multiqc [INFO ] Report : multiqc_report.html [2019-08-27 18:29:49,268] multiqc [INFO ] Data : multiqc_data [2019-08-27 18:29:49,268] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,301] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,313] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,341] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,360] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,391] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,397] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,415] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,418] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,420] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,430] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2714143/tmpwlX7Az/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HNKYVAFXY/merged/multiqc_data' [2019-08-27 18:29:49,596] multiqc [INFO ] MultiQC complete