[2019-02-04 11:26:12,717] 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 [2019-02-04 11:26:12,718] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2019-02-04 11:26:12,718] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-02-04 11:26:12,719] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-02-04 11:26:12,719] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-02-04 11:26:12,719] 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-BTF83/1 [2019-02-04 11:26:12,720] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-02-04 11:26:12,720] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-02-04 11:26:12,720] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-BTF83/1 [2019-02-04 11:26:12,720] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/000000000-BTF83/1 [2019-02-04 11:26:12,720] multiqc [INFO ] Template : default [2019-02-04 11:26:12,720] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-02-04 11:26:12,720] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/000000000-BTF83/1' [2019-02-04 11:26:12,720] 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 [2019-02-04 11:26:12,720] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15007438/tmpr6SXsv [2019-02-04 11:26:13,476] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:13,809] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 95 samples (table) [2019-02-04 11:26:13,821] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-02-04 11:26:13,823] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-02-04 11:26:13,920] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:13,951] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:13,962] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-02-04 11:26:14,096] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:32,666] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:32,698] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:46,647] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:46,697] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:46,750] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:49,688] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:53,420] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:57,234] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:59,858] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:26:59,888] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:27:42,858] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:27:42,896] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:27:45,978] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:27:56,852] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:01,059] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:01,176] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:01,203] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:01,253] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:04,412] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:23,177] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-02-04 11:28:23,228] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:23,255] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:26,362] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:29,560] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:32,602] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:35,401] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:38,169] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:38,210] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:28:57,252] multiqc.modules.fastqc.fastqc [INFO ] Found 190 reports [2019-02-04 11:29:38,976] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BTF83/1',) [2019-02-04 11:29:39,263] multiqc [INFO ] Report : multiqc_report.html [2019-02-04 11:29:39,265] multiqc [INFO ] Data : multiqc_data [2019-02-04 11:29:39,265] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,274] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,279] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,284] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,288] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,293] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,301] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,307] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,311] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,316] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,322] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15007438/tmpr6SXsv/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/000000000-BTF83/1/multiqc_data' [2019-02-04 11:29:39,503] multiqc [INFO ] MultiQC complete