[2018-12-06 14:15:21,185] 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 [2018-12-06 14:15:21,185] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-12-06 14:15:21,185] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-12-06 14:15:21,186] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-12-06 14:15:21,186] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-12-06 14:15:21,187] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HNJM2BCX2/2 [2018-12-06 14:15:21,187] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-12-06 14:15:21,187] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-12-06 14:15:21,187] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HNJM2BCX2/2 [2018-12-06 14:15:21,187] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HNJM2BCX2/2 [2018-12-06 14:15:21,187] multiqc [INFO ] Template : default [2018-12-06 14:15:21,187] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-12-06 14:15:21,187] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HNJM2BCX2/2' [2018-12-06 14:15:21,187] 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 [2018-12-06 14:15:21,187] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10698618/tmpzTvcjR [2018-12-06 14:15:21,520] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:21,583] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 75 samples (table) [2018-12-06 14:15:21,585] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-12-06 14:15:21,642] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:21,658] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:21,662] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-12-06 14:15:21,741] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:25,707] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:25,724] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:28,118] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:28,138] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:28,174] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:28,787] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:29,404] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:30,034] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:30,545] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:30,565] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:36,972] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:36,994] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:37,519] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:39,373] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:39,885] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:39,971] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:39,991] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:40,026] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:40,537] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:44,242] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-12-06 14:15:44,280] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:44,300] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:44,809] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:45,355] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:45,861] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:46,375] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:46,916] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:46,936] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:15:54,077] multiqc.modules.fastqc.fastqc [INFO ] Found 150 reports [2018-12-06 14:16:14,048] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HNJM2BCX2/2',) [2018-12-06 14:16:14,214] multiqc [INFO ] Report : multiqc_report.html [2018-12-06 14:16:14,217] multiqc [INFO ] Data : multiqc_data [2018-12-06 14:16:14,217] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,220] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,222] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,225] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,229] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,231] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,233] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,237] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,239] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,242] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,245] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10698618/tmpzTvcjR/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HNJM2BCX2/2/multiqc_data' [2018-12-06 14:16:14,372] multiqc [INFO ] MultiQC complete