[2018-10-29 16:40:59,099] 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 [2018-10-29 16:40:59,099] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-10-29 16:40:59,099] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-10-29 16:40:59,137] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-10-29 16:40:59,137] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-10-29 16:40:59,137] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMLHWBGX7/merged [2018-10-29 16:40:59,137] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-10-29 16:40:59,138] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-10-29 16:40:59,138] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMLHWBGX7/merged [2018-10-29 16:40:59,138] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HMLHWBGX7/merged [2018-10-29 16:40:59,138] multiqc [INFO ] Template : default [2018-10-29 16:40:59,138] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-10-29 16:40:59,138] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HMLHWBGX7/merged' [2018-10-29 16:40:59,138] 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 [2018-10-29 16:40:59,138] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9635632/tmpW0uX85 [2018-10-29 16:40:59,247] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data [2018-10-29 16:40:59,982] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:00,095] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 81 samples (table) [2018-10-29 16:41:00,097] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-10-29 16:41:00,249] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:00,292] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:00,300] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-10-29 16:41:00,518] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:07,700] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:07,744] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:11,808] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:11,852] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:11,931] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:12,911] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:13,888] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:14,902] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:15,854] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:15,897] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:25,622] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:25,668] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:26,630] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:29,601] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:30,561] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:30,753] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:30,796] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:30,874] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:31,824] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:37,623] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-10-29 16:41:37,705] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:37,748] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:38,706] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:39,730] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:40,703] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:41,679] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:42,626] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:41:42,670] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:43:29,269] multiqc.modules.fastqc.fastqc [INFO ] Found 322 reports [2018-10-29 16:44:33,962] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMLHWBGX7/merged',) [2018-10-29 16:44:34,409] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2018-10-29 16:44:34,414] multiqc [INFO ] Report : multiqc_report.html [2018-10-29 16:44:34,414] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2018-10-29 16:44:34,631] multiqc [INFO ] Data : multiqc_data [2018-10-29 16:44:34,631] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,639] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,642] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,645] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,648] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,654] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,658] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,661] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,669] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,672] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,675] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9635632/tmpW0uX85/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HMLHWBGX7/merged/multiqc_data' [2018-10-29 16:44:34,833] multiqc [INFO ] MultiQC complete