[2018-10-25 08:30:47,642] 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 [2018-10-25 08:30:47,670] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-10-25 08:30:47,670] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-10-25 08:30:47,693] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-10-25 08:30:47,693] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-10-25 08:30:47,693] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMNG2BCX2/1 [2018-10-25 08:30:47,693] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-10-25 08:30:47,693] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-10-25 08:30:47,693] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMNG2BCX2/1 [2018-10-25 08:30:47,694] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HMNG2BCX2/1 [2018-10-25 08:30:47,694] multiqc [INFO ] Template : default [2018-10-25 08:30:47,694] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-10-25 08:30:47,694] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HMNG2BCX2/1' [2018-10-25 08:30:47,694] 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 [2018-10-25 08:30:47,694] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9553627/tmpmOuqp_ [2018-10-25 08:30:48,320] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:48,396] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 61 samples (table) [2018-10-25 08:30:48,399] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-10-25 08:30:48,463] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:48,484] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:48,494] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-10-25 08:30:48,580] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:52,530] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:52,552] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:55,126] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:55,148] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:55,184] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:55,822] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:56,440] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:57,048] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:57,675] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:30:57,697] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:04,317] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:04,342] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:04,878] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:06,441] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:06,978] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:07,056] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:07,079] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:07,115] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:07,672] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:11,433] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-10-25 08:31:11,470] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:11,491] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:12,042] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:12,586] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:13,136] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:13,706] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:14,232] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:14,256] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:22,827] multiqc.modules.fastqc.fastqc [INFO ] Found 122 reports [2018-10-25 08:31:50,431] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMNG2BCX2/1',) [2018-10-25 08:31:50,613] multiqc [INFO ] Report : multiqc_report.html [2018-10-25 08:31:50,614] multiqc [INFO ] Data : multiqc_data [2018-10-25 08:31:50,615] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,618] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,629] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,633] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,643] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,647] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,649] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,652] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,655] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,658] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,661] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9553627/tmpmOuqp_/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HMNG2BCX2/1/multiqc_data' [2018-10-25 08:31:50,849] multiqc [INFO ] MultiQC complete