[2018-11-10 22:54:09,244] 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 [2018-11-10 22:54:09,278] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-11-10 22:54:09,279] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-11-10 22:54:09,291] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-11-10 22:54:09,291] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-11-10 22:54:09,292] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HVCHNBGX7/merged [2018-11-10 22:54:09,292] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-11-10 22:54:09,292] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-11-10 22:54:09,292] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HVCHNBGX7/merged [2018-11-10 22:54:09,292] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HVCHNBGX7/merged [2018-11-10 22:54:09,292] multiqc [INFO ] Template : default [2018-11-10 22:54:09,292] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-11-10 22:54:09,292] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HVCHNBGX7/merged' [2018-11-10 22:54:09,292] 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 [2018-11-10 22:54:09,292] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9893972/tmpqR4bX8 [2018-11-10 22:54:09,322] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data [2018-11-10 22:54:09,847] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:09,895] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 26 samples (table) [2018-11-10 22:54:09,897] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-11-10 22:54:09,952] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:09,970] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:09,978] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-11-10 22:54:10,052] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:13,557] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:13,575] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:15,534] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:15,553] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:15,598] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:16,068] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:16,543] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:16,965] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:17,363] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:17,381] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:22,352] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:22,372] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:22,761] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:23,959] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:24,352] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:24,419] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:24,438] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:24,469] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:24,887] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:27,771] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-11-10 22:54:27,802] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:27,821] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:28,228] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:28,621] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:29,017] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:29,408] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:29,795] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:54:29,814] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:55:08,575] multiqc.modules.fastqc.fastqc [INFO ] Found 102 reports [2018-11-10 22:55:31,155] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HVCHNBGX7/merged',) [2018-11-10 22:55:31,304] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2018-11-10 22:55:31,318] multiqc [INFO ] Report : multiqc_report.html [2018-11-10 22:55:31,318] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2018-11-10 22:55:31,402] multiqc [INFO ] Data : multiqc_data [2018-11-10 22:55:31,402] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,422] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,432] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,435] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,437] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,458] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,460] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,477] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,479] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,481] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,495] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9893972/tmpqR4bX8/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HVCHNBGX7/merged/multiqc_data' [2018-11-10 22:55:31,652] multiqc [INFO ] MultiQC complete