[2020-02-13 23:26:21,840] 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 [2020-02-13 23:26:21,841] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-02-13 23:26:21,841] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-02-13 23:26:21,861] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-02-13 23:26:21,861] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-02-13 23:26:21,861] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HCFFFBGXF/merged [2020-02-13 23:26:21,861] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-02-13 23:26:21,861] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-02-13 23:26:21,862] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HCFFFBGXF/merged [2020-02-13 23:26:21,862] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HCFFFBGXF/merged [2020-02-13 23:26:21,862] multiqc [INFO ] Template : default [2020-02-13 23:26:21,862] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-02-13 23:26:21,862] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HCFFFBGXF/merged' [2020-02-13 23:26:21,862] 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 [2020-02-13 23:26:21,862] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7427401/tmp4Ys_8i [2020-02-13 23:26:21,903] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HCFFFBGXF/merged/multiqc_data [2020-02-13 23:26:22,631] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:22,669] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2020-02-13 23:26:22,685] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-02-13 23:26:22,687] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-02-13 23:26:22,702] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:22,710] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:22,717] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-02-13 23:26:22,727] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,204] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,213] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,474] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,482] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,491] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,557] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,634] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,710] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,887] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:23,896] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,566] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,577] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,640] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,822] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,879] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,891] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,897] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,904] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:24,961] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,376] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-02-13 23:26:25,386] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,394] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,477] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,544] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,718] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,792] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,853] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:25,861] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:28,714] multiqc.modules.fastqc.fastqc [INFO ] Found 11 reports [2020-02-13 23:26:29,402] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HCFFFBGXF/merged',) [2020-02-13 23:26:29,415] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2020-02-13 23:26:29,470] multiqc [INFO ] Report : multiqc_report.html [2020-02-13 23:26:29,471] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2020-02-13 23:26:29,569] multiqc [INFO ] Data : multiqc_data [2020-02-13 23:26:29,569] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7427401/tmp4Ys_8i/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HCFFFBGXF/merged/multiqc_data' [2020-02-13 23:26:29,587] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7427401/tmp4Ys_8i/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HCFFFBGXF/merged/multiqc_data' [2020-02-13 23:26:29,590] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7427401/tmp4Ys_8i/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HCFFFBGXF/merged/multiqc_data' [2020-02-13 23:26:29,754] multiqc [INFO ] MultiQC complete