[2019-05-13 04:12:10,336] 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 [2019-05-13 04:12:10,337] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-05-13 04:12:10,337] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-05-13 04:12:10,339] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-05-13 04:12:10,339] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-05-13 04:12:10,339] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/CCY3TACXX/5 [2019-05-13 04:12:10,340] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-05-13 04:12:10,340] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-05-13 04:12:10,340] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/CCY3TACXX/5 [2019-05-13 04:12:10,340] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/CCY3TACXX/5 [2019-05-13 04:12:10,340] multiqc [INFO ] Template : default [2019-05-13 04:12:10,340] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-05-13 04:12:10,340] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/CCY3TACXX/5' [2019-05-13 04:12:10,341] 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 [2019-05-13 04:12:10,341] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-1161548/tmpgnMk2C [2019-05-13 04:12:10,966] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:11,017] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-05-13 04:12:11,037] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-05-13 04:12:11,048] multiqc.modules.custom_content.custom_content [INFO ] demux_report-5: Found 10 samples (table) [2019-05-13 04:12:11,070] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:11,080] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:11,088] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-05-13 04:12:11,111] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:11,984] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:12,000] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:12,716] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:12,729] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:12,746] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:12,911] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:13,075] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:13,233] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:13,390] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:13,401] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,002] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,018] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,164] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,591] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,729] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,760] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,772] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,787] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:15,913] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,138] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-05-13 04:12:17,154] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,165] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,301] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,440] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,565] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,689] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,821] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:17,832] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:20,002] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2019-05-13 04:12:20,824] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/CCY3TACXX/5',) [2019-05-13 04:12:20,854] multiqc [INFO ] Report : multiqc_report.html [2019-05-13 04:12:20,855] multiqc [INFO ] Data : multiqc_data [2019-05-13 04:12:20,855] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1161548/tmpgnMk2C/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/CCY3TACXX/5/multiqc_data' [2019-05-13 04:12:20,860] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1161548/tmpgnMk2C/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/CCY3TACXX/5/multiqc_data' [2019-05-13 04:12:20,871] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1161548/tmpgnMk2C/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/CCY3TACXX/5/multiqc_data' [2019-05-13 04:12:21,110] multiqc [INFO ] MultiQC complete