[2019-05-21 15:31:17,237] 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 [2019-05-21 15:31:17,237] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-05-21 15:31:17,238] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-05-21 15:31:17,239] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-05-21 15:31:17,239] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-05-21 15:31:17,239] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H5WNTBCX2/2 [2019-05-21 15:31:17,239] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-05-21 15:31:17,239] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-05-21 15:31:17,239] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H5WNTBCX2/2 [2019-05-21 15:31:17,239] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/H5WNTBCX2/2 [2019-05-21 15:31:17,240] multiqc [INFO ] Template : default [2019-05-21 15:31:17,240] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-05-21 15:31:17,240] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/H5WNTBCX2/2' [2019-05-21 15:31:17,240] 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 [2019-05-21 15:31:17,240] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-1350238/tmph5mA0y [2019-05-21 15:31:17,245] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/H5WNTBCX2/2/multiqc_data [2019-05-21 15:31:17,487] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,508] multiqc.modules.custom_content.custom_content [WARNING] Inconsistent number of columns found in H5WNTBCX2_l02_summary_mqc.txt! Skipping.. [2019-05-21 15:31:17,508] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in H5WNTBCX2_l02_summary_mqc.txt [2019-05-21 15:31:17,512] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2019-05-21 15:31:17,512] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2019-05-21 15:31:17,519] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,523] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,529] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-05-21 15:31:17,532] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,602] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,606] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,697] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,701] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,706] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,729] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,754] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,777] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,802] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:17,807] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,011] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,017] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,041] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,106] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,131] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,138] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,143] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,148] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,171] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,289] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-05-21 15:31:18,294] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,299] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,324] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,348] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,372] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,396] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,420] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,425] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,501] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports [2019-05-21 15:31:18,555] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H5WNTBCX2/2',) [2019-05-21 15:31:18,558] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-05-21 15:31:18,558] multiqc [INFO ] Report : multiqc_report.html [2019-05-21 15:31:18,559] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-05-21 15:31:18,563] multiqc [INFO ] Data : multiqc_data [2019-05-21 15:31:18,563] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1350238/tmph5mA0y/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/H5WNTBCX2/2/multiqc_data' [2019-05-21 15:31:18,566] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1350238/tmph5mA0y/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/H5WNTBCX2/2/multiqc_data' [2019-05-21 15:31:18,568] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1350238/tmph5mA0y/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/H5WNTBCX2/2/multiqc_data' [2019-05-21 15:31:18,729] multiqc [INFO ] MultiQC complete