[2019-11-21 00:02:08,906] 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 [2019-11-21 00:02:08,941] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-11-21 00:02:08,941] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-11-21 00:02:08,982] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-11-21 00:02:08,982] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-11-21 00:02:08,982] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H7GKMBGXC/merged [2019-11-21 00:02:08,982] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-11-21 00:02:08,983] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-11-21 00:02:08,983] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H7GKMBGXC/merged [2019-11-21 00:02:08,983] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/H7GKMBGXC/merged [2019-11-21 00:02:08,983] multiqc [INFO ] Template : default [2019-11-21 00:02:08,983] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-11-21 00:02:08,983] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/H7GKMBGXC/merged' [2019-11-21 00:02:08,984] 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 [2019-11-21 00:02:08,984] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-5732988/tmpUzgevR [2019-11-21 00:02:09,016] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/H7GKMBGXC/merged/multiqc_data [2019-11-21 00:02:09,057] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2019-11-21 00:02:09,646] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:09,725] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 22 samples (table) [2019-11-21 00:02:09,739] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-11-21 00:02:09,742] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-11-21 00:02:09,794] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:09,810] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:09,818] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-11-21 00:02:09,872] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:13,319] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:13,333] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:14,864] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:14,878] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:14,898] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:15,270] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:15,605] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:15,973] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:16,267] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:16,280] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:20,081] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:20,097] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:20,470] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:21,345] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:21,637] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:21,680] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:21,692] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:21,713] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:22,004] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:24,175] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-11-21 00:02:24,196] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:24,209] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:24,502] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:24,790] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:25,082] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:25,377] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:25,668] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:25,681] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:35,229] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H7GKMBGXC_n01_MT_30785.TR2_2_fastqc.zip' - Bad zip file [2019-11-21 00:02:35,229] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-11-21 00:02:41,911] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H7GKMBGXC_n02_MT_30785.TR2_2_fastqc.zip' - Bad zip file [2019-11-21 00:02:41,911] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-11-21 00:02:45,746] multiqc.modules.fastqc.fastqc [INFO ] Found 84 reports [2019-11-21 00:02:54,277] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7GKMBGXC/merged',) [2019-11-21 00:02:54,368] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-11-21 00:02:54,371] multiqc [INFO ] Report : multiqc_report.html [2019-11-21 00:02:54,371] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-11-21 00:02:54,533] multiqc [INFO ] Data : multiqc_data [2019-11-21 00:02:54,533] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5732988/tmpUzgevR/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/H7GKMBGXC/merged/multiqc_data' [2019-11-21 00:02:54,544] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5732988/tmpUzgevR/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/H7GKMBGXC/merged/multiqc_data' [2019-11-21 00:02:54,547] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5732988/tmpUzgevR/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/H7GKMBGXC/merged/multiqc_data' [2019-11-21 00:02:54,767] multiqc [INFO ] MultiQC complete