[2018-05-26 07:46:38,908] 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 [2018-05-26 07:46:38,909] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-05-26 07:46:38,909] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-05-26 07:46:38,911] multiqc [DEBUG ] Loading config settings from: /beegfs/mk5636/scripts/mqc_config.yaml [2018-05-26 07:46:38,911] multiqc [DEBUG ] New config 'custom_content': {'order': ['run_stats', 'demux_report', 'demux_report-1', 'demux_report-2', 'demux_report-3', 'demux_report-4', 'demux_report-5', 'demux_report-6', 'demux_report-7', 'demux_report-8']} [2018-05-26 07:46:38,911] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /beegfs/mk5636/scripts/mqc_config.yaml /beegfs/mk5636/logs/html/HJ5Y2BCX2/2 [2018-05-26 07:46:38,911] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-05-26 07:46:38,911] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-05-26 07:46:38,911] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /beegfs/mk5636/scripts/mqc_config.yaml /beegfs/mk5636/logs/html/HJ5Y2BCX2/2 [2018-05-26 07:46:38,912] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HJ5Y2BCX2/2 [2018-05-26 07:46:38,912] multiqc [INFO ] Template : default [2018-05-26 07:46:38,912] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-05-26 07:46:38,912] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HJ5Y2BCX2/2' [2018-05-26 07:46:38,912] 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 [2018-05-26 07:46:38,912] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-6405894/tmp7GD3HS [2018-05-26 07:46:39,153] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,176] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 2 samples (table) [2018-05-26 07:46:39,178] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-05-26 07:46:39,184] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,188] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,193] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-05-26 07:46:39,197] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,210] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,215] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,261] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,265] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,270] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,283] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,296] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,308] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,320] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,325] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,417] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,423] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,435] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,467] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,480] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,487] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,491] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,496] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,508] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,565] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-05-26 07:46:39,570] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,574] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,587] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,600] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,612] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,625] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,638] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,643] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,783] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HJ5Y2BCX2_l02_n01_undetermined_fastqc.zip' - Bad zip file [2018-05-26 07:46:39,783] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2018-05-26 07:46:39,784] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HJ5Y2BCX2_l02_n02_undetermined_fastqc.zip' - Bad zip file [2018-05-26 07:46:39,784] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2018-05-26 07:46:39,784] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2018-05-26 07:46:39,874] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HJ5Y2BCX2/2',) [2018-05-26 07:46:39,878] multiqc [INFO ] Report : multiqc_report.html [2018-05-26 07:46:39,879] multiqc [INFO ] Data : multiqc_data [2018-05-26 07:46:39,879] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6405894/tmp7GD3HS/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HJ5Y2BCX2/2/multiqc_data' [2018-05-26 07:46:39,881] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6405894/tmp7GD3HS/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HJ5Y2BCX2/2/multiqc_data' [2018-05-26 07:46:39,883] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6405894/tmp7GD3HS/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HJ5Y2BCX2/2/multiqc_data' [2018-05-26 07:46:40,004] multiqc [INFO ] MultiQC complete