[2019-02-10 12:29:05,840] 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
[2019-02-10 12:29:05,841] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml
[2019-02-10 12:29:05,841] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2019-02-10 12:29:05,849] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml
[2019-02-10 12:29:05,849] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}}
[2019-02-10 12:29:05,849] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HT5CKBCX2/1
[2019-02-10 12:29:05,849] multiqc [DEBUG ] Could not connect to multiqc.info for version check
[2019-02-10 12:29:05,849] multiqc [INFO ] This is MultiQC v1.0.dev0
[2019-02-10 12:29:05,849] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HT5CKBCX2/1
[2019-02-10 12:29:05,849] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HT5CKBCX2/1
[2019-02-10 12:29:05,849] multiqc [INFO ] Template : default
[2019-02-10 12:29:05,850] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports.
[2019-02-10 12:29:05,850] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HT5CKBCX2/1'
[2019-02-10 12:29:05,850] 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
[2019-02-10 12:29:05,850] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15212767/tmpylMGnr
[2019-02-10 12:29:05,965] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt
[2019-02-10 12:29:06,281] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:06,364] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 89 samples (table)
[2019-02-10 12:29:06,373] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table)
[2019-02-10 12:29:06,374] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2019-02-10 12:29:06,446] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:06,469] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:06,478] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50
[2019-02-10 12:29:06,576] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:13,056] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:13,084] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:15,981] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:16,008] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:16,049] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:16,735] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:17,414] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:18,219] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:18,891] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:18,914] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:25,477] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:25,503] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:26,260] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:28,372] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:28,925] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:29,010] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:29,031] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:29,070] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:29,620] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:33,587] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found.
[2019-02-10 12:29:33,627] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:33,650] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:34,219] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:34,776] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:35,334] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:36,000] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:36,555] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:36,579] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:29:43,796] multiqc.modules.fastqc.fastqc [INFO ] Found 178 reports
[2019-02-10 12:30:08,381] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HT5CKBCX2/1',)
[2019-02-10 12:30:08,577] multiqc [INFO ] Report : multiqc_report.html
[2019-02-10 12:30:08,578] multiqc [INFO ] Data : multiqc_data
[2019-02-10 12:30:08,578] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,581] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,583] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,586] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,588] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,591] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,593] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,596] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,599] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,602] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,604] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15212767/tmpylMGnr/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HT5CKBCX2/1/multiqc_data'
[2019-02-10 12:30:08,760] multiqc [INFO ] MultiQC complete