[2018-10-11 22:17:19,262] 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
[2018-10-11 22:17:19,262] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml
[2018-10-11 22:17:19,263] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2018-10-11 22:17:19,274] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml
[2018-10-11 22:17:19,274] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}}
[2018-10-11 22:17:19,274] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HK77CBCX2/1
[2018-10-11 22:17:19,274] multiqc [DEBUG ] Could not connect to multiqc.info for version check
[2018-10-11 22:17:19,274] multiqc [INFO ] This is MultiQC v1.0.dev0
[2018-10-11 22:17:19,274] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HK77CBCX2/1
[2018-10-11 22:17:19,274] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HK77CBCX2/1
[2018-10-11 22:17:19,274] multiqc [INFO ] Template : default
[2018-10-11 22:17:19,274] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports.
[2018-10-11 22:17:19,274] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HK77CBCX2/1'
[2018-10-11 22:17:19,275] 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
[2018-10-11 22:17:19,275] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9197202/tmp5oL32h
[2018-10-11 22:17:19,290] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HK77CBCX2/1/multiqc_data
[2018-10-11 22:17:19,606] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:19,635] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 13 samples (table)
[2018-10-11 22:17:19,637] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2018-10-11 22:17:19,663] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:19,674] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:19,681] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50
[2018-10-11 22:17:19,713] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:21,335] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:21,354] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,070] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,082] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,098] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,265] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,438] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,603] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,766] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:22,776] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:24,386] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:24,398] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:24,564] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:25,059] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:25,223] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:25,256] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:25,267] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:25,283] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:25,447] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:26,405] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found.
[2018-10-11 22:17:26,422] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:26,433] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:26,611] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:26,779] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:26,955] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:27,122] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:27,289] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:27,301] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:27,339] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HK77CBCX2_l01_n02_MG_neg.8.7_fastqc.zip' - Bad zip file
[2018-10-11 22:17:27,339] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-10-11 22:17:27,675] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HK77CBCX2_l01_n02_MG_positive_fastqc.zip' - Bad zip file
[2018-10-11 22:17:27,675] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-10-11 22:17:28,005] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HK77CBCX2_l01_n01_MG_neg.8.7_fastqc.zip' - Bad zip file
[2018-10-11 22:17:28,005] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-10-11 22:17:28,688] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HK77CBCX2_l01_n01_MG_positive_fastqc.zip' - Bad zip file
[2018-10-11 22:17:28,688] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-10-11 22:17:28,890] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HK77CBCX2_l01_n02_MG_8724.tr6_fastqc.zip' - Bad zip file
[2018-10-11 22:17:28,891] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-10-11 22:17:28,892] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HK77CBCX2_l01_n01_MG_8724.tr6_fastqc.zip' - Bad zip file
[2018-10-11 22:17:28,892] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-10-11 22:17:29,212] multiqc.modules.fastqc.fastqc [INFO ] Found 44 reports
[2018-10-11 22:17:35,793] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HK77CBCX2/1',)
[2018-10-11 22:17:35,854] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified)
[2018-10-11 22:17:35,882] multiqc [INFO ] Report : multiqc_report.html
[2018-10-11 22:17:35,883] multiqc [WARNING] Deleting : multiqc_data (-f was specified)
[2018-10-11 22:17:35,913] multiqc [INFO ] Data : multiqc_data
[2018-10-11 22:17:35,913] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9197202/tmp5oL32h/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HK77CBCX2/1/multiqc_data'
[2018-10-11 22:17:35,916] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9197202/tmp5oL32h/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HK77CBCX2/1/multiqc_data'
[2018-10-11 22:17:35,935] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9197202/tmp5oL32h/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HK77CBCX2/1/multiqc_data'
[2018-10-11 22:17:36,063] multiqc [INFO ] MultiQC complete