[2018-12-12 17:46:55,153] 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
[2018-12-12 17:46:55,154] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2018-12-12 17:46:55,154] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2018-12-12 17:46:55,167] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml
[2018-12-12 17:46:55,167] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}}
[2018-12-12 17:46:55,168] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-BPJBB/1
[2018-12-12 17:46:55,168] multiqc [DEBUG ] Could not connect to multiqc.info for version check
[2018-12-12 17:46:55,168] multiqc [INFO ] This is MultiQC v1.0.dev0
[2018-12-12 17:46:55,168] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/000000000-BPJBB/1
[2018-12-12 17:46:55,168] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/000000000-BPJBB/1
[2018-12-12 17:46:55,168] multiqc [INFO ] Template : default
[2018-12-12 17:46:55,168] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports.
[2018-12-12 17:46:55,168] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/000000000-BPJBB/1'
[2018-12-12 17:46:55,168] 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
[2018-12-12 17:46:55,168] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10836345/tmpkXsmcN
[2018-12-12 17:46:55,178] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/000000000-BPJBB/1/multiqc_data
[2018-12-12 17:46:55,469] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,618] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 7 samples (table)
[2018-12-12 17:46:55,621] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2018-12-12 17:46:55,638] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,648] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,658] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50
[2018-12-12 17:46:55,670] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,781] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,791] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,922] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,929] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,936] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:55,969] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,004] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,038] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,072] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,079] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,355] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,364] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,396] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,483] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,517] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,529] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,536] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,544] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,578] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,746] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found.
[2018-12-12 17:46:56,755] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,762] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,795] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,829] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,861] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,894] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,927] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,934] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:56,974] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n01_mcb3_fastqc.zip' - Bad zip file
[2018-12-12 17:46:56,975] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,005] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n02_mcb3_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,005] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,007] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n02_mcb_wt_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,007] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,008] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n01_mcb_wt_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,008] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,010] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n01_Mcb1_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,010] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,011] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n02_Mcb1_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,011] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,013] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n01_mcb2_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,013] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,014] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n01_Mcb4_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,014] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,016] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n02_mcb2_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,016] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,017] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n01_mcb5_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,017] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,019] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n02_mcb5_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,019] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,020] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read '000000000-BPJBB_l01_n02_Mcb4_fastqc.zip' - Bad zip file
[2018-12-12 17:46:57,020] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error:
File is not a zip file
[2018-12-12 17:46:57,021] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
[2018-12-12 17:46:57,153] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/000000000-BPJBB/1',)
[2018-12-12 17:46:57,157] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified)
[2018-12-12 17:46:57,159] multiqc [INFO ] Report : multiqc_report.html
[2018-12-12 17:46:57,159] multiqc [WARNING] Deleting : multiqc_data (-f was specified)
[2018-12-12 17:46:57,276] multiqc [INFO ] Data : multiqc_data
[2018-12-12 17:46:57,277] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10836345/tmpkXsmcN/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/000000000-BPJBB/1/multiqc_data'
[2018-12-12 17:46:57,281] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10836345/tmpkXsmcN/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/000000000-BPJBB/1/multiqc_data'
[2018-12-12 17:46:57,285] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10836345/tmpkXsmcN/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/000000000-BPJBB/1/multiqc_data'
[2018-12-12 17:46:57,564] multiqc [INFO ] MultiQC complete