[2017-10-23 22:13:43,979] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml
[2017-10-23 22:13:43,991] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2017-10-23 22:13:43,992] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2017-10-23 22:13:44,001] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml
[2017-10-23 22:13:44,001] 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']}
[2017-10-23 22:13:44,001] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HL2YMBGX3/merged
[2017-10-23 22:13:44,749] multiqc [WARNING] MultiQC Version v1.2 now available!
[2017-10-23 22:13:44,750] multiqc [INFO ] This is MultiQC v1.0.dev0
[2017-10-23 22:13:44,750] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HL2YMBGX3/merged
[2017-10-23 22:13:44,750] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HL2YMBGX3/merged
[2017-10-23 22:13:44,750] multiqc [INFO ] Template : default
[2017-10-23 22:13:44,751] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HL2YMBGX3/merged'
[2017-10-23 22:13:44,751] multiqc [DEBUG ] Analysing modules: custom_content, peddy, methylQA, qualimap, preseq, quast, rna_seqc, rseqc, busco, goleft_indexcov, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, bismark, hicup, salmon, kallisto, slamdunk, star, tophat, bowtie2, bowtie1, adapterRemoval, cutadapt, trimmomatic, skewer, sortmerna, fastq_screen, fastqc, clusterflow
[2017-10-23 22:13:44,751] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpkxnr3v2y
[2017-10-23 22:13:46,267] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2017-10-23 22:13:46,275] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table)
[2017-10-23 22:13:46,285] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,289] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,293] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50
[2017-10-23 22:13:46,293] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,298] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,302] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,306] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,323] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,341] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,345] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,348] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,353] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,367] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,371] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,374] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,382] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,385] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,392] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,397] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,401] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,405] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,408] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,412] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,416] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,419] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found.
[2017-10-23 22:13:46,424] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,428] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,431] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,435] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,444] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,447] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,451] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,455] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,458] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:46,462] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:47,784] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports
[2017-10-23 22:13:47,943] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HL2YMBGX3/merged',)
[2017-10-23 22:13:47,958] multiqc [INFO ] Compressing plot data
[2017-10-23 22:13:48,195] multiqc [INFO ] Report : multiqc_report.html
[2017-10-23 22:13:48,196] multiqc [INFO ] Data : multiqc_data
[2017-10-23 22:13:48,197] multiqc [DEBUG ] Moving data file from '/tmp/tmpkxnr3v2y/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HL2YMBGX3/merged/multiqc_data'
[2017-10-23 22:13:48,269] multiqc [DEBUG ] Moving data file from '/tmp/tmpkxnr3v2y/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HL2YMBGX3/merged/multiqc_data'
[2017-10-23 22:13:48,272] multiqc [DEBUG ] Moving data file from '/tmp/tmpkxnr3v2y/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HL2YMBGX3/merged/multiqc_data'
[2017-10-23 22:13:48,428] multiqc [INFO ] MultiQC complete