[2018-06-25 12:02:26,519] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-06-25 12:02:26,519] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-06-25 12:02:26,520] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-06-25 12:02:26,522] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-06-25 12:02:26,522] 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']} [2018-06-25 12:02:26,522] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/000000000-BJT65/1 [2018-06-25 12:02:27,190] multiqc [WARNING] MultiQC Version v1.5 now available! [2018-06-25 12:02:27,190] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-06-25 12:02:27,191] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/000000000-BJT65/1 [2018-06-25 12:02:27,191] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-BJT65/1 [2018-06-25 12:02:27,191] multiqc [INFO ] Template : default [2018-06-25 12:02:27,191] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-06-25 12:02:27,191] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/000000000-BJT65/1' [2018-06-25 12:02:27,192] 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 [2018-06-25 12:02:27,192] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpte6iz9r9 [2018-06-25 12:02:28,232] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-06-25 12:02:28,234] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 1 samples (table) [2018-06-25 12:02:28,245] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,249] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,262] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-06-25 12:02:28,262] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,266] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,270] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,275] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,281] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,285] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,288] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,292] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,296] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,302] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,306] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,311] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,317] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,321] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,324] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,329] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,333] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,337] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,341] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,344] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,348] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,352] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-06-25 12:02:28,355] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,359] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,362] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,366] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,370] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,378] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,382] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,385] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,389] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,392] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,432] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2018-06-25 12:02:28,479] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-BJT65/1',) [2018-06-25 12:02:28,485] multiqc [INFO ] Compressing plot data [2018-06-25 12:02:28,558] multiqc [INFO ] Report : multiqc_report.html [2018-06-25 12:02:28,594] multiqc [INFO ] Data : multiqc_data [2018-06-25 12:02:28,594] multiqc [DEBUG ] Moving data file from '/tmp/tmpte6iz9r9/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-BJT65/1/multiqc_data' [2018-06-25 12:02:28,622] multiqc [DEBUG ] Moving data file from '/tmp/tmpte6iz9r9/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-BJT65/1/multiqc_data' [2018-06-25 12:02:28,626] multiqc [DEBUG ] Moving data file from '/tmp/tmpte6iz9r9/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-BJT65/1/multiqc_data' [2018-06-25 12:02:29,368] multiqc [INFO ] MultiQC complete