[2017-11-14 17:39:34,374] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-11-14 17:39:34,375] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2017-11-14 17:39:34,375] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-11-14 17:39:34,390] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-11-14 17:39:34,390] 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']} [2017-11-14 17:39:34,390] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HMKLYBGX3/merged [2017-11-14 17:39:34,628] multiqc [WARNING] MultiQC Version v1.3 now available! [2017-11-14 17:39:34,628] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-11-14 17:39:34,628] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HMKLYBGX3/merged [2017-11-14 17:39:34,628] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMKLYBGX3/merged [2017-11-14 17:39:34,628] multiqc [INFO ] Template : default [2017-11-14 17:39:34,630] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HMKLYBGX3/merged' [2017-11-14 17:39:34,630] 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 [2017-11-14 17:39:34,630] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpdidg4o_w [2017-11-14 17:39:36,568] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2017-11-14 17:39:36,570] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-11-14 17:39:36,577] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,580] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,585] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-11-14 17:39:36,586] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,589] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,593] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,597] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,608] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,613] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,617] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,621] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,625] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,629] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,633] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,636] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,646] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,649] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,661] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,676] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,681] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,684] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,688] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,692] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,695] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,699] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-11-14 17:39:36,702] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,706] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,710] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,713] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,717] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,721] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,724] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,728] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,731] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:36,735] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:38,247] multiqc.modules.fastqc.fastqc [INFO ] Found 11 reports [2017-11-14 17:39:38,420] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HMKLYBGX3/merged',) [2017-11-14 17:39:38,435] multiqc [INFO ] Compressing plot data [2017-11-14 17:39:38,636] multiqc [INFO ] Report : multiqc_report.html [2017-11-14 17:39:38,652] multiqc [INFO ] Data : multiqc_data [2017-11-14 17:39:38,652] multiqc [DEBUG ] Moving data file from '/tmp/tmpdidg4o_w/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMKLYBGX3/merged/multiqc_data' [2017-11-14 17:39:38,674] multiqc [DEBUG ] Moving data file from '/tmp/tmpdidg4o_w/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMKLYBGX3/merged/multiqc_data' [2017-11-14 17:39:38,683] multiqc [DEBUG ] Moving data file from '/tmp/tmpdidg4o_w/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMKLYBGX3/merged/multiqc_data' [2017-11-14 17:39:39,175] multiqc [INFO ] MultiQC complete