[2017-08-10 18:42:05,172] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-08-10 18:42:05,172] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2017-08-10 18:42:05,172] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-08-10 18:42:05,174] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-08-10 18:42:05,174] 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']} [2017-08-10 18:42:05,174] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-08-10 18:42:05,408] multiqc [WARNING] MultiQC Version v1.1 now available! [2017-08-10 18:42:05,409] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-08-10 18:42:05,409] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-08-10 18:42:05,409] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN2WTAFXX/merged [2017-08-10 18:42:05,409] multiqc [INFO ] Template : default [2017-08-10 18:42:05,410] multiqc [INFO ] Searching '.' [2017-08-10 18:42:05,411] 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 [2017-08-10 18:42:05,411] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp4mfqn4fr [2017-08-10 18:42:08,771] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 24 samples (table) [2017-08-10 18:42:08,773] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-08-10 18:42:08,776] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,779] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,783] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-08-10 18:42:08,783] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,786] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-08-10 18:42:08,790] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,793] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-08-10 18:42:08,798] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,801] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,804] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-08-10 18:42:08,808] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-08-10 18:42:08,811] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,814] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,818] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,821] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,826] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,830] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-08-10 18:42:08,833] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-08-10 18:42:08,837] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,841] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,844] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,847] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-08-10 18:42:08,850] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-08-10 18:42:08,853] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,857] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-08-10 18:42:08,860] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,863] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,866] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,869] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,873] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,876] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:08,879] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-08-10 18:42:08,882] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-08-10 18:42:08,885] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-08-10 18:42:08,889] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:11,091] multiqc.modules.fastqc.fastqc [INFO ] Found 48 reports [2017-08-10 18:42:11,817] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-08-10 18:42:11,883] multiqc [INFO ] Compressing plot data [2017-08-10 18:42:12,693] multiqc [INFO ] Report : multiqc_report.html [2017-08-10 18:42:12,711] multiqc [INFO ] Data : multiqc_data [2017-08-10 18:42:12,711] multiqc [DEBUG ] Moving data file from '/tmp/tmp4mfqn4fr/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN2WTAFXX/merged/multiqc_data' [2017-08-10 18:42:12,714] multiqc [DEBUG ] Moving data file from '/tmp/tmp4mfqn4fr/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN2WTAFXX/merged/multiqc_data' [2017-08-10 18:42:12,718] multiqc [DEBUG ] Moving data file from '/tmp/tmp4mfqn4fr/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN2WTAFXX/merged/multiqc_data' [2017-08-10 18:42:12,820] multiqc [INFO ] MultiQC complete