[2017-04-12 11:28:18,434] multiqc [DEBUG ] No MultiQC config found: /opt/local/tubo/env/python3/lib/python3.4/site-packages/multiqc_config.yaml [2017-04-12 11:28:18,434] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2017-04-12 11:28:18,434] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-04-12 11:28:18,435] multiqc [DEBUG ] Command used: /opt/local/tubo/env/python3/bin/multiqc . [2017-04-12 11:28:18,766] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-04-12 11:28:18,767] multiqc [DEBUG ] Command : /opt/local/tubo/env/python3/bin/multiqc . [2017-04-12 11:28:18,767] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5WJNBCXY-test/2 [2017-04-12 11:28:18,767] multiqc [INFO ] Template : default [2017-04-12 11:28:18,767] multiqc [INFO ] Searching '.' [2017-04-12 11:28:18,768] 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 [2017-04-12 11:28:18,768] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp08xj3gcw [2017-04-12 11:28:19,104] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-04-12 11:28:19,117] multiqc.modules.custom_content.custom_content [INFO ] H5WJNBCXY_l02_summary: Found 1 samples (table) [2017-04-12 11:28:19,122] multiqc.modules.custom_content.custom_content [INFO ] H5WJNBCXY_l02_demux_report: Found 6 samples (table) [2017-04-12 11:28:19,135] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,139] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,145] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-04-12 11:28:19,160] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,190] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-04-12 11:28:19,195] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,286] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,291] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,298] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-04-12 11:28:19,320] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-04-12 11:28:19,342] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,363] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,384] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,389] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,577] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,583] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-04-12 11:28:19,605] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-04-12 11:28:19,667] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,688] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,703] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,708] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-04-12 11:28:19,717] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-04-12 11:28:19,743] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,857] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-04-12 11:28:19,865] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,869] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,891] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,912] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,933] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:19,954] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-04-12 11:28:19,975] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-04-12 11:28:19,980] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:20,207] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2017-04-12 11:28:20,341] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-04-12 11:28:20,363] multiqc [INFO ] Report : multiqc_report.html [2017-04-12 11:28:20,364] multiqc [INFO ] Data : multiqc_data [2017-04-12 11:28:20,365] multiqc [DEBUG ] Moving data file from '/tmp/tmp08xj3gcw/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5WJNBCXY-test/2/multiqc_data' [2017-04-12 11:28:20,369] multiqc [DEBUG ] Moving data file from '/tmp/tmp08xj3gcw/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5WJNBCXY-test/2/multiqc_data' [2017-04-12 11:28:20,373] multiqc [DEBUG ] Moving data file from '/tmp/tmp08xj3gcw/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5WJNBCXY-test/2/multiqc_data' [2017-04-12 11:28:20,495] multiqc [INFO ] MultiQC complete