[2017-05-17 14:25:48,507] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-05-17 14:25:48,507] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2017-05-17 14:25:48,507] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-05-17 14:25:48,507] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc . [2017-05-17 14:25:48,769] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-05-17 14:25:48,769] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc . [2017-05-17 14:25:48,769] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HK2HHAFXX/merged [2017-05-17 14:25:48,770] multiqc [INFO ] Template : default [2017-05-17 14:25:48,770] multiqc [INFO ] Searching '.' [2017-05-17 14:25:48,771] 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 [2017-05-17 14:25:48,771] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp_rewnupb [2017-05-17 14:25:49,748] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2017-05-17 14:25:49,751] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,755] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,758] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-05-17 14:25:49,759] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,762] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-05-17 14:25:49,765] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,768] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-05-17 14:25:49,774] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,777] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,780] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-05-17 14:25:49,784] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-05-17 14:25:49,787] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,790] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,794] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,797] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,802] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,806] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-05-17 14:25:49,809] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-05-17 14:25:49,813] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,816] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,820] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,823] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-05-17 14:25:49,826] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-05-17 14:25:49,829] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,832] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-05-17 14:25:49,836] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,839] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,842] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,845] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,848] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,852] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:49,855] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-05-17 14:25:49,858] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-05-17 14:25:49,861] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-05-17 14:25:49,864] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:50,009] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2017-05-17 14:25:50,056] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-05-17 14:25:50,063] multiqc [INFO ] Compressing plot data [2017-05-17 14:25:50,131] multiqc [INFO ] Report : multiqc_report.html [2017-05-17 14:25:50,174] multiqc [INFO ] Data : multiqc_data [2017-05-17 14:25:50,174] multiqc [DEBUG ] Moving data file from '/tmp/tmp_rewnupb/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HK2HHAFXX/merged/multiqc_data' [2017-05-17 14:25:50,237] multiqc [DEBUG ] Moving data file from '/tmp/tmp_rewnupb/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HK2HHAFXX/merged/multiqc_data' [2017-05-17 14:25:50,241] multiqc [DEBUG ] Moving data file from '/tmp/tmp_rewnupb/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HK2HHAFXX/merged/multiqc_data' [2017-05-17 14:25:50,413] multiqc [INFO ] MultiQC complete