[2017-07-24 17:57:08,719] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-07-24 17:57:08,720] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2017-07-24 17:57:08,720] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-07-24 17:57:08,720] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc . [2017-07-24 17:57:09,471] multiqc [WARNING] MultiQC Version v1.1 now available! [2017-07-24 17:57:09,471] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-07-24 17:57:09,471] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc . [2017-07-24 17:57:09,472] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMN35AFXX/merged [2017-07-24 17:57:09,472] multiqc [INFO ] Template : default [2017-07-24 17:57:09,472] multiqc [INFO ] Searching '.' [2017-07-24 17:57:09,472] 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 [2017-07-24 17:57:09,472] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpemwhuq3i [2017-07-24 17:57:13,678] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-07-24 17:57:13,703] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2017-07-24 17:57:13,715] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,718] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,721] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-07-24 17:57:13,722] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,725] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-07-24 17:57:13,746] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,748] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-07-24 17:57:13,753] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,755] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,758] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-07-24 17:57:13,761] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-07-24 17:57:13,764] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,767] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,771] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,774] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,787] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,790] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-07-24 17:57:13,794] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-07-24 17:57:13,805] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,809] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,813] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,815] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-07-24 17:57:13,819] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-07-24 17:57:13,822] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,825] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-07-24 17:57:13,828] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,832] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,835] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,838] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,852] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,865] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:13,883] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-07-24 17:57:13,886] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-07-24 17:57:13,894] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-07-24 17:57:13,897] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:15,685] multiqc.modules.fastqc.fastqc [INFO ] Found 58 reports [2017-07-24 17:57:17,113] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-07-24 17:57:17,192] multiqc [INFO ] Compressing plot data [2017-07-24 17:57:18,064] multiqc [INFO ] Report : multiqc_report.html [2017-07-24 17:57:18,076] multiqc [INFO ] Data : multiqc_data [2017-07-24 17:57:18,077] multiqc [DEBUG ] Moving data file from '/tmp/tmpemwhuq3i/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMN35AFXX/merged/multiqc_data' [2017-07-24 17:57:18,138] multiqc [DEBUG ] Moving data file from '/tmp/tmpemwhuq3i/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMN35AFXX/merged/multiqc_data' [2017-07-24 17:57:18,142] multiqc [DEBUG ] Moving data file from '/tmp/tmpemwhuq3i/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMN35AFXX/merged/multiqc_data' [2017-07-24 17:57:18,341] multiqc [INFO ] MultiQC complete