[2017-06-08 11:34:54,308] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-06-08 11:34:54,308] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2017-06-08 11:34:54,308] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-06-08 11:34:54,309] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-06-08 11:34:54,309] multiqc [DEBUG ] New config 'custom_content': {'order': ['run_stats', 'demux_report']} [2017-06-08 11:34:54,309] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-06-08 11:34:54,540] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-06-08 11:34:54,541] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-06-08 11:34:54,541] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN3YYBGX2/merged [2017-06-08 11:34:54,541] multiqc [INFO ] Template : default [2017-06-08 11:34:54,542] multiqc [INFO ] Searching '.' [2017-06-08 11:34:54,542] 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 [2017-06-08 11:34:54,543] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpxxje1tko [2017-06-08 11:34:55,403] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 1 samples (table) [2017-06-08 11:34:55,405] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-06-08 11:34:55,408] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,412] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,415] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-06-08 11:34:55,416] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,419] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-06-08 11:34:55,422] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,426] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-06-08 11:34:55,431] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,435] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,438] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-06-08 11:34:55,441] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-06-08 11:34:55,445] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,448] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,451] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,455] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,460] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,464] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-06-08 11:34:55,467] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-06-08 11:34:55,471] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,475] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,478] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,481] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-06-08 11:34:55,485] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-06-08 11:34:55,488] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,491] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-06-08 11:34:55,494] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,498] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,501] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,504] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,507] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,511] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,514] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-06-08 11:34:55,517] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-06-08 11:34:55,520] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-06-08 11:34:55,524] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,701] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports [2017-06-08 11:34:55,723] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-06-08 11:34:55,726] multiqc [INFO ] Compressing plot data [2017-06-08 11:34:55,749] multiqc [INFO ] Report : multiqc_report.html [2017-06-08 11:34:55,765] multiqc [INFO ] Data : multiqc_data [2017-06-08 11:34:55,765] multiqc [DEBUG ] Moving data file from '/tmp/tmpxxje1tko/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN3YYBGX2/merged/multiqc_data' [2017-06-08 11:34:55,796] multiqc [DEBUG ] Moving data file from '/tmp/tmpxxje1tko/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN3YYBGX2/merged/multiqc_data' [2017-06-08 11:34:55,799] multiqc [DEBUG ] Moving data file from '/tmp/tmpxxje1tko/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HN3YYBGX2/merged/multiqc_data' [2017-06-08 11:34:56,063] multiqc [INFO ] MultiQC complete