[2018-06-19 16:30:37,165] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-06-19 16:30:37,165] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-06-19 16:30:37,166] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-06-19 16:30:37,190] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-06-19 16:30:37,191] 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']} [2018-06-19 16:30:37,191] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HVJJYBGX5/merged [2018-06-19 16:30:37,508] multiqc [WARNING] MultiQC Version v1.5 now available! [2018-06-19 16:30:37,508] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-06-19 16:30:37,508] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HVJJYBGX5/merged [2018-06-19 16:30:37,508] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVJJYBGX5/merged [2018-06-19 16:30:37,509] multiqc [INFO ] Template : default [2018-06-19 16:30:37,509] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-06-19 16:30:37,509] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HVJJYBGX5/merged' [2018-06-19 16:30:37,509] 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 [2018-06-19 16:30:37,510] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpllm8_h5h [2018-06-19 16:30:39,644] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2018-06-19 16:30:39,646] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-06-19 16:30:39,651] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,655] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,661] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-06-19 16:30:39,661] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,665] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,678] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,702] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,726] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,745] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,752] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,758] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,764] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,770] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,776] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,782] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,794] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,799] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,805] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,813] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,819] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,824] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,829] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,834] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,840] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,845] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-06-19 16:30:39,850] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,854] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,859] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,864] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,870] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,874] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,880] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,890] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,895] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:39,900] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:41,150] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2018-06-19 16:30:41,341] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HVJJYBGX5/merged',) [2018-06-19 16:30:41,359] multiqc [INFO ] Compressing plot data [2018-06-19 16:30:41,556] multiqc [INFO ] Report : multiqc_report.html [2018-06-19 16:30:41,579] multiqc [INFO ] Data : multiqc_data [2018-06-19 16:30:41,579] multiqc [DEBUG ] Moving data file from '/tmp/tmpllm8_h5h/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVJJYBGX5/merged/multiqc_data' [2018-06-19 16:30:41,664] multiqc [DEBUG ] Moving data file from '/tmp/tmpllm8_h5h/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVJJYBGX5/merged/multiqc_data' [2018-06-19 16:30:41,667] multiqc [DEBUG ] Moving data file from '/tmp/tmpllm8_h5h/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVJJYBGX5/merged/multiqc_data' [2018-06-19 16:30:41,941] multiqc [INFO ] MultiQC complete