[2018-08-10 13:42:45,134] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-08-10 13:42:45,134] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-08-10 13:42:45,134] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-08-10 13:42:45,161] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-08-10 13:42:45,162] 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']} [2018-08-10 13:42:45,162] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/H3VL5AFXY/merged [2018-08-10 13:42:45,656] multiqc [WARNING] MultiQC Version v1.6 now available! [2018-08-10 13:42:45,656] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-08-10 13:42:45,657] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/H3VL5AFXY/merged [2018-08-10 13:42:45,657] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged [2018-08-10 13:42:45,657] multiqc [INFO ] Template : default [2018-08-10 13:42:45,657] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-08-10 13:42:45,657] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/H3VL5AFXY/merged' [2018-08-10 13:42:45,657] 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 [2018-08-10 13:42:45,658] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmplh29f2ar [2018-08-10 13:42:45,758] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /home/mk5636/fastqc-delivery/H3VL5AFXY/merged/multiqc_data [2018-08-10 13:42:57,498] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 192 samples (table) [2018-08-10 13:42:57,500] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-08-10 13:42:57,512] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,516] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,521] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-08-10 13:42:57,521] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,524] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,529] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,543] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,560] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,567] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,571] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,574] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,579] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,583] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,587] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,590] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,598] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,601] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,605] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,611] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,616] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,619] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,623] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,627] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,630] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,634] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-08-10 13:42:57,638] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,641] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,645] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,649] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,653] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,657] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,660] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,664] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,668] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:42:57,671] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:43:03,685] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2018-08-10 13:43:17,672] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VL5AFXY/merged',) [2018-08-10 13:43:18,055] multiqc [INFO ] Compressing plot data [2018-08-10 13:43:18,056] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2018-08-10 13:43:18,105] multiqc [INFO ] Report : multiqc_report.html [2018-08-10 13:43:18,105] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2018-08-10 13:43:18,226] multiqc [INFO ] Data : multiqc_data [2018-08-10 13:43:18,226] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,266] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,284] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,534] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,539] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,553] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,978] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,983] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,987] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,991] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:18,995] multiqc [DEBUG ] Moving data file from '/tmp/tmplh29f2ar/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VL5AFXY/merged/multiqc_data' [2018-08-10 13:43:19,223] multiqc [INFO ] MultiQC complete