[2018-02-22 14:29:21,491] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-02-22 14:29:21,492] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-02-22 14:29:21,492] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-02-22 14:29:21,494] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-02-22 14:29:21,494] 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']} [2018-02-22 14:29:21,494] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2018-02-22 14:29:21,571] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-02-22 14:29:21,571] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-02-22 14:29:21,571] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2018-02-22 14:29:21,571] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged [2018-02-22 14:29:21,572] multiqc [INFO ] Template : default [2018-02-22 14:29:21,572] multiqc [INFO ] Searching '.' [2018-02-22 14:29:21,573] 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 [2018-02-22 14:29:21,573] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpntzxkd1r [2018-02-22 14:29:55,925] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-02-22 14:29:56,255] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 334 samples (table) [2018-02-22 14:29:56,258] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,262] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,265] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-02-22 14:29:56,266] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,269] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2018-02-22 14:29:56,272] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,275] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2018-02-22 14:29:56,280] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,284] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,287] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2018-02-22 14:29:56,290] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2018-02-22 14:29:56,294] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,297] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,300] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,303] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,309] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,312] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2018-02-22 14:29:56,316] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2018-02-22 14:29:56,320] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,323] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,327] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,330] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2018-02-22 14:29:56,333] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2018-02-22 14:29:56,336] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,340] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-02-22 14:29:56,343] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,346] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,349] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,352] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,356] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,359] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:29:56,363] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2018-02-22 14:29:56,366] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2018-02-22 14:29:56,369] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2018-02-22 14:29:56,372] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:30:16,914] multiqc.modules.fastqc.fastqc [INFO ] Found 668 reports [2018-02-22 14:30:57,618] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2018-02-22 14:30:57,622] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 668 samples [2018-02-22 14:30:57,624] multiqc [INFO ] Compressing plot data [2018-02-22 14:30:57,788] multiqc [INFO ] Report : multiqc_report.html [2018-02-22 14:30:57,829] multiqc [INFO ] Data : multiqc_data [2018-02-22 14:30:57,830] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:57,851] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:57,942] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,033] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,043] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,091] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,106] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,170] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,175] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,180] multiqc [DEBUG ] Moving data file from '/tmp/tmpntzxkd1r/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged/multiqc_data' [2018-02-22 14:30:58,400] multiqc [INFO ] MultiQC complete