[2017-05-16 16:20:35,285] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-05-16 16:20:35,285] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2017-05-16 16:20:35,285] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-05-16 16:20:35,286] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-05-16 16:20:35,286] multiqc [DEBUG ] New config 'custom_content': {'order': ['run_stats', 'demux_report']} [2017-05-16 16:20:35,286] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-05-16 16:20:35,457] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-05-16 16:20:35,458] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-05-16 16:20:35,458] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX [2017-05-16 16:20:35,458] multiqc [INFO ] Template : default [2017-05-16 16:20:35,459] multiqc [INFO ] Searching '.' [2017-05-16 16:20:35,459] 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 [2017-05-16 16:20:35,459] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp741a7nz2 [2017-05-16 16:20:42,598] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 7 samples (table) [2017-05-16 16:20:42,606] multiqc.modules.custom_content.custom_content [INFO ] demux_report-3: Found 7 samples (table) [2017-05-16 16:20:42,615] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 8 samples (table) [2017-05-16 16:20:42,627] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 11 samples (table) [2017-05-16 16:20:42,635] multiqc.modules.custom_content.custom_content [INFO ] demux_report-7: Found 7 samples (table) [2017-05-16 16:20:42,642] multiqc.modules.custom_content.custom_content [INFO ] demux_report-6: Found 7 samples (table) [2017-05-16 16:20:42,650] multiqc.modules.custom_content.custom_content [INFO ] demux_report-5: Found 7 samples (table) [2017-05-16 16:20:42,657] multiqc.modules.custom_content.custom_content [INFO ] demux_report-8: Found 7 samples (table) [2017-05-16 16:20:42,665] multiqc.modules.custom_content.custom_content [INFO ] demux_report-4: Found 7 samples (table) [2017-05-16 16:20:42,668] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,672] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,675] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-05-16 16:20:42,675] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,679] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-05-16 16:20:42,682] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,685] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-05-16 16:20:42,690] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,693] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,697] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-05-16 16:20:42,700] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-05-16 16:20:42,703] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,706] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,710] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,713] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,719] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,722] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-05-16 16:20:42,725] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-05-16 16:20:42,729] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,733] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,736] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,739] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-05-16 16:20:42,742] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-05-16 16:20:42,746] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,749] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-05-16 16:20:42,752] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,755] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,758] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,762] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,765] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,768] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:42,771] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-05-16 16:20:42,774] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-05-16 16:20:42,778] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-05-16 16:20:42,781] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:46,648] multiqc.modules.fastqc.fastqc [INFO ] Found 120 reports [2017-05-16 16:20:54,374] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-05-16 16:20:54,535] multiqc [INFO ] Compressing plot data [2017-05-16 16:20:54,535] multiqc [INFO ] Report : multiqc_report.html [2017-05-16 16:20:54,548] multiqc [INFO ] Data : multiqc_data [2017-05-16 16:20:54,549] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,581] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,586] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,591] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,596] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,619] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,623] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,628] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,631] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,634] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,637] multiqc [DEBUG ] Moving data file from '/tmp/tmp741a7nz2/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/C9LUHACXX/multiqc_data' [2017-05-16 16:20:54,809] multiqc [INFO ] MultiQC complete