[2017-07-20 20:14:11,196] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-07-20 20:14:11,196] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2017-07-20 20:14:11,196] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-07-20 20:14:11,201] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-07-20 20:14:11,201] 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']} [2017-07-20 20:14:11,201] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HT5LJBCXY/2 [2017-07-20 20:14:11,948] multiqc [WARNING] MultiQC Version v1.1 now available! [2017-07-20 20:14:11,948] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-07-20 20:14:11,949] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HT5LJBCXY/2 [2017-07-20 20:14:11,949] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2 [2017-07-20 20:14:11,949] multiqc [INFO ] Template : default [2017-07-20 20:14:11,950] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HT5LJBCXY/2' [2017-07-20 20:14:11,950] 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 [2017-07-20 20:14:11,951] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpbqhmku3t [2017-07-20 20:14:22,435] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-07-20 20:14:22,533] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 96 samples (table) [2017-07-20 20:14:22,537] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,540] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,544] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-07-20 20:14:22,544] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,547] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,550] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,554] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,559] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,562] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,565] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,569] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,572] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,575] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,578] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,582] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,587] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,591] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,594] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,598] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,601] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,605] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,608] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,611] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,614] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,617] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-07-20 20:14:22,621] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,624] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,627] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,630] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,633] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,636] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,640] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,643] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,646] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:22,649] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:25,511] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2017-07-20 20:14:34,791] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HT5LJBCXY/2',) [2017-07-20 20:14:35,124] multiqc [INFO ] Compressing plot data [2017-07-20 20:14:35,125] multiqc [INFO ] Report : multiqc_report.html [2017-07-20 20:14:35,137] multiqc [INFO ] Data : multiqc_data [2017-07-20 20:14:35,137] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,176] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,181] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,185] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,189] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,193] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,197] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,200] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,204] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,207] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,210] multiqc [DEBUG ] Moving data file from '/tmp/tmpbqhmku3t/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HT5LJBCXY/2/multiqc_data' [2017-07-20 20:14:35,352] multiqc [INFO ] MultiQC complete