[2018-05-14 23:41:27,709] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-05-14 23:41:27,709] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-05-14 23:41:27,710] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-05-14 23:41:27,720] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-05-14 23:41:27,721] 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']} [2018-05-14 23:41:27,721] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HG5M3BCX2/1 [2018-05-14 23:41:28,142] multiqc [WARNING] MultiQC Version v1.5 now available! [2018-05-14 23:41:28,142] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-05-14 23:41:28,143] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HG5M3BCX2/1 [2018-05-14 23:41:28,143] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1 [2018-05-14 23:41:28,143] multiqc [INFO ] Template : default [2018-05-14 23:41:28,143] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-05-14 23:41:28,143] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HG5M3BCX2/1' [2018-05-14 23:41:28,144] 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 [2018-05-14 23:41:28,144] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpfbfebpd8 [2018-05-14 23:41:41,605] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 96 samples (table) [2018-05-14 23:41:41,607] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-05-14 23:41:41,636] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,640] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,645] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-05-14 23:41:41,645] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,649] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,654] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,663] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,677] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,682] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,686] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,700] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,704] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,708] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,713] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,721] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,743] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,750] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,757] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,767] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,774] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,781] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,787] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,793] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,799] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,804] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-05-14 23:41:41,810] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,815] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,821] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,826] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,831] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,836] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,852] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,857] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,862] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:41,866] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:46,391] multiqc.modules.fastqc.fastqc [INFO ] Found 200 reports [2018-05-14 23:41:58,879] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/1',) [2018-05-14 23:41:59,216] multiqc [INFO ] Compressing plot data [2018-05-14 23:41:59,218] multiqc [INFO ] Report : multiqc_report.html [2018-05-14 23:41:59,246] multiqc [INFO ] Data : multiqc_data [2018-05-14 23:41:59,247] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,298] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,441] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,482] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,487] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,503] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,511] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,516] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,520] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,525] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,531] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbfebpd8/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/1/multiqc_data' [2018-05-14 23:41:59,832] multiqc [INFO ] MultiQC complete