[2018-05-15 00:28:31,958] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-05-15 00:28:31,958] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-05-15 00:28:31,959] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-05-15 00:28:31,961] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-05-15 00:28:31,961] 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']} [2018-05-15 00:28:31,961] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HG5M3BCX2/2 [2018-05-15 00:28:32,355] multiqc [WARNING] MultiQC Version v1.5 now available! [2018-05-15 00:28:32,355] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-05-15 00:28:32,355] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HG5M3BCX2/2 [2018-05-15 00:28:32,355] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2 [2018-05-15 00:28:32,356] multiqc [INFO ] Template : default [2018-05-15 00:28:32,356] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-05-15 00:28:32,356] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HG5M3BCX2/2' [2018-05-15 00:28:32,356] 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 [2018-05-15 00:28:32,356] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpfbm1kts0 [2018-05-15 00:28:42,514] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-05-15 00:28:42,652] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 96 samples (table) [2018-05-15 00:28:42,657] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,660] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,664] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-05-15 00:28:42,664] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,667] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,671] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,674] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,679] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,683] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,686] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,689] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,693] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,696] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,699] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,703] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,708] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,712] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,715] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,719] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,723] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,726] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,729] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,733] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,736] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,739] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-05-15 00:28:42,742] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,746] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,749] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,752] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,755] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,758] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,762] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,765] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,768] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:42,771] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:45,699] multiqc.modules.fastqc.fastqc [INFO ] Found 166 reports [2018-05-15 00:28:54,861] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HG5M3BCX2/2',) [2018-05-15 00:28:55,136] multiqc [INFO ] Compressing plot data [2018-05-15 00:28:55,137] multiqc [INFO ] Report : multiqc_report.html [2018-05-15 00:28:55,153] multiqc [INFO ] Data : multiqc_data [2018-05-15 00:28:55,153] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,228] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,339] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,366] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,371] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,399] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,420] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,425] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,429] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,432] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,436] multiqc [DEBUG ] Moving data file from '/tmp/tmpfbm1kts0/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HG5M3BCX2/2/multiqc_data' [2018-05-15 00:28:55,591] multiqc [INFO ] MultiQC complete