[2017-12-23 22:46:59,560] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-12-23 22:46:59,560] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2017-12-23 22:46:59,560] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-12-23 22:46:59,565] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-12-23 22:46:59,565] 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']} [2017-12-23 22:46:59,566] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HW32WAFXX/merged [2017-12-23 22:47:00,321] multiqc [WARNING] MultiQC Version v1.3 now available! [2017-12-23 22:47:00,321] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-12-23 22:47:00,322] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HW32WAFXX/merged [2017-12-23 22:47:00,322] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged [2017-12-23 22:47:00,322] multiqc [INFO ] Template : default [2017-12-23 22:47:00,323] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HW32WAFXX/merged' [2017-12-23 22:47:00,323] 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 [2017-12-23 22:47:00,324] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpwykvwavi [2017-12-23 22:47:14,903] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-12-23 22:47:14,999] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 96 samples (table) [2017-12-23 22:47:15,003] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,006] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,010] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-12-23 22:47:15,010] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,013] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,016] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,020] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,025] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,028] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,032] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,035] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,038] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,042] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,045] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,048] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,054] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,058] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,061] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,065] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,069] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,072] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,075] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,079] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,082] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,085] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-12-23 22:47:15,088] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,092] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,095] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,098] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,101] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,105] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,108] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,111] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,115] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:15,118] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:23,919] multiqc.modules.fastqc.fastqc [INFO ] Found 244 reports [2017-12-23 22:47:39,780] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HW32WAFXX/merged',) [2017-12-23 22:47:40,114] multiqc [INFO ] Compressing plot data [2017-12-23 22:47:40,114] multiqc [INFO ] Report : multiqc_report.html [2017-12-23 22:47:40,140] multiqc [INFO ] Data : multiqc_data [2017-12-23 22:47:40,140] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,171] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,187] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,196] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,216] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,222] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,227] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,281] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,285] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,289] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,294] multiqc [DEBUG ] Moving data file from '/tmp/tmpwykvwavi/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW32WAFXX/merged/multiqc_data' [2017-12-23 22:47:40,519] multiqc [INFO ] MultiQC complete