[2018-08-03 10:19:38,710] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-08-03 10:19:38,710] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-08-03 10:19:38,711] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-08-03 10:19:38,721] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-08-03 10:19:38,721] 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']} [2018-08-03 10:19:38,721] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/H3VNWAFXY/merged [2018-08-03 10:19:39,066] multiqc [WARNING] MultiQC Version v1.5 now available! [2018-08-03 10:19:39,066] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-08-03 10:19:39,066] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -f -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/H3VNWAFXY/merged [2018-08-03 10:19:39,066] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged [2018-08-03 10:19:39,066] multiqc [INFO ] Template : default [2018-08-03 10:19:39,066] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-08-03 10:19:39,066] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/H3VNWAFXY/merged' [2018-08-03 10:19:39,066] 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 [2018-08-03 10:19:39,067] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp5q71dwqu [2018-08-03 10:19:48,721] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-08-03 10:19:48,804] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 96 samples (table) [2018-08-03 10:19:48,808] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,812] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,816] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-08-03 10:19:48,816] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,820] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,823] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,833] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,846] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,862] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,865] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,869] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,873] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,876] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,880] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,883] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,891] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,899] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,903] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,913] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,917] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,921] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,924] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,927] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,931] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,934] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-08-03 10:19:48,949] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,953] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,956] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,959] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,963] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,966] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,969] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,972] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,976] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:48,979] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:19:55,573] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2018-08-03 10:20:08,255] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/H3VNWAFXY/merged',) [2018-08-03 10:20:08,538] multiqc [INFO ] Compressing plot data [2018-08-03 10:20:08,539] multiqc [INFO ] Report : multiqc_report.html [2018-08-03 10:20:08,579] multiqc [INFO ] Data : multiqc_data [2018-08-03 10:20:08,579] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:08,592] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:08,619] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:08,754] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:08,759] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:08,790] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:09,056] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:09,060] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:09,063] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:09,066] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:09,070] multiqc [DEBUG ] Moving data file from '/tmp/tmp5q71dwqu/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3VNWAFXY/merged/multiqc_data' [2018-08-03 10:20:09,278] multiqc [INFO ] MultiQC complete