[2017-04-12 13:23:54,690] multiqc [DEBUG ] No MultiQC config found: /opt/local/tubo/env/python3/lib/python3.4/site-packages/multiqc_config.yaml [2017-04-12 13:23:54,691] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2017-04-12 13:23:54,693] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-04-12 13:23:54,693] multiqc [DEBUG ] Command used: /opt/local/tubo/env/python3/bin/multiqc /home/mk5636/fastqc-delivery/000000000-ATLLR/1 [2017-04-12 13:23:57,302] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2017-04-12 13:23:57,302] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-04-12 13:23:57,302] multiqc [DEBUG ] Command : /opt/local/tubo/env/python3/bin/multiqc /home/mk5636/fastqc-delivery/000000000-ATLLR/1 [2017-04-12 13:23:57,302] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1 [2017-04-12 13:23:57,302] multiqc [INFO ] Template : default [2017-04-12 13:23:57,304] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/000000000-ATLLR/1' [2017-04-12 13:23:57,304] multiqc [DEBUG ] Analysing modules: rna_seqc, custom_content, peddy, methylQA, qualimap, preseq, quast, rseqc, busco, goleft_indexcov, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, bismark, hicup, salmon, kallisto, slamdunk, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc, clusterflow [2017-04-12 13:23:57,304] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp119k1gga [2017-04-12 13:23:58,467] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:23:58,548] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2017-04-12 13:23:58,741] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:23:58,789] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:23:58,799] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-04-12 13:23:59,022] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:02,148] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:02,200] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:04,403] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:04,453] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:04,554] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:05,072] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:05,543] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:06,030] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:06,503] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:06,551] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:11,343] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:11,391] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:11,847] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:13,321] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:13,796] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:14,019] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:14,066] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:14,160] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:14,822] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:17,704] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-04-12 13:24:17,800] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:17,849] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:18,332] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:18,809] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:19,278] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:19,769] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:20,244] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:20,292] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:23,251] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2017-04-12 13:24:41,149] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/000000000-ATLLR/1',) [2017-04-12 13:24:41,490] multiqc [INFO ] Report : multiqc_report.html [2017-04-12 13:24:41,493] multiqc [INFO ] Data : multiqc_data [2017-04-12 13:24:41,493] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,504] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,510] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,521] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,531] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,541] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,550] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,556] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,562] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,570] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,576] multiqc [DEBUG ] Moving data file from '/tmp/tmp119k1gga/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/000000000-ATLLR/1/multiqc_data' [2017-04-12 13:24:41,959] multiqc [INFO ] MultiQC complete