[2018-01-12 16:27:11,025] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2018-01-12 16:27:11,025] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2018-01-12 16:27:11,025] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-01-12 16:27:11,027] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2018-01-12 16:27:11,027] 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']} [2018-01-12 16:27:11,027] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2018-01-12 16:27:11,696] multiqc [WARNING] MultiQC Version v1.4 now available! [2018-01-12 16:27:11,697] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-01-12 16:27:11,697] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2018-01-12 16:27:11,697] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMYHGBBXX/5 [2018-01-12 16:27:11,697] multiqc [INFO ] Template : default [2018-01-12 16:27:11,697] multiqc [INFO ] Searching '.' [2018-01-12 16:27:11,698] 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 [2018-01-12 16:27:11,698] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpvb9ux2k4 [2018-01-12 16:27:13,533] multiqc.modules.custom_content.custom_content [INFO ] demux_report-5: Found 12 samples (table) [2018-01-12 16:27:13,534] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-01-12 16:27:13,537] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,540] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,544] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-01-12 16:27:13,544] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,546] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2018-01-12 16:27:13,549] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,552] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2018-01-12 16:27:13,556] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,558] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,561] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2018-01-12 16:27:13,564] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2018-01-12 16:27:13,566] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,569] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,572] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,574] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,579] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,582] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2018-01-12 16:27:13,584] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2018-01-12 16:27:13,588] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,591] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,593] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,596] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2018-01-12 16:27:13,598] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2018-01-12 16:27:13,601] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,604] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-01-12 16:27:13,606] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,609] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,612] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,614] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,617] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,619] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:13,622] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2018-01-12 16:27:13,625] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2018-01-12 16:27:13,627] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2018-01-12 16:27:13,630] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:14,290] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2018-01-12 16:27:14,662] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2018-01-12 16:27:14,698] multiqc [INFO ] Compressing plot data [2018-01-12 16:27:15,092] multiqc [INFO ] Report : multiqc_report.html [2018-01-12 16:27:15,120] multiqc [INFO ] Data : multiqc_data [2018-01-12 16:27:15,120] multiqc [DEBUG ] Moving data file from '/tmp/tmpvb9ux2k4/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMYHGBBXX/5/multiqc_data' [2018-01-12 16:27:15,159] multiqc [DEBUG ] Moving data file from '/tmp/tmpvb9ux2k4/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMYHGBBXX/5/multiqc_data' [2018-01-12 16:27:15,162] multiqc [DEBUG ] Moving data file from '/tmp/tmpvb9ux2k4/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMYHGBBXX/5/multiqc_data' [2018-01-12 16:27:15,286] multiqc [INFO ] MultiQC complete