[2017-04-30 22:14:03,305] multiqc [DEBUG ] No MultiQC config found: /opt/local/tubo/env/python3/lib/python3.4/site-packages/multiqc_config.yaml [2017-04-30 22:14:03,306] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2017-04-30 22:14:03,306] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-04-30 22:14:03,314] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-04-30 22:14:03,314] multiqc [DEBUG ] New config 'custom_content': {'order': ['run_stats', 'demux_report']} [2017-04-30 22:14:03,314] multiqc [DEBUG ] Command used: /opt/local/tubo/env/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-04-30 22:14:03,597] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-04-30 22:14:03,597] multiqc [DEBUG ] Command : /opt/local/tubo/env/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml . [2017-04-30 22:14:03,597] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5J5LBGX2/merged [2017-04-30 22:14:03,597] multiqc [INFO ] Template : default [2017-04-30 22:14:03,598] multiqc [INFO ] Searching '.' [2017-04-30 22:14:03,598] 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, sortmerna [2017-04-30 22:14:03,598] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpzcp3v50p [2017-04-30 22:14:04,458] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-04-30 22:14:04,503] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-04-30 22:14:04,507] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 1 samples (table) [2017-04-30 22:14:04,526] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,534] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,549] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-04-30 22:14:04,557] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,571] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-04-30 22:14:04,576] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,615] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,621] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,640] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-04-30 22:14:04,651] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-04-30 22:14:04,675] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,687] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,698] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,733] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,805] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,813] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-04-30 22:14:04,823] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-04-30 22:14:04,854] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,865] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,877] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,885] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-04-30 22:14:04,895] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-04-30 22:14:04,907] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,946] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-04-30 22:14:04,954] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,962] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,976] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,987] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:04,998] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:05,018] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-04-30 22:14:05,030] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-04-30 22:14:05,038] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:05,233] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports [2017-04-30 22:14:05,274] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-04-30 22:14:05,287] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-04-30 22:14:05,293] multiqc [INFO ] Report : multiqc_report.html [2017-04-30 22:14:05,294] multiqc [INFO ] Data : multiqc_data [2017-04-30 22:14:05,295] multiqc [DEBUG ] Moving data file from '/tmp/tmpzcp3v50p/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5J5LBGX2/merged/multiqc_data' [2017-04-30 22:14:05,301] multiqc [DEBUG ] Moving data file from '/tmp/tmpzcp3v50p/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5J5LBGX2/merged/multiqc_data' [2017-04-30 22:14:05,304] multiqc [DEBUG ] Moving data file from '/tmp/tmpzcp3v50p/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5J5LBGX2/merged/multiqc_data' [2017-04-30 22:14:05,541] multiqc [INFO ] MultiQC complete