[2017-07-26 00:29:18,387] multiqc [DEBUG ] No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml [2017-07-26 00:29:18,387] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2017-07-26 00:29:18,388] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-07-26 00:29:18,401] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml [2017-07-26 00:29:18,401] 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']} [2017-07-26 00:29:18,401] multiqc [DEBUG ] Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HWFTLBGX2/merged [2017-07-26 00:29:19,318] multiqc [WARNING] MultiQC Version v1.1 now available! [2017-07-26 00:29:19,318] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-07-26 00:29:19,318] multiqc [DEBUG ] Command : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HWFTLBGX2/merged [2017-07-26 00:29:19,318] multiqc [DEBUG ] Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HWFTLBGX2/merged [2017-07-26 00:29:19,319] multiqc [INFO ] Template : default [2017-07-26 00:29:19,319] multiqc [INFO ] Searching '/home/mk5636/fastqc-delivery/HWFTLBGX2/merged' [2017-07-26 00:29:19,319] 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 [2017-07-26 00:29:19,320] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpjbj9662d [2017-07-26 00:29:20,919] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 12 samples (table) [2017-07-26 00:29:20,920] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2017-07-26 00:29:20,934] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:20,938] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:20,950] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-07-26 00:29:20,950] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:20,954] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:20,966] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:20,981] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:20,996] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,007] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,011] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,014] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,017] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,023] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,027] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,030] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,047] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,050] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,053] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,058] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,062] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,065] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,069] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,072] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,075] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,078] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-07-26 00:29:21,090] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,094] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,097] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,100] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,104] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,107] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,110] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,122] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,126] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:21,129] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:22,739] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2017-07-26 00:29:22,925] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/home/mk5636/fastqc-delivery/HWFTLBGX2/merged',) [2017-07-26 00:29:22,942] multiqc [INFO ] Compressing plot data [2017-07-26 00:29:23,187] multiqc [INFO ] Report : multiqc_report.html [2017-07-26 00:29:23,209] multiqc [INFO ] Data : multiqc_data [2017-07-26 00:29:23,209] multiqc [DEBUG ] Moving data file from '/tmp/tmpjbj9662d/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HWFTLBGX2/merged/multiqc_data' [2017-07-26 00:29:23,226] multiqc [DEBUG ] Moving data file from '/tmp/tmpjbj9662d/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HWFTLBGX2/merged/multiqc_data' [2017-07-26 00:29:23,233] multiqc [DEBUG ] Moving data file from '/tmp/tmpjbj9662d/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HWFTLBGX2/merged/multiqc_data' [2017-07-26 00:29:23,498] multiqc [INFO ] MultiQC complete