[2018-09-11 15:39:43,299] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python2.7/site-packages/multiqc-1.0.dev0-py2.7.egg/multiqc_config.yaml [2018-09-11 15:39:43,299] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/samwhite/.multiqc_config.yaml [2018-09-11 15:39:43,299] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-09-11 15:39:43,299] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/bin/multiqc . [2018-09-11 15:39:43,299] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-09-11 15:39:43,300] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-09-11 15:39:43,300] multiqc [DEBUG ] Command : /gscratch/srlab/programs/bin/multiqc . [2018-09-11 15:39:43,300] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimmed_fastqc [2018-09-11 15:39:43,300] multiqc [INFO ] Template : default [2018-09-11 15:39:43,300] multiqc [INFO ] Searching '.' [2018-09-11 15:39:43,300] multiqc [DEBUG ] Analysing modules: 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 [2018-09-11 15:39:43,300] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpMwIWHy [2018-09-11 15:39:43,616] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2018-09-11 15:39:43,622] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,626] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,628] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-09-11 15:39:43,634] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,675] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2018-09-11 15:39:43,678] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,761] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,764] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,769] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2018-09-11 15:39:43,790] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2018-09-11 15:39:43,811] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,832] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,853] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:43,856] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,028] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,031] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2018-09-11 15:39:44,048] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2018-09-11 15:39:44,096] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,112] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,118] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,121] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2018-09-11 15:39:44,124] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2018-09-11 15:39:44,141] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,232] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-09-11 15:39:44,236] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,238] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,255] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,271] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,288] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,305] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2018-09-11 15:39:44,321] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2018-09-11 15:39:44,324] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,700] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2018-09-11 15:39:44,828] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:44,829] multiqc [INFO ] Report : multiqc_report.html [2018-09-11 15:39:44,830] multiqc [INFO ] Data : multiqc_data [2018-09-11 15:39:44,831] multiqc [DEBUG ] Moving data file from '/tmp/tmpMwIWHy/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimmed_fastqc/multiqc_data' [2018-09-11 15:39:44,832] multiqc [DEBUG ] Moving data file from '/tmp/tmpMwIWHy/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimmed_fastqc/multiqc_data' [2018-09-11 15:39:44,833] multiqc [DEBUG ] Moving data file from '/tmp/tmpMwIWHy/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimmed_fastqc/multiqc_data' [2018-09-11 15:39:44,911] multiqc [INFO ] MultiQC complete