[2018-09-11 15:39:45,452] 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 15:39:45,452] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/samwhite/.multiqc_config.yaml [2018-09-11 15:39:45,452] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-09-11 15:39:45,453] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/bin/multiqc . [2018-09-11 15:39:45,453] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-09-11 15:39:45,453] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-09-11 15:39:45,453] multiqc [DEBUG ] Command : /gscratch/srlab/programs/bin/multiqc . [2018-09-11 15:39:45,453] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore [2018-09-11 15:39:45,453] multiqc [INFO ] Template : default [2018-09-11 15:39:45,453] multiqc [INFO ] Searching '.' [2018-09-11 15:39:45,453] 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 15:39:45,453] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp9I76tg [2018-09-11 15:39:45,461] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_CAGATC_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,461] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_GCCAAT_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_TTAGGC_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_TGACCA_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_ACAGTG_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8_ACTTGA_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_CGATGT_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_ATCACG_L001_R1_001_trimmed.fq.gz [2018-09-11 15:39:45,708] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2018-09-11 15:39:45,712] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,714] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,716] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-09-11 15:39:45,719] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,727] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2018-09-11 15:39:45,729] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,742] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,744] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,747] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2018-09-11 15:39:45,750] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2018-09-11 15:39:45,754] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,757] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,761] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,764] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,784] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,787] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2018-09-11 15:39:45,790] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2018-09-11 15:39:45,798] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,802] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,806] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,808] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2018-09-11 15:39:45,811] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2018-09-11 15:39:45,814] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,826] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-09-11 15:39:45,828] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,831] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,834] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,838] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,851] multiqc.modules.cutadapt.cutadapt [INFO ] Found 8 reports [2018-09-11 15:39:45,858] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2018-09-11 15:39:45,861] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2018-09-11 15:39:45,863] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,866] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,869] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2018-09-11 15:39:45,870] multiqc [INFO ] Report : multiqc_report.html [2018-09-11 15:39:45,871] multiqc [INFO ] Data : multiqc_data [2018-09-11 15:39:45,871] multiqc [DEBUG ] Moving data file from '/tmp/tmp9I76tg/multiqc_data/multiqc_cutadapt.txt' to '/gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/multiqc_data' [2018-09-11 15:39:45,872] multiqc [DEBUG ] Moving data file from '/tmp/tmp9I76tg/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/multiqc_data' [2018-09-11 15:39:45,873] multiqc [DEBUG ] Moving data file from '/tmp/tmp9I76tg/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/multiqc_data' [2018-09-11 15:39:45,956] multiqc [INFO ] MultiQC complete