[2017-09-15 10:37:21,703] multiqc [DEBUG ] No MultiQC config found: /Users/sr320/anaconda/lib/python2.7/site-packages/multiqc-1.0.dev0-py2.7.egg/multiqc_config.yaml [2017-09-15 10:37:21,704] multiqc [DEBUG ] No MultiQC config found: /Users/sr320/.multiqc_config.yaml [2017-09-15 10:37:21,722] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-09-15 10:37:21,722] multiqc [DEBUG ] Command used: /Users/sr320/anaconda/bin/multiqc /Volumes/web/halfshell/working-directory/17-09-07/ [2017-09-15 10:37:21,723] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2017-09-15 10:37:21,723] multiqc [INFO ] This is MultiQC v1.0.dev0 [2017-09-15 10:37:21,723] multiqc [DEBUG ] Command : /Users/sr320/anaconda/bin/multiqc /Volumes/web/halfshell/working-directory/17-09-07/ [2017-09-15 10:37:21,723] multiqc [DEBUG ] Working dir : /Volumes/Alanine/wd/17-09-15 [2017-09-15 10:37:21,723] multiqc [INFO ] Template : default [2017-09-15 10:37:21,723] multiqc [INFO ] Searching '/Volumes/web/halfshell/working-directory/17-09-07/' [2017-09-15 10:37:21,723] 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 [2017-09-15 10:37:21,723] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmp4AH1d9 [2017-09-15 10:37:22,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R1_001.fastq.gz [2017-09-15 10:37:22,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R2_001.fastq.gz [2017-09-15 10:37:22,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R1_001.fastq.gz [2017-09-15 10:37:22,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R2_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R1_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R2_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R1_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R2_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R1_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R2_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R1_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R2_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R1_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R2_001.fastq.gz [2017-09-15 10:37:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R1_001.fastq.gz [2017-09-15 10:37:22,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R2_001.fastq.gz [2017-09-15 10:37:22,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R1_001.fastq.gz [2017-09-15 10:37:22,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R2_001.fastq.gz [2017-09-15 10:37:22,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R1_001.fastq.gz [2017-09-15 10:37:22,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R2_001.fastq.gz [2017-09-15 10:37:23,772] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2017-09-15 10:37:23,814] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:37:23,833] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:37:23,844] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-09-15 10:37:23,862] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:37:35,026] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:37:35,051] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:37:59,995] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:00,022] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:00,032] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:00,693] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:00,912] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:01,098] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:01,297] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:01,304] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:05,775] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:05,798] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:08,247] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:09,973] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:12,432] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:12,451] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:12,514] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:12,522] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:15,394] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:17,751] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-09-15 10:38:17,762] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:17,768] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:17,909] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:18,181] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:19,234] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:19,686] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:19,830] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:19,836] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:21,745] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2017-09-15 10:38:24,222] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/Volumes/web/halfshell/working-directory/17-09-07/',) [2017-09-15 10:38:24,225] multiqc [INFO ] Report : multiqc_report.html [2017-09-15 10:38:24,226] multiqc [INFO ] Data : multiqc_data [2017-09-15 10:38:24,226] multiqc [DEBUG ] Moving data file from '/var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmp4AH1d9/multiqc_data/multiqc_fastqc.txt' to '/Volumes/Alanine/wd/17-09-15/multiqc_data' [2017-09-15 10:38:24,226] multiqc [DEBUG ] Moving data file from '/var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmp4AH1d9/multiqc_data/multiqc_general_stats.txt' to '/Volumes/Alanine/wd/17-09-15/multiqc_data' [2017-09-15 10:38:24,227] multiqc [DEBUG ] Moving data file from '/var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmp4AH1d9/multiqc_data/multiqc_sources.txt' to '/Volumes/Alanine/wd/17-09-15/multiqc_data' [2017-09-15 10:38:24,505] multiqc [INFO ] MultiQC complete