[2018-03-14 08:38:30,748] multiqc [DEBUG ] No MultiQC config found: /Users/sr320/anaconda/lib/python2.7/site-packages/multiqc-1.0.dev0-py2.7.egg/multiqc_config.yaml [2018-03-14 08:38:30,748] multiqc [DEBUG ] No MultiQC config found: /Users/sr320/.multiqc_config.yaml [2018-03-14 08:38:30,748] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-03-14 08:38:30,748] multiqc [DEBUG ] Command used: /Users/sr320/anaconda/bin/multiqc . [2018-03-14 08:38:30,748] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-03-14 08:38:30,748] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-03-14 08:38:30,748] multiqc [DEBUG ] Command : /Users/sr320/anaconda/bin/multiqc . [2018-03-14 08:38:30,749] multiqc [DEBUG ] Working dir : /Volumes/Serine/wd/18-03-14 [2018-03-14 08:38:30,749] multiqc [INFO ] Template : default [2018-03-14 08:38:30,749] multiqc [INFO ] Searching '.' [2018-03-14 08:38:30,749] 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 [2018-03-14 08:38:30,749] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmpxRfBXW [2018-03-14 08:38:30,754] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: .DS_Store [2018-03-14 08:38:30,754] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 10_32_S32_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,754] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 10_32_S32_L001_R1_001.fastq.gz [2018-03-14 08:38:30,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 10_32_S32_L001_R2_001.fastq.gz [2018-03-14 08:38:30,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 11_37_S37_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 11_37_S37_L001_R1_001.fastq.gz [2018-03-14 08:38:30,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 11_37_S37_L001_R2_001.fastq.gz [2018-03-14 08:38:30,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12_38_S38_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12_38_S38_L001_R1_001.fastq.gz [2018-03-14 08:38:30,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12_38_S38_L001_R2_001.fastq.gz [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13_33_S33_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13_33_S33_L001_R1_001.fastq.gz [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13_33_S33_L001_R2_001.fastq.gz [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 14_34_S34_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 14_34_S34_L001_R1_001.fastq.gz [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 14_34_S34_L001_R2_001.fastq.gz [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 15_39_S39_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 15_39_S39_L001_R1_001.fastq.gz [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 15_39_S39_L001_R2_001.fastq.gz [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16_40_S40_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16_40_S40_L001_R1_001.fastq.gz [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16_40_S40_L001_R2_001.fastq.gz [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 17_9_S9_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 17_9_S9_L001_R1_001.fastq.gz [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 17_9_S9_L001_R2_001.fastq.gz [2018-03-14 08:38:30,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 18_10_S10_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 18_10_S10_L001_R1_001.fastq.gz [2018-03-14 08:38:30,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 18_10_S10_L001_R2_001.fastq.gz [2018-03-14 08:38:30,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19_7_S7_L001-bsmap_out_Cv3.sam [2018-03-14 08:38:30,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19_7_S7_L001_R1_001.fastq.gz [2018-03-14 08:38:30,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19_7_S7_L001_R2_001.fastq.gz [2018-03-14 08:38:30,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_25_S25_L001_R1_001.fastq.gz [2018-03-14 08:38:30,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_25_S25_L001_R2_001.fastq.gz [2018-03-14 08:38:30,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20_8_S8_L001_R1_001.fastq.gz [2018-03-14 08:38:30,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20_8_S8_L001_R2_001.fastq.gz [2018-03-14 08:38:30,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_26_S26_L001_R1_001.fastq.gz [2018-03-14 08:38:30,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_26_S26_L001_R2_001.fastq.gz [2018-03-14 08:38:30,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_27_S27_L001_R1_001.fastq.gz [2018-03-14 08:38:30,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_27_S27_L001_R2_001.fastq.gz [2018-03-14 08:38:30,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_28_S28_L001_R1_001.fastq.gz [2018-03-14 08:38:30,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_28_S28_L001_R2_001.fastq.gz [2018-03-14 08:38:30,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_35_S35_L001_R1_001.fastq.gz [2018-03-14 08:38:30,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_35_S35_L001_R2_001.fastq.gz [2018-03-14 08:38:30,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_36_S36_L001_R1_001.fastq.gz [2018-03-14 08:38:30,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_36_S36_L001_R2_001.fastq.gz [2018-03-14 08:38:30,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_29_S29_L001_R1_001.fastq.gz [2018-03-14 08:38:30,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_29_S29_L001_R2_001.fastq.gz [2018-03-14 08:38:30,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8_30_S30_L001_R2_001.fastq.gz [2018-03-14 08:38:30,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 9_31_S31_L001_R1_001.fastq.gz [2018-03-14 08:38:30,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 9_31_S31_L001_R2_001.fastq.gz [2018-03-14 08:38:30,768] multiqc [DEBUG ] Ignoring file as too large: GCA_002022765.4_C_virginica-3.0_genomic.fna [2018-03-14 08:38:30,768] multiqc [DEBUG ] Ignoring file as is encoded: GCA_002022765.4_C_virginica-3.0_genomic.fna.gz [2018-03-14 08:38:30,768] multiqc [DEBUG ] Ignoring file as too large: GCF_002022765.2_C_virginica-3.0_genomic.fna [2018-03-14 08:38:30,769] multiqc [DEBUG ] Ignoring file as is encoded: GCF_002022765.2_C_virginica-3.0_genomic.fna.gz [2018-03-14 08:38:31,624] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2018-03-14 08:38:31,649] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:31,659] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:31,664] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-03-14 08:38:31,697] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:31,809] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2018-03-14 08:38:31,825] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:32,283] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:32,300] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:32,314] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2018-03-14 08:38:32,413] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2018-03-14 08:38:32,512] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:32,610] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:32,714] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:32,731] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:33,659] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:33,667] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2018-03-14 08:38:33,758] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2018-03-14 08:38:34,040] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:34,130] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:34,161] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:34,170] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2018-03-14 08:38:34,183] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2018-03-14 08:38:34,273] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:34,789] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-03-14 08:38:34,811] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:34,819] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:34,906] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:34,991] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:35,076] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:35,161] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2018-03-14 08:38:35,245] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2018-03-14 08:38:35,253] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:36,697] multiqc.modules.fastqc.fastqc [INFO ] Found 39 reports [2018-03-14 08:38:39,812] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2018-03-14 08:38:39,816] multiqc [INFO ] Report : multiqc_report.html [2018-03-14 08:38:39,817] multiqc [INFO ] Data : multiqc_data [2018-03-14 08:38:39,817] multiqc [DEBUG ] Moving data file from '/var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmpxRfBXW/multiqc_data/multiqc_fastqc.txt' to '/Volumes/Serine/wd/18-03-14/multiqc_data' [2018-03-14 08:38:39,818] multiqc [DEBUG ] Moving data file from '/var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmpxRfBXW/multiqc_data/multiqc_general_stats.txt' to '/Volumes/Serine/wd/18-03-14/multiqc_data' [2018-03-14 08:38:39,818] multiqc [DEBUG ] Moving data file from '/var/folders/32/gn3lrlb11ds54r71vtpk47pm0000gn/T/tmpxRfBXW/multiqc_data/multiqc_sources.txt' to '/Volumes/Serine/wd/18-03-14/multiqc_data' [2018-03-14 08:38:40,095] multiqc [INFO ] MultiQC complete