Hello list

rnaSeq <- easyRNASeq(filesDirectory=getwd(),
    filenames="accepted_hits.bam.bai",
    organism="Dmelanogaster",
    chr.sizes=as.list(seqlengths(Dmelanogaster)),
    readLength=36L,
    annotationMethod="gtf",
    annotationFile="/myrnaseqB/genes.gtf",
      format="bam", gapped=TRUE,
    count="exons",
    outputFormat="RNAseq")    

I keep getting this error:
Checking arguments... 
Error in easyRNASeq(filesDirectory = getwd(), filenames = "accepted_hits.bam.bai",  : 
  Index files (bai) are required. They are missing for the files: /myrnaseqB/C2_R2_thout/accepted_hits.bam.bai
  
even after 
> sortBam("accepted_hits.bam","accepted_hits") 
> indexBam(files="accepted_hits.bam")
> file.exists("/myrnaseqB/C2_R2_thout/accepted_hits.bam.bai")
[1] TRUE

Please help. I will not be able to upgrade or reinstall. IT dept does that on their schedule.

Silav
--------------------------------------------------------- 
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] easyRNASeq_1.2.5       ShortRead_1.14.4       latticeExtra_0.6-24    RColorBrewer_1.0-5    
 [5] lattice_0.20-10        Rsamtools_1.8.6        DESeq_1.8.3            locfit_1.5-8          
 [9] BSgenome_1.24.0        GenomicRanges_1.8.13   Biostrings_2.24.1      IRanges_1.14.4        
[13] edgeR_2.6.12           limma_3.12.3           biomaRt_2.12.0         Biobase_2.16.0        
[17] genomeIntervals_1.12.0 BiocGenerics_0.2.0     intervals_0.13.3      

loaded via a namespace (and not attached):
 [1] annotate_1.34.1      AnnotationDbi_1.18.4 bitops_1.0-4.2       DBI_0.2-5            genefilter_1.38.0   
 [6] geneplotter_1.34.0   grid_2.15.0          hwriter_1.3          RCurl_1.95-3         RSQLite_0.11.2      
[11] splines_2.15.0       stats4_2.15.0        survival_2.37-2      tools_2.15.0         XML_3.95-0.1        
[16] xtable_1.7-0         zlibbioc_1.2.0      
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