[BioC] NuPoP cannot recognize my fasta file

[Catherine [guest]]

Hi,
Thank you in advance for any help.
Here is my code and results
> writeXStringSet(DNAcutout1.seq, "DNAcutout2.fa", append=FALSE, compress=FALSE, compression_level=NA, format="fasta")
and when I read it, it looks fine
> readDNAStringSet(file="DNAcutout1.fa", format="fasta")
  A DNAStringSet instance of length 3615
       width seq                                        names               
   [1]   831 TTTCGGCTGTTTAAGAGTCT...CGTCCACTCGTGTGATAGG chr2L:27661:28491
   [2]   760 CCGCGCCAAGAACAACCGTT...AGTAATCATTACAAACTTT chr2L:28501:29260
   [3]   610 TTAATACATAATATGTATGC...AAGCTTTCGAGAAAAGAAT chr2L:66591:67200
   [4]   851 CCTCAAGCCCCCAAAATCCG...GGTCGAGCCTTGACGTTGA chr2L:90861:91711
   [5]   570 AACGTTCGAAAAAGTAACAT...CTAAACTATTCCAAGCATT chr2L:160751:161320
   ...   ... ...

but when I use the NuPoP, it has errors, and I have no idea what went wrong.
> library(NuPoP)
> predNuPoP("DNAcutout1.fa", species=5, model=4)
[1] "The input file is not in FASTA format, or contains characters other than A/a, C/c, G/g, T/t, N/n, stop!"
> 


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (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 
[7] methods   base     

other attached packages:
[1] NuPoP_1.14.1                          
[2] BSgenome.Dmelanogaster.UCSC.dm3_1.3.99
[3] BSgenome_1.32.0                       
[4] Biostrings_2.32.1                     
[5] XVector_0.4.0                         
[6] GenomicRanges_1.16.3                  
[7] GenomeInfoDb_1.0.2                    
[8] IRanges_1.22.10                       
[9] BiocGenerics_0.10.0                   
[10] BiocInstaller_1.14.2                  
[11] RSQLite_0.11.4                        
[12] DBI_0.2-7                             

loaded via a namespace (and not attached):
[1] bitops_1.0-6     Rsamtools_1.16.1 stats4_3.1.0    
[4] tools_3.1.0      zlibbioc_1.10.0 

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