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 -- Sent via the guest posting facility at bioconductor.org.

Can you send me the DNA sequence file? so I can check into it. On 8/1/14, 4:35 PM, "Catherine [guest]" <guest at="" bioconductor.org=""> wrote: >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 > >-- >Sent via the guest posting facility at bioconductor.org.