Dcas Tool - Has Anyone Been Successful At Getting It To Locate The Univec Database?

Question

[Susan Corbett]

I'm a newbie here, but I think I've done my homework and am still coming up short. When I run a core workflow (on Windows 7), I get the message "Can not find the UniVec database." The configuration asks for a location for the UniVec database, but not a specific filename. I've tried just UniVec as well as UniVec.fas and UniVec.fsa in multiple locations just in case it is ignoring my setting and looking for it in one of the other directories involved in the process. I uninstalled/re-installed and noticed that my settings remained intact then found that settings were kept in a .cas subdir of my user dir. I submitted a question to dCAS support a couple days ago, but have yet to receive a response.

Any thoughts would be greatly appreciated.

Answer 1

[Hamish]

In an effort to replicate your issue, and to have a look at the Desktop cDNA Annotation System (dCAS), I've installed dCAS based on the installation instructions on the web site.

1. I already have NCBI BLAST 2.2.25+ installed in C:Program FilesNCBIblast-2.2.25+. This used the installer based x86_64 (x64) version instead of the archive based distribution.

2. I downloaded the BLAST databases from http://exon.niaid.nih.gov/cas/dbsupport.jsp. I had a couple of problems with NR.ZIP due to it being >2GB but finally managed a complete download.

3. I unpacked the BLAST database ZIP files into F:scratchNCBI_BLAST_data. Note there are no spaces in this path, this was to avoid the issues described in "makeblastdb with whitespace in -out filename".

4. I installed CAP3 into my Cygwin home directory (I already had Cygwin installed), under '~/usr/'.

5. Installed dCAS 1.4.3.

6. Configured dCAS, with the following (note had to add BLAST databases before I could "Save" the configuration):

7. "Workspace": C:UsershamishDocumentsdCAS\
8. "Blast Home Directory": C:Program FilesNCBIblast-2.2.25+
9. "Cap3 Directory": G:cygwinhomehamishusrCAP3\
10. "UniVec Database": F:scratchNCBI_BLAST_dataunivec

11. "Blast Databases": added 'nr', 'go', 'kog', 'mit-pla', 'pfam', 'rrna' and 'smart'. These are recognised by dCAS and appropriate BLAST parameters suggested.

12. Downloaded the sample data and unpacked it under the "Workspace" directory.

13. Created a new "Core Workflow". Configured the various steps to use the sample data as the cDNA library and to run all the analysis with the default options.

14. Ran the workflow, which completed successfully and produced the Excel sheet summarising the results.

As far as I can see it all works, and there weren't any problems with finding the databases. However I was careful to avoid the possible issues caused by having file paths containing spaces when using NCBI BLAST, so it may be that this is your issue.