Problem running RepeatModeler (using WUBlast)

[najoshi]

Hi all,

I am trying to run RepeatModeler on a fasta file that has about 415000 reads. What is strange is that the program runs through 4 rounds with no problem, but then in the 5th round I get this error for every time the WUBlast search engine is called:

WUBlastSearchEngine::search: FATAL: Missing or invalid slice specified with "dbslice" option.

This, in turn, causes RECON to fail and the whole thing dies. I tried running it with just 20000 of the reads, and it ran just fine. Is there a limit to the number of reads that can be used? Or if there is some malformed read in the fasta file, would that cause a WUBlast
error? Any help would be highly appreciated. Thanks!

- Nik.

--
Nikhil Joshi
Bioinformatics Programmer
UC Davis Genome Center
University of California, Davis
Davis, CA
http://bioinformatics.ucdavis.edu

[byou678]

Please help

When I do RNAseq Quality Trimmming using 'Trim.pl' scripts in Terminal, these Options appear:

--type <num> 0=standard trimming, 1=adaptive trimming, 2=windowed adaptive trimming. Default 0

--qual-threshold <num> quality threshold for trimming, default 20
-- length-threshold <num> length threshold for trimming, default 20
... ...

Could you explain the differences of 0=standard trimming, 1=adaptive trimming, 2=windowed adaptive trimming? and the criteria about setting length-threshold??

Thanks a lot in advance. Sorry for bother you but I need the help.