On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I've seen that kind of error from NCBI BLAST+ before - do you know which of the BLAST tools was this, and what the query was?
The repo was: repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus
The query was: Output from velvetoptimiser /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser
OK, so this was a nucleotide FASTA file from an assembly, right?
Yes
What were you searching with BLAST? e.g. BLASTN against NT, BLASTX against NR, etc.
Search was blastn, task megablast of the assembly as query against an in-house made (and installed into galaxy) of a blastn database for Chromosomes 1 to 7 of Neurospora crassa Database was produced with: makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index and "installed" into the "blastdb.loc" file as required
Can you run this blastn search 'by hand' at the terminal? Does that crash too? The error sounds very similar to this report which turned out to be due to a corrupted BLAST database - so also try recreating your DB: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962 Peter