On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo <raram...@tamu.edu> wrote:
> On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock <p.j.a.c...@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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to