[Biopython] Local blast error on mac

[Anthony Underwood]

Thanks for the quick reply Peter. It's possible that the query file was opened to write the sequence to and then not closed (the code is on my work computer so I can not check right now). I will try changing this and report back.

Thanks again,

Anthony
On 29 Jan 2013, at 21:33, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Tue, Jan 29, 2013 at 9:20 PM, Anthony Underwood <email2ants at gmail.com> wrote:
>> Running local blast+ through biopython on a mac I get the following error
>> 
>> Traceback (most recent call last):
>> ...
>> Bio.Application.ApplicationError: Command '/usr/local/ncbi/blast/bin/blastp -out gene_id_blast_output.txt -outfmt 5 -query gene_id_sequences.fasta -db /Volumes/DataRAID/blast_databases/uniprot_sprot -evalue 0.001' returned non-zero exit status -11
> 
> See http://docs.python.org/2/library/subprocess.html
> "A negative value -N indicates that the child was terminated by signal
> N (Unix only)."
> 
> This means blastp died with signal 11, typically a segmentation fault.
> 
>> If I run the command on its own
>> 
>> "/usr/local/ncbi/blast/bin/blastp -out gene_id_blast_output.txt -outfmt 5 -query gene_id_sequences.fasta -db /Volumes/DataRAID/blast_databases/uniprot_sprot -evalue 0.001"
>> 
>> This runs fine and it produces XML output.
> 
> Very strange. There is nothing odd there with slashes, spaces or quotes
> (the usual suspects).
> 
> Is there anything else happening in the Python code which might
> interact with BLAST? For example changing directory, changing
> environment variables, or keeping a handle open to one of the files
> BLAST is using?
> 
> You can check that by writing a tiny Python script which just
> sets up the BLAST wrapper and exec
> 
> How long does it take to run outside Python? Is there enough time
> to monitor the task list when run via Python, and perhaps get some
> clue like tight memory or something?
> 
> Other than that, I'm not sure off hand what to suggest.
> 
> Peter