[Biopython] Local blast error on mac

[Peter Cock]

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