Error during cablastp about cablastp HOT 5 CLOSED

I believe this relates to using the subject flag to specify a fasta file to search rather than using makeblastdb and creating a binary database.

I've meant for a while to make this change in cablastp-search (I already made it in cablastp-deltasearch and cablastp-psisearch). I'll try to push a fix tomorrow.

On Nov 14, 2013, at 5:07 PM, nsarode [email protected] wrote:

Here is another one for ya.

Not sure if the real error is "signal: bus error (core dumped)" or "stderr: num_threads' is currently ignored when 'subject' is specified."

Blasting query on coarse database...
blastp -db /blast_databases/cablastp_database/capblastp-cogs_db_aa/blastdb-coarse -num_threads 9 -outfmt 5 -dbsize 47558392
Decompressing blast hits...
Blasting query on fine database...
blastp -subject /tmp/cablastp-fine-fasta604138705 -dbsize 47558392 -num_threads 9 -max_target_seqs 10 -out /blastoutput/stn_ALL_prodigal.prot_2.blast -outfmt 6 qseqid sseqid pident qcovs length mismatch qstart qend sstart send evalue bitscore
Error blasting fine database: Error running 'blastp -subject /tmp/cablastp-fine-fasta604138705 -dbsize 47558392 -num_threads 9 -max_target_seqs 10 -out /blastoutput/stn_ALL_prodigal.prot_2.blast -outfmt 6 qseqid sseqid pident qcovs length mismatch qstart qend sstart send evalue bitscore': 'signal: bus error (core dumped)'.

stderr:
'num_threads' is currently ignored when 'subject' is specified.

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Hi Noah,
Could you confirm if you did manage to make this change ?

Thanks
Neha

from cablastp.

I haven't yet, but that's actually unrelated to the issue you were having, which is why I sidelined it. The issue is one of relative paths, which I believe Andrew (BurntSushi) figured out. We will try to get both of these taken care of soon.

from cablastp.

Thanks for letting me know.
The relative path issue that you mentioned, is it the one where I need to run the blastp search from the database directory ? Because I was doing it this time when I got the same error. But if you are talking about something else, then I will just wait for the update.

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I have pushed what hopefully fixes the 'subject' issue for you. This does not yet solve the need to run the search from the database directory.

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