I'm getting an error when running blastn against the nt database:
Error: (117.2) CThread::Wrapper: CThread::Main() failed
NCBI C++ Exception:
Error: (CSeqDBException::eArgErr) Sequence not returned.
The actual command line is
/export/ocbn/ncbi/blast/bin/blastn -query orf02468.fas -db /export/ocbn/ncbi/nt/nt -num_threads 64
This is run on a SUN SPARC box (Victoria Fall) with 16 cores and 128 threads.
Any help, appreciated.
•
written
by
Paulo Nuin
The first thing is to be certain that your sequences are in the proper format. I know this is obvious, but I have had some jobs fail because what I thought was FASTA format, for example, was not or not interpreted as such. Examples of sources ofthat error included the sequence getting appended to the def line, the def line beginning with >_ and the > at start of def line read as something else.
You've probably checked this already, but it is where I would begin.
•
written
by
Larry_Parnell
Just downloaded nt from NCBI and tried formatting the database on the same machine, the error still happens. Moving back to Wu-BLAST.
Log in to answer this question.
did you formatdb /export/ocbn/ncbi/nt/nt with the same distribution ? on the same machine ?
Database was downloaded from NCBI's ftp site already formatted. I donwloaded the FASTA file and will try with one formatted locally.