Formatdb Return Code 1

Question

[User 0437]

I am using a program that itself uses formatdb to create a blast database. For two of my input databases, the program runs fine. For one of my input databases, i get this formatdb return code, and formatdb fails to create a blastable database.

System call "formatdb -p F -t iBOLphase1.0sap -i iBOLphase1.0sap.fasta" return code 1

Would anyone know what return code 1 signifies? Any clue would help me find whatever it is in the database that is preventing completion.

Thanks

doug

[Jan Kosinski]

what error do you get if you run "formatdb -p F -t iBOL_phase1.0_sap -i iBOL_phase1.0_sap.fasta"" outside the program, directly from shell? what can you see if you add "strace" command before "formatdb" (I mean "strace formatdb -p ...")

[Michael Schubert]

Additionally check if you FASTA file is valid, that's the most common error.

Answer 1

[Hamish]

An exit code of 1 (in fact any non-zero value) indicates that an error occurred. The case of formatdb an more useful error message will likely have been output to standard error and to the log file generated by the program (format.log). The error message will contain more information about the nature of the problem.

As Michael says the most likely cause of a formatdb failure is an input formatting problem, so check that the data is in the fasta sequence format and does not contain any control characters ('cat -v file.fasta').