BFAST index error

kursuni · 09-26-2011, 06:57 PM

I have a fasta file and am trying to index it after creating reference genome.
the command I used is as follows:

$ bfast index chr1.fa

and the error is:

************************************************************
Checking input parameters supplied by the user ...
************************************************************
In function "BfastIndexValidateInputs": Fatal Error[IllegalFileName]. Variable/Value: fastaFileName.
Message: Required command line argument.
***** Exiting due to errors *****
************************************************************

What would I be doing wrong ?

sdvie · 09-27-2011, 01:39 AM

Generating indices for bfast is quite complex, and the bfast index command requires several input arguments apart from the fasta file of the reference to be indexed.

Check the manual "bfast-book.pdf" (included in the bfast package, in my version it is under bfast+bwa-0.6.4e/share/doc/bfast+bwa) that explains very well what you have to do.

Cheers,
Sophia

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09-26-2011, 06:57 PM	#1
kursuni Member Location: Hoboken, NJ Join Date: May 2011 Posts: 15	BFAST index error I have a fasta file and am trying to index it after creating reference genome. the command I used is as follows: $ bfast index chr1.fa and the error is: ********************************************************** Checking input parameters supplied by the user ... ******************************************************** In function "BfastIndexValidateInputs": Fatal Error[IllegalFileName]. Variable/Value: fastaFileName. Message: Required command line argument. * Exiting due to errors * ********************************************************** What would I be doing wrong ?

09-27-2011, 01:39 AM	#2
sdvie Member Location: Spain Join Date: Jul 2010 Posts: 68	Generating indices for bfast is quite complex, and the bfast index command requires several input arguments apart from the fasta file of the reference to be indexed. Check the manual "bfast-book.pdf" (included in the bfast package, in my version it is under bfast+bwa-0.6.4e/share/doc/bfast+bwa) that explains very well what you have to do. Cheers, Sophia