Question: Error Reading Reference Genome Using Bfast
0
gravatar for Jordan
8.0 years ago by
Jordan1.2k
Pittsburgh
Jordan1.2k wrote:

Hi,

I'm getting an error while executing the following step in BFAST.

    bfast fasta2brg -f ~/Refs/human_hg19.fa

"************************************************************"

Checking input parameters supplied by the user ...

Validating fastaFileName /Refs/human_hg19.fa. 

"************************************************************"

In function "BfastFasta2BRGValidateInputs": Fatal Error[IllegalFileName]. Variable/Value: fastaFileName.

Message: Command line argument.

 *****Exiting due to errors *****

"************************************************************"

Does anyone why this occurs? Thanks!

reference • 1.6k views
ADD COMMENTlink modified 8.0 years ago • written 8.0 years ago by Jordan1.2k

expand the "~" to the full file-path.

ADD REPLYlink written 8.0 years ago by brentp23k
0
gravatar for Istvan Albert
8.0 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

I think the answer is pretty much that your file does not exist at the location that you specified or that it contains something else than what it should.

ADD COMMENTlink written 8.0 years ago by Istvan Albert ♦♦ 86k

I checked the path. It is pointing to the right file. And this same human reference file has been used for a different analysis. It never gave any errors before.

ADD REPLYlink written 8.0 years ago by Jordan1.2k
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