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kingsfordgroup / sailfish

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
http://www.cs.cmu.edu/~ckingsf/software/sailfish
GNU General Public License v3.0
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Salmon beta #37

Closed blahah closed 10 years ago

blahah commented 10 years ago

I get the following error when running ./salmon index transcripts.fa with the binary provided in the download from the v1.0.1 release:

$ ./salmon index --transcripts opti.final.fa
Version Info: This is the most recent version

Exception : [boost::bad_any_cast: failed conversion using boost::any_cast]
./salmon index was invoked improperly.
For usage information, try ./salmon index --help
Exiting.

I'll build locally and see if the issue persists.

rob-p commented 10 years ago

Hi @Blahah: The problem is that you need to give it an output directory (where it should put the index). Can you try:

./salmon index --transcripts opti.final.fa -i salmonIndex

or some such and see if that works?

Thanks! Rob

P.S. I realize that boost::bad_any_cast is not an appropriate error message --- I'll go fix that in the source now ;P.

blahah commented 10 years ago

d'oh

rob-p commented 10 years ago

No worries. I just discovered the "required()" function call in Boost's program options. I'll start putting these where they are needed to provide more reasonable error messages!