grabherrgroup / kraken Goto Github PK

Hi,

this is not per-se a bug, but the newly introduced option "-f" is actually non-optional. Kraken simply won't do anything without setting this. This is from the most recent commit at the time of writing this.

From the description, this is not entirely clear. And maybe this is also not a good thing since it assumes that the user knows all the feature types that should be mapped (there are quite a few in the GFF ontology). At minimum, this is tedious if I simply want to map everything.

Maybe this can be made truly optional so that Kraken will lift everything, unless a user sets "-f".

Cheers,
Marc

Hi gang,

tried Kraken again after a little while. Compiled on a Centos6 host, everything seemed fine.
Running the example included with the code base as well as my own data produces an empty mapped.gtf. Log output reads:

cat application.log
- 08:53:32.092 INFO: Running GTF transfer
- 08:53:33.246 INFO: Done - writing GTF output

Any ideas? I first thought something was wrong with my Satsuma file or input GTF, but since the example data fails as well...