search

TheSEED / RASTtk-Distribution

KBase distribution module for RASTtk.
http://www.nature.com/articles/srep08365
13 stars 6 forks source link

problem with genomeTO_to_feature_data #3

Closed jotech closed 7 years ago

jotech commented 7 years ago

Hi, after creating my genome gto file (fasta) and using the rastk annotation, I would like have a look on the features:

rast-create-genome --scientific-name "Ochrobactrum sp." --genetic-code 11 --domain Bacteria --contigs /home/jo/rast/MYb71.fasta > out.gto
rast-process-genome < out.gto > out.gto2
genomeTO_to_feature_data < out.gto2 > features

But the genomeTO_to_feature_data leads to the following error:

JSONRPC error:
[genome.zip](https://github.com/TheSEED/RASTtk-Distribution/files/1404989/genome.zip)

Can't use an undefined value as an ARRAY reference
JSONRPC error code: -32603
JSONRPC error data:Can't use an undefined value as an ARRAY reference at /disks/kb/deployment/lib/Bio/KBase/GenomeAnnotation/GenomeAnnotationImpl.pm line 5127.

Trace begun at /usr/share/rasttk/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm line 4237
Bio::KBase::GenomeAnnotation::Client::genomeTO_to_feature_data('Bio::KBase::GenomeAnnotation::Client=HASH(0x55ae6c3817c0)', 'HASH(0x55ae6c390980)') called at /usr/share/rasttk/deployment/plbin/genomeTO_to_feature_data.pl line 99

If I'm using out.gto instead of out.gto2, then no error occur but the file features is empty afterwards. What's going wrong?

olsonanl commented 7 years ago

Hi - there's a bug on the server side. I've fixed and will redeploy this afternoon.

olsonanl commented 7 years ago

OK, this should be working properly now.

jotech commented 7 years ago

Hi, it is working now, thank you!