JSONRPC error on rast-process-genome

[mberacochea]

I'm having some issues with rast-process-genome. Any help is appreciated.

~> rast-process-genome < uyso24_contigs_ordered.gto > uyso24_contigs_ordered.gto2
JSONRPC error:
Error invoking method call_features_CDS_prodigal: error calling CDSs: 65280
on command rast_call_CDSs_using_prodigal --input /disks/tmp/i1fhSIPFq8 --output /disks/tmp/d1zqr_Thr0 --id-prefix fig|992418.8 --id-type peg
Use of uninitialized value in pattern match (m//) at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 52, <$in_fh> line 1.
Use of uninitialized value in concatenation (.) or string at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.
Invalid domain: "" at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.


JSONRPC error code: -32603
JSONRPC error data:Error invoking method call_features_CDS_prodigal: error calling CDSs: 65280
on command rast_call_CDSs_using_prodigal --input /disks/tmp/i1fhSIPFq8 --output /disks/tmp/d1zqr_Thr0 --id-prefix fig|992418.8 --id-type peg
Use of uninitialized value in pattern match (m//) at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 52, <$in_fh> line 1.
Use of uninitialized value in concatenation (.) or string at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.
Invalid domain: "" at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.




Trace begun at /Applications/RASTtk.app/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm line 20857
Bio::KBase::GenomeAnnotation::Client::run_pipeline('Bio::KBase::GenomeAnnotation::Client=HASH(0x7bc23780)', 'HASH(0x7bc30cd0)', 'HASH(0x7bc30de0)') called at /Applications/RASTtk.app/deployment/plbin/rast-process-genome.pl line 142

[fireornight]

hey, I'm having the same problem. Did you figure a way to solve it? Thanks.

[mberacochea]

It just started to work a few days later, I didn't change anything.

[olsonanl]

I'd be interested to see if you run into the same problems running the genome through the PATRIC genome annotation service; this uses the same RASTtk backend as the command line tools but leaves more tracing information in place. It's at https://patricbrc.org. See http://docs.patricbrc.org/tutorial/genome_annotation/annotation.html for a tutorial on genome annotation.

How large are your input data files? They are not eukaryotic genomes, are they?

[fireornight]

@mberacochea Thanks. Hopeful it will be the same for my case.
@olsonanl The input data is only ~60kb and it is not eukaryotic genomes. I'll try partrcbrc. Thanks.

[olsonanl]

Is it plasmid or phage or something? It's possible prodigal didn't find anything.

[Antonior26]

Hey! I had the same problem, any news on this?

[olsonanl]

@Antonior26 - when did you have the problem? What sequence data did you give the service?