[maker-devel] Most scaffolds fail with BadParameter error, Maker on TACC Lonestar

[Card, Daren C]

Hello,

I’ve tried to run Maker on TACC Lonestar (4, trying to squeeze some last things in before deprecation), but I haven’t had much success. I get Maker to run, but only 28 proteins/transcripts are annotated and most scaffolds fail to finish properly, according to the …master_datastore_index.log. In my STDERR, I see a consistent error show up for many scaffolds:

------------- EXCEPTION: Bio::Root::BadParameter -------------
MSG: ' 7.5' is not a valid score
VALUE:  7.5
STACK: Error::throw
STACK: Bio::Root::Root::throw /opt/apps/maker/2.30/bin/../perl/lib/Bio/Root/Root.pm:486
STACK: Bio::SeqFeature::Generic::score /opt/apps/maker/2.30/bin/../perl/lib/Bio/SeqFeature/Generic.pm:468
STACK: GFFDB::_ary_to_features /opt/apps/maker/2.30/bin/../lib/GFFDB.pm:891
STACK: GFFDB::phathits_on_chunk /opt/apps/maker/2.30/bin/../lib/GFFDB.pm:534
STACK: Process::MpiChunk::_go /opt/apps/maker/2.30/bin/../lib/Process/MpiChunk.pm:756
STACK: Process::MpiChunk::run /opt/apps/maker/2.30/bin/../lib/Process/MpiChunk.pm:341
STACK: main::node_thread /opt/apps/maker/2.30/bin/maker:1433
STACK: threads::new /opt/apps/maker/2.30/bin/../perl/lib/forks.pm:799
STACK: /opt/apps/maker/2.30/bin/maker:901
--------------------------------------------------------------
--> rank=18, hostname=c304-113.ls4.tacc.utexas.edu
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:scaffold279|size418813

The ‘7.5’ value can vary between errors, but other than that and the scaffold ID, the rest of the error message is the same. I obviously don’t have the expertise to diagnose the issue here, but I’m hoping someone can help me sort this out.

A quick, unrelated question, is whether the Yandell lab (or anyone else) has a script that will produce a CDS file (multi-FASTA file) from a GFF annotation and FASTA genome sequence. I’m trying to produce a CDS from some NCBI genomes (annoying that it isn’t already included from NCBI), but the script I produced to do this is giving some suspect results. I figured if anyone had a well-tested script for this purpose, it would be someone on this list.

Best,
Daren


Daren Card
Ph.D. Candidate
Castoe Lab
University of Texas at Arlington
dcard at uta.edu
www.darencard.net