Question: Error While Running Forge (Snap-Hmm) To Generate Prameters
0
gravatar for arnstrm
4.6 years ago by
arnstrm1.7k
Ames, IA
arnstrm1.7k wrote:

Hello all,

I am using maker2 to annotate the genome. For gene prediction, I am trying to use snap-hmm. While training snap, to generate parameters file I used the command

forge export.ann export.dna

and I received the following error:

ZOE ERROR (from forge): impossible error7
ZOE library version 2013-02-16

I can't figure out what this error means. I couldn't find anything in maker-devel discussion group either. If anyone can help me, I greatly appreciate the help.

Thanks very much and have a great weekend!

training • 2.3k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by arnstrm1.7k
4
gravatar for arnstrm
4.6 years ago by
arnstrm1.7k
Ames, IA
arnstrm1.7k wrote:

I contacted the author and here is the work around for this problem. In short, I have to follow these commands to reach the error (forge step)

$ gff3_merge -d genome_master_datastore_index.log -g
$ mkdir snap_training
$ mv genome.all.gff ./snap_training/
$ cd snap_training/ 
$ maker2zff -n genome.all.gff
$ fathom -validate genome.ann genome.dna
# prints to stdout after validation, several pages long.
$ fathom -gene-stats genome.ann genome.dna
  1365 sequences
  0.413186 avg GC fraction (min=0.339882 max=0.666334)
  24265 genes (plus=12222 minus=12043)
  4313 (0.177746) single-exon
  19952 (0.822254) multi-exon
  181.480927 mean exon (min=1 max=11937)
  792.193176 mean intron (min=30 max=48985)
 $ fathom -categorize 1000 genome.ann genome.dna
 $ fathom -export 1000 uni.ann uni.dna
 $ mkdir parameters
 $ cd parameters
 $ forge ../export.ann ../export.dna
   ZOE ERROR (from forge): impossible error7
   ZOE library version 2013-02-16

If your models have a lot of errors, then the step fathom -export 1000 uni.ann uni.dna will ignore only upto 1000 errors. To ignore more that that, you need to specify the option -export 1000 -plus. this will solve the problem. So use:

 $ fathom -export 1000 -plus uni.ann uni.dna
ADD COMMENTlink written 4.6 years ago by arnstrm1.7k

your answer saved my time. Thank you!

ADD REPLYlink written 2.9 years ago by Prakki Rama2.2k
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