[maker-devel] maker crash - indexing fasta?

[Yannick Wurm]

Hi Carson,

upgrading to perl 5.10.1 and bioperl 1.6 did not do the trick, even with the '-f' option.
(all this is on a 64 bit linux machine)

It would thus be great if you could share the prerelease maker 2...

thank you very much,

Yannick




On 17 Mar 2010, at 18:48, Carson Holt wrote:

> Sorry about the late reply, my mail filters had apparently filtered out this message.  There are two things to check right away.  First make sure you have BioPerl version 1.6 installed.  Indexing errors can occur on version 1.5.  Also rerun your test with the –f option.  The –f option will force MAKER to completely destroy and rebuild old indexes and blast reports before running.  If both of those fail, I can give you pre-release access to MAKER 2.0 which has much more robust indexing of fasta files.
> 
> Carson
> 
> 
> On 3/14/10 12:43 PM, "Yannick Wurm" <yannick.wurm at unil.ch> wrote:
> 
> Hello,
> 
> I'm trying to get maker to work locally.
> The test data seems to run correctly.
> So then I try running it on my data.
> I have a single 2.8mb scaffold in a fasta file.
> I provide a fasta of all ESTs for our organism, and a fasta of uniprot proteins that hit the scaffold.
> 
> 
> The run fails with the following message:
> /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_gnE.scaf
> fold02061_datastore/Si_gnE.scaffold02061/theVoid.Si_gnE.scaffold02061/Si_gnE.scaffold02061.0.Si_gnE.scaffold02061.Bx.sp_al
> l.prots.blastx
> deleted:0 hits
> cleaning blastx...
>  in cluster:shadow cluster...
>     i_size:7 j_size:1
>  sorting hits in shadow cluster...
> ... finished.
>  i_size:7   current i:0
>  i_size:7   current i:1
>  i_size:7   current i:2
>  i_size:7   current i:3
>  i_size:7   current i:4
>  i_size:7   current i:5
>  i_size:7   current i:6
>  in cluster:shadow cluster...
>     i_size:0 j_size:0
>  sorting hits in shadow cluster...
> ... finished.
> cleaning clusters....
> total clusters:1 now processing 0
>  ...processing 0 of 7
>  ...processing 1 of 7
>  ...processing 2 of 7
>  ...processing 3 of 7
>  ...processing 4 of 7
>  ...processing 5 of 7
> 
> WARNING: Cannot find> sp|O00267|SPT5H_HUMAN, trying to re-index the fasta.
> stop here:sp|O00267|SPT5H_HUMAN
> #----------------------
> FATAL: failed!!
> #----------------------
> ERROR: Fasta index error
> 
> ERROR: Failed while doing exonerate of proteins!!
> 
> ERROR: Chunk failed at level 14
> !!
> FAILED CONTIG:Si_gnE.scaffold02061
> 
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> #---------------------------------------------------------------------
> The contig failed 2 time!!
> Maker will not try again!!
> The contig will be stored in a fasta file that you can use for debugging.
> SeqID: Si_gnE.scaffold02061
> Length: 2869475
> FASTA: /sfs1/home/frt/ywurm/assemblyValidation/results/2010-03-12/gp9scaffold/maker/Si_gnE.scaffold02061.maker.output/Si_g
> nE.scaffold02061_datastore/Si_gnE.scaffold02061/Si_gnE.scaffold02061.died.fasta
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> :
> 
> I've attached some log files and runinfo in the zip.
> 



--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html


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