[maker-devel] maker crash - indexing fasta?

[Yannick Wurm]

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. 
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If any one has a suggestion on how to make things work.... Thanks!!

yannick





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