[AMOS-help] Question about amosvalidate (IID does not exist in bank)

[Florence M. <flo...@u-...>]

Hello everyone,

I have a question that will probably seems naive : does amosvalidate support 
bank assemblies with mate-pair AND single end reads?
I ask that because I'm encountering some problems with amosvalidate : it 
stops at the step 330 with the following error message :

!!! 2011-06-23 11:13:05  Doing step 330
!!! 2011-06-23 11:13:05  Running: ./amos-3.0.0/bin/cestat-cov -i -f 4 
out2.bnk > out2.ce.feat
Opening out2.bnk... [5.03s]
Indexing Contigs   ERROR in openBank():
WHAT: IID '4463371' does not exist in bank
LINE: 594
FILE: Bank_AMOS.cc
Processing contigs... Loading mates ..FATAL: IID '4463371' does not exist in 
bank
  there has been a fatal error, abort
!!! 2011-06-23 11:13:10  Command: ./amos-3.0.0/bin/cestat-cov -i -f 4 
out2.bnk > out2.ce.feat exited with status: 1
!!! END - Elapsed time: 0d 0h 1m 59s

In other case, I thought it can be because this read hasn't been aligned to 
the assembly so amosvalidate can't find it... In this case, how can I do to 
run amosvalidate entirely?

Thank you in advance for your help.

Best regards,

Florence Maurier