[maker-devel] Fwd: [Lab] maker question

[Barry Moore]

I think this thread accidentally got moved to the lab mailing list, so  
I'm forwarding it back to the maker mailing list.

Barry

Begin forwarded message:

> From: cwilks <cwilks at stanford.edu>
> Date: October 7, 2009 10:13:16 PM MDT
> To: Carson Holt <carson.holt at genetics.utah.edu>, "lab at yandell- 
> lab.org" <lab at yandell-lab.org>
> Subject: Re: [Lab] maker question
>
> Hi Carson,
>
> Thanks for the quick response.  We're definitely using Bioperl 1.6  
> (we followed the quick 'n dirty instructions in the maker readme).   
> As for the maker version, we downloaded the 001 version, which  
> appears to be still the current one, however, the one I just  
> downloaded (after I got your email) appears to be [slightly?]  
> different, so I'm currently re-running the data I referred to below  
> again with that one.  I'll let you know if and when it finishes.
>
> Thanks again,
> Chris
>
> ----- Original Message -----
> From: Carson Holt
> To: cwilks ; lab at yandell-lab.org
> Sent: Wednesday, October 07, 2009 11:28 AM
> Subject: Re: maker question
>
> Could you check two things for me.  First, make sure your using  
> BioPerl 1.6 and not 1.5.  MAKER fails with 1.5.  Second make sure  
> you have the most recent version of MAKER downloaded and installed  
> from our lab website ( http://www.yandell-lab.org ).  I’ll take a  
> look at the data in the ftp link you sent.
>
> Thanks,
> Carson
>
>
> On 10/6/09 7:37 PM, "cwilks" <cwilks at stanford.edu> wrote:
>
> Hi Carson,
>
> We're attempting to use Maker to possibly supplement our annotation
> process here at The Arabipdopsis Information resource (TAIR) and we've
> run into an issue and hoping you might be able to help us out.
>
> We've got some files (shown below, they're accessible if you want to  
> run
> them yourself), which are partial versions of our chromosome 2
> annotation (they're partial because we tried on the whole chromosome
> first and that failed as well).  We keep getting the error shown  
> below,
> although when we tried it on a very small (<=10,000 bps) start  
> region of
> chromosome 2, it worked, but when we tried ~half of chromosome 2 we  
> got
> the same error as doing the whole thing.
>
> Let me know if you need anything else, we would be grateful for any  
> help
> you can offer.
>
> Thanks,
> Chris Wilks
> TAIR
>
>
> ftp://ftp.arabidopsis.org/home/tair/User_Requests/maker:
>
> Three files:
> ATH2_partial2.fas = contig file (1)
> tair9w.cdnas.chr2.txt.fas.partial2 = est file
> tair9w.proteins.chr2.txt.fas.partial2 = protein seq file
>
>
> tail end of the STDOUT of the maker run on those files.
>
> Choosing best annotations
> re reading blast report.
> /var/opt/oracle/short_reads/maker_arab_test/ 
> ATH2_partial2.maker.output/ATH2_partial2_datastore/Chr2/theVoid.Chr2/ 
> Chr2.67.tair9w.cdnas.chr2.txt.fas.partial2.blastn
> deleted:8 hits
> re reading blast report.
> /var/opt/oracle/short_reads/maker_arab_test/ 
> ATH2_partial2.maker.output/ATH2_partial2_datastore/Chr2/theVoid.Chr2/ 
> Chr2.67.tair9w.proteins.chr2.txt.fas.partial2.blastx
> deleted:0 hits
> merging blast reports...
> ...finished
> re-running blast against gi|17980420|gb|AF417474|AF417474...
> #----------------------
> FATAL: failed!!
> #----------------------
> Can't use string ("Chr2.6699345.6720856") as a HASH ref while "strict
> refs" in use
> ERROR: Failed while processing the chunk divide!!
>
> ERROR: Chunk failed at level 13
>
>
>
>
> --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: Chr2
> Length: 9874921
> FASTA:
> /var/opt/oracle/short_reads/maker_arab_test/ 
> ATH2_partial2.maker.output/ATH2_partial2_datastore/Chr2/ 
> Chr2.died.fasta
> #---------------------------------------------------------------------
>
>
> _______________________________________________
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> Lab at yandell-lab.org
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