[maker-devel] failing contigs

[Mikael Brandström Durling]

You are most likely right. When you mention that I remember that I stumbled across that particular problem in another analysis pipeline based on blast I wrote long ago. Interesting that such an arbitrary limit has not been lifted. 
Thanks for the hint. I will try mangling the fasta ids to something shorter. 
Mikael

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Sent from a crippled computer (a.k.a a phone)

22 feb 2013 kl. 22:40 skrev "Daniel Ence" <dence at genetics.utah.edu>:

> Hi Mikael, 
> 
> Sometimes really long fasta ID's (like the one in your example) cause blast to fail. I'm not super familiar with how short they need to be, but I know I've had this issue in the past. If you can try shortening the IDs, and then retry maker, I think that will solve your problem.
> 
> Thanks,
> Daniel
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ________________________________________
> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Mikael Brandström Durling [mikael.durling at slu.se]
> Sent: Friday, February 22, 2013 6:40 AM
> To: maker-devel at yandell-lab.org
> Subject: [maker-devel] failing contigs
> 
> Hi,
> 
> while at trying to find why things don't work for me, I have encountered another problem. Sometimes contigs fail with these lines found in the logs:
> 
> WARNING: Cannot find >0_0_CCPB1339.b1_CCOZ_CCPA_CCPB_CCPC_EXTA, trying to re-index the fasta.
> […]
> stop here:0_0_CCPB1339.b1_CCOZ_CCPA_CCPB_CCPC_EXTA
> doing blastx repeats
> ERROR: Failed while collecting blastn reports
> ERROR: Chunk failed at level:1, tier_type:3
> FAILED CONTIG:scaffold_01
> 
> polishig ESTs
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:scaffold_01
> 
> If I then grep for that specific EST in the fasta file, the sequence is there. Sometimes the issue is resolved by deleting the mpi_blastdb and restarting MAKER, sometimes not.
> 
> Mikael
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