[maker-devel] failing contigs

[Daniel Ence]

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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