[maker-devel] failing contigs

[Mikael Brandström Durling]

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