#80 'Read of CDB_File failed' error from BsmlReader
When doing a large database load I get the following error message:
Read of CDB_File failed: Protocol error at /usr/local/projects/ergatis/package-devel/lib/perl5/BSML/BsmlReader.pm line 2054.
at /usr/local/projects/ergatis/package-devel/lib/perl5/BSML/BsmlParserSerialSearch.pm line 189
Usually this will kill several of the BSML parse steps but the vast majority will go through fine. I will need to rerun (perhaps twice) and all will eventually finish.
My understanding is that this is a problem with how the BSML modules index fasta files. Currently we are using a tied hash where the hash contains the headers of the fasta file as keys. (If I am reading this right in BsmlReader ~ line 2040.
It appears that there is some kind of race condition happening here where perhaps tie needs to get a lock on the cdb file. I have not confirmed this with an strace.
Discussion
