[maker-devel] 2.27 and 2.28 incompatible

[Malcolm Hinsley]

To try to fix SQL lock file errors I installed 2.28 and made the mistake
of running on a directory made by 2.27 (to run snap and augustus for the
first time).

Every contig fails due to errors like:


------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't open file 04723bc0c22478764d90bbaebca96d23
STACK: Error::throw
STACK: Bio::Root::Root::throw
/nfs/panda/ensemblgenomes/external/bioperl/BioPerl-1.6.901//Bio/Root/Root.pm:472
STACK: Bio::DB::Fasta::fh
/nfs/panda/ensemblgenomes/external/bioperl/BioPerl-1.6.901//Bio/DB/Fasta.pm:948
STACK: Bio::DB::Fasta::subseq
/nfs/panda/ensemblgenomes/external/bioperl/BioPerl-1.6.901//Bio/DB/Fasta.pm:929
STACK: Bio::PrimarySeq::Fasta::seq
/nfs/panda/ensemblgenomes/external/bioperl/BioPerl-1.6.901//Bio/DB/Fasta.pm:1089
STACK: FastaSeq::seq
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/FastaSeq.pm:50
STACK: Process::MpiChunk::_go
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/Process/MpiChunk.pm:478
STACK: Process::MpiChunk::run
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/Process/MpiTiers.pm:286
STACK: /nfs/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/maker:667
-----------------------------------------------------------
--> rank=NA, hostname=ebi3-198.ebi.ac.uk
 at
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/Error.pm
line 38
        Error::_throw_Error_Simple('HASH(0x388cb78)') called at
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../
lib/Error.pm line 306
        Error::subs::run_clauses('HASH(0x388cbf0)', '\x{a}-------------
EXCEPTION: Bio::Root::Exception -------------\x{a}...', undef,
'ARRAY(0x38a0d18)') called at
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/Error.pm
line 426
        Error::subs::try('CODE(0x38f93f8)', 'HASH(0x388cbf0)') called at
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich
2/bin/../lib/FastaSeq.pm line 95
        FastaSeq::seq('FastaSeq=HASH(0x388dda0)') called at
/nfs/production/panda/ensemblgenomes/external/maker/2.28_mpich2/bin/../lib/
Process/MpiChunk.pm line 478
        Process::MpiChunk::_go('Process::MpiChunk=HASH(0x38a0e50)',
'run', 'HASH(0x38a0ec8)', 0, 0) called at /nfs/production/panda/ens
emblgenomes/external/maker/2.28_mpich2/bin/../lib/Process/MpiChunk.pm
line 341
        Process::MpiChunk::run('Process::MpiChunk=HASH(0x38a0e50)', 0)
called at /nfs/production/panda/ensemblgenomes/external/maker/2.
28_mpich2/bin/../lib/Process/MpiChunk.pm line 357
        Process::MpiChunk::run_all('Process::MpiChunk=HASH(0x38a0e50)',
0) called at /nfs/production/panda/ensemblgenomes/external/make
r/2.28_mpich2/bin/../lib/Process/MpiTiers.pm line 286
        Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x3867960)',
0) called at /nfs/panda/ensemblgenomes/external/maker/2.28_mpic
h2/bin/maker line 667

Is there an easy to reset the datastore/ file names so that i can switch
over to 2.28 without starting over? (eg maker -dsindex)
I killed the job and ran 2.27 instead which seems to be jim dandy.

-- 
malcolm hinsley | EnsEMBL Genomes | +44 (0)1223 49 4669
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
United Kingdom