[maker-devel] 'not a SCALAR reference' error

[Malcolm Hinsley]

Hi

I'm running maker 2.31 with mpich 3 and have run once with est and 
protein2genome, then trained augustus and snap and run the first 
iteration of ab-initio predictors, which finished cleanly with no 
errors/ failures.

Having retrained augustus and snap I'm trying to run maker -a using the 
same augustus species and snap.hmm pathname... previously this has 
worked fine.


I get a lot of errors like this (it looks like every scaffold fails):

doing repeat masking
ERROR: Not a SCALAR reference
  at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/Fasta.pm 
line 382 thread 1.
         Fasta::_formatSeq(FastaSeq=HASH(0x4426298), 60) called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/Fasta.pm 
line 369 thread 1
         Fasta::toFastaRef(">scaffold29 CHUNK number:0 size:100000 
offset:0", REF(0x42e48f0)) called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/FastaChunk.pm 
line 217 thread 1
         FastaChunk::fasta_ref(FastaChunk=HASH(0x42c76a8)) called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/FastaChunk.pm 
line 168 thread 1
         FastaChunk::write_file(FastaChunk=HASH(0x42c76a8), 
"/gpfs/nobackup/ensembl_genomes/mhinsley/c.sonorensis/maker/v8"...) 
called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/GI.pm 
line 3138 thread 1
         GI::repeatmask(FastaChunk=HASH(0x42c76a8), 
"/gpfs/nobackup/ensembl_genomes/mhinsley/c.sonorensis/maker/v8"..., 
"scaffold29", "", 
"/nfs/production/panda/ensemblgenomes/external/RepeatMasker-op"..., 
"/gpfs/nobackup/ensembl_genomes/mhinsley/c.sonorensis/maker/c."..., 1, 
runlog=HASH(0x430e730)) called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/Process/MpiChunk.pm 
line 785 thread 1
         Process::MpiChunk::__ANON__() called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/Error.pm 
line 415 thread 1
         eval {...} called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/Error.pm 
line 407 thread 1
         Error::subs::try(CODE(0x4437a90), HASH(0x4425fc8)) called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/Process/MpiChunk.pm 
line 4215 thread 1
         Process::MpiChunk::_go(Process::MpiChunk=HASH(0x426e0a0), 
"run", HASH(0x42a5410), 0, 1) called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/../lib/Process/MpiChunk.pm 
line 341 thread 1
         Process::MpiChunk::run(Process::MpiChunk=HASH(0x426e0a0), 29) 
called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/maker line 
1457 thread 1
main::node_thread("/gpfs/nobackup/ensembl_genomes/mhinsley/c.sonorensis/maker/v8"...) 
called at 
/nfs/panda/ensemblgenomes/perl/perlbrew/perls/5.14.2/lib/site_perl/5.14.2/x86_64-linux-thread-multi/forks.pm 
line 799 thread 1
         eval {...} called at 
/nfs/panda/ensemblgenomes/perl/perlbrew/perls/5.14.2/lib/site_perl/5.14.2/x86_64-linux-thread-multi/forks.pm 
line 799 thread 1
         threads::new("threads", CODE(0x4168d70), 
"/gpfs/nobackup/ensembl_genomes/mhinsley/c.sonorensis/maker/v8"...) 
called at 
/nfs/production/panda/ensemblgenomes/external/maker/2.31_mpich3/bin/maker line 
917 thread 1
--> rank=29, hostname=ebi5-229.ebi.ac.uk
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:scaffold29

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold29


I see from the mailing list that there's a known issue w/ forks..pm 
(which is at the bottom of this stack) relating to perl 5.18, but I'm 
running 5.14.


Any ideas?





On 17/06/14 22:09, Carson Holt wrote:
> There is a change in Perl 5.18 that makes the forks.pm module incompatible.
> The forks.pm model maintainers have yet to update their module to resolve
> the issue, so it only works on perl version prior to 5.18.
> One work around it to manually edit forks.pm line 1736 yourself.
>
> Change it from this -->
> $write = each %WRITE;
>
> To this (make sure to include the {} brackets)-->
> {
>       no warnings qw(internal);
>       $write = each %WRITE;
> }
>
> --Carson
>

-- 
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