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

[Carson Holt]

Make sure you are using the latest version of MAKER 3.31.6.  Also you may
have to use MPICH2.  MPICH3 is actually a different MPI protocol and I
have not had success running MAKER with it.

--Carson


On 6/19/14, 3:07 AM, "Malcolm Hinsley" <mhinsley at ebi.ac.uk> wrote:

>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/ma
>ker/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
>
>
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