[maker-devel] maker-2.23

Thu Feb 23 08:26:50 MST 2012

All MAKER versions after 2.2 use the CPAN forks.pm module rather than
threads.pm.  forks.pm is just a drop in replacement for threads.pm so you
can use the same syntax for forks as you do with threads.  Even if you have
perl compiled with threads MAKER still uses forks.pm (I am referring to the
about the module forks.pm and not forks themselves).  The place where you
get the error suggests the problem is at the C level, so the forks.pm module
from CPAN and Storable.pm are the  two most likely culprits.  Reinstalling
both of those would be the first thing to do.  If you have threaded perl you
can just change the 'use' statement at the start of MAKER, but if you don't
have threaded perl, just reinstall forks.pm.  Don't worry about changing the
perl installation.

Thanks,
Carson

From:  Rodolfo Aramayo <raramayo at tamu.edu>
Date:  Thu, 23 Feb 2012 09:17:36 -0600
To:  Carson Holt <carsonhh at gmail.com>
Cc:  MAKER <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker-2.23

Thanks Carson...please see below

On Thu, Feb 23, 2012 at 08:56, Carson Holt <carsonhh at gmail.com> wrote:
> Try two things for me.  Install/Re-install the latest version of the CPAN
> Storable module.  Install/Re-install forks and forks::shared from CPAN.
> Alternatively change 'use forks' to 'use threads' and 'use forks::shared' to
> 'use threads::shared' in the MAKER executable.  Those modules are supposed to
> be drop in replacements for each other.

which modules? I assume threads will be dropped, right?
and if this is the case what are the advantages/disadvantages of using Perl
5, version 12, subversion 3 (v5.12.3) built for darwin-thread-multi-2level
should I change to non-threads version?? or it does not matter

Thanks

--R

> 
> Thanks,
> Carson
> 
> From:  Rodolfo Aramayo <raramayo at tamu.edu>
> Date:  Thu, 23 Feb 2012 08:47:32 -0600
> To:  MAKER <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] maker-2.23
> 
> I am running into an unusual problem
> If I run Maker in the maker01 directory, say "/Volumes/g0006/maker/maker01"
> things go well no problem so far...but if I start a second maker inside the
> maker02 directory:  "/Volumes/g0006/maker/maker02"
> the second maker quits with a: "[3]+  Abort trap              nohup maker" and
> in the nohup file I see the following:
> 
> ##############################################################################
> ############################
> ...
> ...
> ...
> ...
> #-------------------------------#
> re reading genemark report.
> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi
> nal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6
> /70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059
> /NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum%2Emod.genemark
> running  genemark.
> #--------- command -------------#
> Widget::genemark:
> /opt/local/bin/perl
> /usr/local/bioinfosoft/maker-2.23/bin/../lib/Widget/genemark/gmhmm_wrap -m
> /Volumes/a0003/bioinfodata/genemark/hmm/Ralstonia_solanacearum_plasmid_pGMI100
> 0MP.mod -g /usr/local/bioinfosoft/genemark/gmhmmp -p
> /usr/local/bioinfosoft/genemark/probuild -o
> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi
> nal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6
> /70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059
> /NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum_plasmid_pGMI100
> 0MP%2Emod.genemark
> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi
> nal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6
> /70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059
> /query.fasta
> #-------------------------------#
> formating database...
> #--------- command -------------#
> Widget::formater:
> /usr/local/bin/makeblastdb -dbtype prot -in
> /tmp/maker_hZ_8Uc/uniprot_sprot%2Efasta.mpi.10.0
> #-------------------------------#
> running  blast search.
> #--------- command -------------#
> Widget::blastx:
> /usr/local/bin/blastx -db /tmp/maker_hZ_8Uc/uniprot_sprot%2Efasta.mpi.10.0
> -query /tmp/maker_hZ_8Uc/rank0/NODE_2_length_2929_cov_50%2E101059.0
> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300
> -searchsp 20000000 -num_threads 7 -seg yes -soft_masking true -lcase_masking
> -show_gis -out 
> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi
> nal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6
> /70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059
> /NODE_2_length_2929_cov_50%2E101059.0.uniprot_sprot%2Efasta.blastx.temp_dir/un
> iprot_sprot%2Efasta.mpi.10.0.blastx
> #-------------------------------#
> deleted:97 hits
> perl(12478) malloc: *** error for object 0x1033bada0: pointer being freed was
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
> freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> 
> ##############################################################################
> ############################
> 
> I am using Maker 2.23
> 
> I see this problem in Maker with and without mpich2 compilation
> I am using:
> 
> Perl 5, version 12, subversion 3 (v5.12.3) built for
> darwin-thread-multi-2level
> 
> 
> Any ideas?
> 
> Thanks
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org

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