[maker-devel] maker-2.23

[Carson Holt]

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.

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_
final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastor
e/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.g
enemark
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_pGMI1
000MP.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_
final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastor
e/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
_pGMI1000MP%2Emod.genemark
/Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_
final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastor
e/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_
final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastor
e/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.tem
p_dir/uniprot_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
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