[maker-devel] maker-2.23

[Rodolfo Aramayo]

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_final_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_pGMI1000MP.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_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_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_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_final_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/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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>
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