Thanks Carson...please see below<br><br><div class="gmail_quote">On Thu, Feb 23, 2012 at 08:56, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>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.</div>
</div></blockquote><div><br>which modules? I assume threads will be dropped, right?<br>and if this is the case what are the advantages/disadvantages of using <span>Perl 5, version 12, subversion 3 (v5.12.3) built for darwin-thread-multi-2level<br>
should I change to non-threads version?? or it does not matter<br><br>Thanks<br><br>--R<br><br></span></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Rodolfo Aramayo <<a href="mailto:raramayo@tamu.edu" target="_blank">raramayo@tamu.edu</a>><br><span style="font-weight:bold">Date: </span> Thu, 23 Feb 2012 08:47:32 -0600<br>
<span style="font-weight:bold">To: </span> MAKER <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] maker-2.23<br>
</div><div><div class="h5"><div><br></div>I am running into an unusual problem<br>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"<div>the second maker quits with a: "[3]+ Abort trap nohup maker" and in the nohup file I see the following:<br><br>##########################################################################################################<br>
...<br>...<br>...<br>...<br>#-------------------------------#<br>re reading genemark report.<br>/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<br>
running genemark.<br>#--------- command -------------#<br>Widget::genemark:<br>/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<br>
#-------------------------------#<br>formating database...<br>#--------- command -------------#<br>Widget::formater:<br>/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_hZ_8Uc/uniprot_sprot%2Efasta.mpi.10.0<br>#-------------------------------#<br>
running blast search.<br>#--------- command -------------#<br>Widget::blastx:<br>/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<br>
#-------------------------------#<br>deleted:97 hits<br>perl(12478) malloc: *** error for object 0x1033bada0: pointer being freed was not allocated<br>*** set a breakpoint in malloc_error_break to debug<br>perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>
*** set a breakpoint in malloc_error_break to debug<br>perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>*** set a breakpoint in malloc_error_break to debug<br>
perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>*** set a breakpoint in malloc_error_break to debug<br>perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>
*** set a breakpoint in malloc_error_break to debug<br>perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>*** set a breakpoint in malloc_error_break to debug<br>
perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>*** set a breakpoint in malloc_error_break to debug<br>perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>
*** set a breakpoint in malloc_error_break to debug<br>perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for freed object - object was probably modified after being freed.<br>*** set a breakpoint in malloc_error_break to debug<br>
<br>##########################################################################################################<br><br>I am using Maker 2.23<br><br>I see this problem in Maker with and without mpich2 compilation<br>I am using:<br>
<br>Perl 5, version 12, subversion 3 (v5.12.3) built for darwin-thread-multi-2level<br><br><br>Any ideas?<br><br>Thanks</div></div></div>_______________________________________________
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