Thanks Carson,<br><br>So I did the following:<br><br>Deleted the Maker installation<br>Re-configure, re-compiled and re-installed mpich2<br>Re-installed CPAN and all the CPAN-modules required by Maker<br>Re-compiled and re-installed Maker<br>
Re-installed Genemark<br> and now things work!<br><br>The question remains, why did this failed?<br>The only thing I can think of, the only thing I noticed, is the fact that forks::shared and threads::shared were installed by CPAN as if they had not been installed before??<br>
But they were...so..perhaps CPAN modules got broken during a major MacPorts upgrade I did over the weekend, where many, many MacPorts perl modules were upgraded<br><br>Like they say: <b>No Good Deed Shall Go Unpunished!<br>
<br></b>It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software<b><br></b><br>Thanks for your help<br><br>--Rodolfo<br><br><br><br><div class="gmail_quote">On Thu, Feb 23, 2012 at 11:08, 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>Does it indicate at any level what the compilation error is?</div>
<div><br></div><div>Could you pack up your job and send it to me? I'll just try it on a couple of system types. A malloc error with perl would normally happen at the C level, so it's a matter of identifying what module is being called.</div>
<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 11:00:37 -0600<div>
<div class="h5"><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </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> Re: [maker-devel] maker-2.23<br></div></div></div><div><div class="h5"><div><br></div>Carson,<br><br>Reinstalled storable, forks and forks::shared<br>Re-compiled maker<br>Same problem<br>
<br>Change from forks/forks::shared to threads/threads::shared in the compiled executable and<br>Running maker gives me:<br><br>"Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors."<br>
<br>Ideas?<br><br>Thanks<br><br>--R<br><br><br><br><br><br><div class="gmail_quote">On Thu, Feb 23, 2012 at 09:26, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">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>All MAKER versions after 2.2 use the CPAN <a href="http://forks.pm" target="_blank">forks.pm</a> module rather than <a href="http://threads.pm" target="_blank">threads.pm</a>. <a href="http://forks.pm" target="_blank">forks.pm</a> is just a drop in replacement for <a href="http://threads.pm" target="_blank">threads.pm</a> 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 <a href="http://forks.pm" target="_blank">forks.pm</a> (I am referring to the about the module <a href="http://forks.pm" target="_blank">forks.pm</a> and not forks themselves). The place where you get the error suggests the problem is at the C level, so the <a href="http://forks.pm" target="_blank">forks.pm</a> 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 <a href="http://forks.pm" target="_blank">forks.pm</a>. Don't worry about changing the perl installation.</div>
<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 09:17:36 -0600<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </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> Re: [maker-devel] maker-2.23<br></div><div><div><div><br></div>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" target="_blank">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><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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