<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><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><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Rodolfo Aramayo <<a href="mailto:raramayo@tamu.edu">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">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] maker-2.23<br></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 id=":19s">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>_______________________________________________
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