From raramayo at tamu.edu Thu Feb 23 08:47:32 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 08:47:32 -0600 Subject: [maker-devel] maker-2.23 Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 08:56:55 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 09:56:55 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: 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 Date: Thu, 23 Feb 2012 08:47:32 -0600 To: MAKER 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 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 09:17:36 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 09:17:36 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 09:26:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 10:26:50 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: All MAKER versions after 2.2 use the CPAN forks.pm module rather than threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to the about the module forks.pm and not forks themselves). The place where you get the error suggests the problem is at the C level, so the forks.pm 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 forks.pm. Don't worry about changing the perl installation. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 09:17:36 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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_fi > nal_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_pGMI100 > 0MP.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_fi > nal_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_pGMI100 > 0MP%2Emod.genemark > /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi > nal_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_fi > nal_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/un > iprot_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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 11:00:37 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 11:00:37 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module rather than > threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to > the about the module forks.pm and not forks themselves). The place where > you get the error suggests the problem is at the C level, so the forks.pmmodule 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 forks.pm. > Don't worry about changing the perl installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 11:08:12 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:08:12 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: Does it indicate at any level what the compilation error is? 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. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 11:00:37 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module > rather than threads.pm . forks.pm is > just a drop in replacement for threads.pm 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 forks.pm (I am > referring to the about the module forks.pm and not forks > themselves). The place where you get the error suggests the problem is at the > C level, so the forks.pm 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 forks.pm . Don't worry about changing the perl > installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum%2Emod.genem >> ark >> 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_pGMI10 >> 00MP.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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum_plasmid_pGM >> I1000MP%2Emod.genemark >> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f >> inal_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_50.101 >> 059/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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.0.uniprot_sprot%2Efasta.blastx.temp_di >> r/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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From olaf.mueller at duke.edu Thu Feb 23 11:16:58 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:16:58 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F46748A.8000505@duke.edu> Hi, I've done a preliminary run on an alga genome with maker 2.23beta, using only mRNA-seq tophat/cufflinks input and no additional evidence source. As prerequisite a cufflinks transcripts.gtf (merged from different read sample mappings) has been converted with maker cufflinks2gff3 (strandless transcripts/exons removed). I provided the resulting gff3 via pred_gff and model_gff to maker, and also didn't call est2genome or other predictors. During maker run for some scaffolds, I receive this error message for some chunks, while gathering GFF3 input into hits: Gathering GFF3 input into hits - chunk:0 panic: fold_constants JMPENV_PUSH returned 2 at /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 Gathering GFF3 input into hits - chunk:2 ... The index log nevertheless reports these scaffolds as finished and annotations are generated. Do I have to be concerned about this message because it is related to my cufflinks input? Thanks Olaf From carsonhh at gmail.com Thu Feb 23 11:31:28 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:31:28 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F46748A.8000505@duke.edu> Message-ID: The error is caused by a perl module that is loaded at runtime to access the system's Process Table. This is an error that sometimes happens in cluster environments like SGE. It's not related to the GFF3. It's more related to the specific system running MAKER at the time and can be semi-random. MAKER has auto-retry on contigs, so it would have done it's best to recover from any failure. If the master_index_datastore.log file shows all input contigs as being of status FINISHED, you are fine. If you are on a cluster and you continually get the error you may need to install the Proc::ProcessTable locally on that specific node and not just globally for the cluster. Errors with fold_constants happen when you compile on one system and then run on another. The issue can sometimes be related to floating points being slightly different between the two systems. So clusters that have non-identical architectures within the same cluster can have these types of errors more often. Thanks, Carson On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >Hi, > >I've done a preliminary run on an alga genome with maker 2.23beta, using >only mRNA-seq tophat/cufflinks input and no additional evidence source. > >As prerequisite a cufflinks transcripts.gtf (merged from different read >sample mappings) has been converted with maker cufflinks2gff3 >(strandless transcripts/exons removed). I provided the resulting gff3 >via pred_gff and model_gff to maker, and also didn't call est2genome or >other predictors. > >During maker run for some scaffolds, I receive this error message for >some chunks, while gathering GFF3 input into hits: > >Gathering GFF3 input into hits - chunk:0 >panic: fold_constants JMPENV_PUSH returned 2 at >/home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >Gathering GFF3 input into hits - chunk:2 >... > >The index log nevertheless reports these scaffolds as finished and >annotations are generated. Do I have to be concerned about this message >because it is related to my cufflinks input? > >Thanks >Olaf > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From olaf.mueller at duke.edu Thu Feb 23 11:41:15 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:41:15 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F467A3B.4040002@duke.edu> Thanks Carson, That's good to know. I'm running maker on a single machine (dual Xeon quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on this computer without MPICH2 hooked in. Best Olaf On 02/23/2012 12:31 PM, Carson Holt wrote: > The error is caused by a perl module that is loaded at runtime to access > the system's Process Table. This is an error that sometimes happens in > cluster environments like SGE. It's not related to the GFF3. It's more > related to the specific system running MAKER at the time and can be > semi-random. MAKER has auto-retry on contigs, so it would have done it's > best to recover from any failure. If the master_index_datastore.log file > shows all input contigs as being of status FINISHED, you are fine. > > If you are on a cluster and you continually get the error you may need to > install the Proc::ProcessTable locally on that specific node and not just > globally for the cluster. Errors with fold_constants happen when you > compile on one system and then run on another. The issue can sometimes be > related to floating points being slightly different between the two > systems. So clusters that have non-identical architectures within the > same cluster can have these types of errors more often. > > Thanks, > Carson > > > > On 12-02-23 12:16 PM, "Olaf Mueller" wrote: > >> Hi, >> >> I've done a preliminary run on an alga genome with maker 2.23beta, using >> only mRNA-seq tophat/cufflinks input and no additional evidence source. >> >> As prerequisite a cufflinks transcripts.gtf (merged from different read >> sample mappings) has been converted with maker cufflinks2gff3 >> (strandless transcripts/exons removed). I provided the resulting gff3 >> via pred_gff and model_gff to maker, and also didn't call est2genome or >> other predictors. >> >> During maker run for some scaffolds, I receive this error message for >> some chunks, while gathering GFF3 input into hits: >> >> Gathering GFF3 input into hits - chunk:0 >> panic: fold_constants JMPENV_PUSH returned 2 at >> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >> Gathering GFF3 input into hits - chunk:2 >> ... >> >> The index log nevertheless reports these scaffolds as finished and >> annotations are generated. Do I have to be concerned about this message >> because it is related to my cufflinks input? >> >> Thanks >> Olaf >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Olaf Mueller, PhD Duke University Department of Biology, PO Box 90338 369 Biological Sciences Bldg. Science Drive Durham, NC 27708, USA phone: (919) 660-7402 email: olaf.mueller at duke.edu From esther.t.chan at gmail.com Thu Feb 23 11:42:02 2012 From: esther.t.chan at gmail.com (Esther) Date: Thu, 23 Feb 2012 09:42:02 -0800 (PST) Subject: [maker-devel] Error from a malformed gff file Message-ID: Hi, I'm interested in re-annotating gene models with new evidence using MAKER in a first generation genome (budding yeast). I have been able to run it fine in de novo and reference mode as described by Holt and Yandell in the Maize example in their 2011 BMC Bioinformatics paper but I'm having troubles running in re-annotation mode using a gff file with the model_gff parameter. The gff file I'm using is from SGD (http://downloads.yeastgenome.org/curation/chromosomal_feature/ saccharomyces_cerevisiae.gff) which should be GFF3 compliant according to this validator: https://github.com/solgenomics/gff3_validator. I get an error due to a malformed gff file, but without knowledge of which line(s) are offending, it's hard for me to fix the problem. Is there a way to find that information? The error message I get is as follows: Making transcripts Processing transcripts into genes Calculating annotation quality statistics ERROR: The feature being compared appears to be missing some of it's structure. This can happen when you use a malformed GFF3 file as input to one of MAKER's evidence passthrough options. Failed on maker-chrIII-pred_gff_blastx- gene-0.1018-mRNA-1 (from shadow_AED::get_AED) Thanks, Esther From carsonhh at gmail.com Thu Feb 23 11:56:06 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:56:06 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F467A3B.4040002@duke.edu> Message-ID: You should be fine then. It may never even happen again (semi-random), but if it does, you can try reinstalling the Proc::ProcessTable module from CPAN. You can also change line 89 from 'require Proc::ProcessTable' to 'use Proc::ProcessTable', which would load at the start rather than at runtime (safe to do on your system because Proc::ProcessTable is already there). Thanks, Carson On 12-02-23 12:41 PM, "Olaf Mueller" wrote: >Thanks Carson, > >That's good to know. I'm running maker on a single machine (dual Xeon >quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on >this computer without MPICH2 hooked in. > >Best >Olaf > >On 02/23/2012 12:31 PM, Carson Holt wrote: >> The error is caused by a perl module that is loaded at runtime to access >> the system's Process Table. This is an error that sometimes happens in >> cluster environments like SGE. It's not related to the GFF3. It's more >> related to the specific system running MAKER at the time and can be >> semi-random. MAKER has auto-retry on contigs, so it would have done >>it's >> best to recover from any failure. If the master_index_datastore.log >>file >> shows all input contigs as being of status FINISHED, you are fine. >> >> If you are on a cluster and you continually get the error you may need >>to >> install the Proc::ProcessTable locally on that specific node and not >>just >> globally for the cluster. Errors with fold_constants happen when you >> compile on one system and then run on another. The issue can sometimes >>be >> related to floating points being slightly different between the two >> systems. So clusters that have non-identical architectures within the >> same cluster can have these types of errors more often. >> >> Thanks, >> Carson >> >> >> >> On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >> >>> Hi, >>> >>> I've done a preliminary run on an alga genome with maker 2.23beta, >>>using >>> only mRNA-seq tophat/cufflinks input and no additional evidence source. >>> >>> As prerequisite a cufflinks transcripts.gtf (merged from different read >>> sample mappings) has been converted with maker cufflinks2gff3 >>> (strandless transcripts/exons removed). I provided the resulting gff3 >>> via pred_gff and model_gff to maker, and also didn't call est2genome or >>> other predictors. >>> >>> During maker run for some scaffolds, I receive this error message for >>> some chunks, while gathering GFF3 input into hits: >>> >>> Gathering GFF3 input into hits - chunk:0 >>> panic: fold_constants JMPENV_PUSH returned 2 at >>> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >>> Gathering GFF3 input into hits - chunk:2 >>> ... >>> >>> The index log nevertheless reports these scaffolds as finished and >>> annotations are generated. Do I have to be concerned about this message >>> because it is related to my cufflinks input? >>> >>> Thanks >>> Olaf >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > >-- >Olaf Mueller, PhD >Duke University >Department of Biology, PO Box 90338 >369 Biological Sciences Bldg. >Science Drive >Durham, NC 27708, USA > >phone: (919) 660-7402 >email: olaf.mueller at duke.edu > From raramayo at tamu.edu Fri Feb 24 09:43:08 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Fri, 24 Feb 2012 09:43:08 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: *No Good Deed Shall Go Unpunished! *It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software* * Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > >> All MAKER versions after 2.2 use the CPAN forks.pm module rather than >> threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks themselves). >> The place where you get the error suggests the problem is at the C level, >> so the forks.pm 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 >> forks.pm. Don't worry about changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Feb 24 09:49:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 24 Feb 2012 10:49:46 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: I'm glad it is working now. There is nothing harder than tracking down errors in Perl that are really coming from a C compiled source outside of Perl (malloc, folding_constents, etc.). Thanks, Carson From: Rodolfo Aramayo Date: Fri, 24 Feb 2012 09:43:08 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: No Good Deed Shall Go Unpunished! It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: >> All MAKER versions after 2.2 use the CPAN forks.pm module >> rather than threads.pm . forks.pm is >> just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks >> themselves). The place where you get the error suggests the problem is at >> the C level, so the forks.pm 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 forks.pm . Don't worry about >> changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joana.guimaraes at inrb.pt Tue Feb 28 04:25:24 2012 From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=) Date: Tue, 28 Feb 2012 10:25:24 -0000 Subject: [maker-devel] maker run error Message-ID: Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastore_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Feb 28 06:48:09 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 28 Feb 2012 07:48:09 -0500 Subject: [maker-devel] maker run error In-Reply-To: Message-ID: You're using ABBlast. MAKER doesn't support it yet. Maybe now would be a good time to do it though. It would take about 10 hours to implement and test. I could probably look into it this weekend. Thanks, Carson From: "Maria Joana F. B. A. Guimar?es" Date: Tue, 28 Feb 2012 10:25:24 -0000 To: Subject: [maker-devel] maker run error maker run error Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastor e_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb. out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 07:47:32 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 08:47:32 -0600 Subject: [maker-devel] maker-2.23 Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 07:56:55 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 09:56:55 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: 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 Date: Thu, 23 Feb 2012 08:47:32 -0600 To: MAKER 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 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 08:17:36 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 09:17:36 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 08:26:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 10:26:50 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: All MAKER versions after 2.2 use the CPAN forks.pm module rather than threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to the about the module forks.pm and not forks themselves). The place where you get the error suggests the problem is at the C level, so the forks.pm 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 forks.pm. Don't worry about changing the perl installation. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 09:17:36 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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_fi > nal_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_pGMI100 > 0MP.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_fi > nal_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_pGMI100 > 0MP%2Emod.genemark > /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi > nal_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_fi > nal_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/un > iprot_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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 10:00:37 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 11:00:37 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module rather than > threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to > the about the module forks.pm and not forks themselves). The place where > you get the error suggests the problem is at the C level, so the forks.pmmodule 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 forks.pm. > Don't worry about changing the perl installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 10:08:12 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:08:12 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: Does it indicate at any level what the compilation error is? 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. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 11:00:37 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module > rather than threads.pm . forks.pm is > just a drop in replacement for threads.pm 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 forks.pm (I am > referring to the about the module forks.pm and not forks > themselves). The place where you get the error suggests the problem is at the > C level, so the forks.pm 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 forks.pm . Don't worry about changing the perl > installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum%2Emod.genem >> ark >> 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_pGMI10 >> 00MP.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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum_plasmid_pGM >> I1000MP%2Emod.genemark >> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f >> inal_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_50.101 >> 059/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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.0.uniprot_sprot%2Efasta.blastx.temp_di >> r/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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From olaf.mueller at duke.edu Thu Feb 23 10:16:58 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:16:58 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F46748A.8000505@duke.edu> Hi, I've done a preliminary run on an alga genome with maker 2.23beta, using only mRNA-seq tophat/cufflinks input and no additional evidence source. As prerequisite a cufflinks transcripts.gtf (merged from different read sample mappings) has been converted with maker cufflinks2gff3 (strandless transcripts/exons removed). I provided the resulting gff3 via pred_gff and model_gff to maker, and also didn't call est2genome or other predictors. During maker run for some scaffolds, I receive this error message for some chunks, while gathering GFF3 input into hits: Gathering GFF3 input into hits - chunk:0 panic: fold_constants JMPENV_PUSH returned 2 at /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 Gathering GFF3 input into hits - chunk:2 ... The index log nevertheless reports these scaffolds as finished and annotations are generated. Do I have to be concerned about this message because it is related to my cufflinks input? Thanks Olaf From carsonhh at gmail.com Thu Feb 23 10:31:28 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:31:28 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F46748A.8000505@duke.edu> Message-ID: The error is caused by a perl module that is loaded at runtime to access the system's Process Table. This is an error that sometimes happens in cluster environments like SGE. It's not related to the GFF3. It's more related to the specific system running MAKER at the time and can be semi-random. MAKER has auto-retry on contigs, so it would have done it's best to recover from any failure. If the master_index_datastore.log file shows all input contigs as being of status FINISHED, you are fine. If you are on a cluster and you continually get the error you may need to install the Proc::ProcessTable locally on that specific node and not just globally for the cluster. Errors with fold_constants happen when you compile on one system and then run on another. The issue can sometimes be related to floating points being slightly different between the two systems. So clusters that have non-identical architectures within the same cluster can have these types of errors more often. Thanks, Carson On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >Hi, > >I've done a preliminary run on an alga genome with maker 2.23beta, using >only mRNA-seq tophat/cufflinks input and no additional evidence source. > >As prerequisite a cufflinks transcripts.gtf (merged from different read >sample mappings) has been converted with maker cufflinks2gff3 >(strandless transcripts/exons removed). I provided the resulting gff3 >via pred_gff and model_gff to maker, and also didn't call est2genome or >other predictors. > >During maker run for some scaffolds, I receive this error message for >some chunks, while gathering GFF3 input into hits: > >Gathering GFF3 input into hits - chunk:0 >panic: fold_constants JMPENV_PUSH returned 2 at >/home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >Gathering GFF3 input into hits - chunk:2 >... > >The index log nevertheless reports these scaffolds as finished and >annotations are generated. Do I have to be concerned about this message >because it is related to my cufflinks input? > >Thanks >Olaf > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From olaf.mueller at duke.edu Thu Feb 23 10:41:15 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:41:15 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F467A3B.4040002@duke.edu> Thanks Carson, That's good to know. I'm running maker on a single machine (dual Xeon quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on this computer without MPICH2 hooked in. Best Olaf On 02/23/2012 12:31 PM, Carson Holt wrote: > The error is caused by a perl module that is loaded at runtime to access > the system's Process Table. This is an error that sometimes happens in > cluster environments like SGE. It's not related to the GFF3. It's more > related to the specific system running MAKER at the time and can be > semi-random. MAKER has auto-retry on contigs, so it would have done it's > best to recover from any failure. If the master_index_datastore.log file > shows all input contigs as being of status FINISHED, you are fine. > > If you are on a cluster and you continually get the error you may need to > install the Proc::ProcessTable locally on that specific node and not just > globally for the cluster. Errors with fold_constants happen when you > compile on one system and then run on another. The issue can sometimes be > related to floating points being slightly different between the two > systems. So clusters that have non-identical architectures within the > same cluster can have these types of errors more often. > > Thanks, > Carson > > > > On 12-02-23 12:16 PM, "Olaf Mueller" wrote: > >> Hi, >> >> I've done a preliminary run on an alga genome with maker 2.23beta, using >> only mRNA-seq tophat/cufflinks input and no additional evidence source. >> >> As prerequisite a cufflinks transcripts.gtf (merged from different read >> sample mappings) has been converted with maker cufflinks2gff3 >> (strandless transcripts/exons removed). I provided the resulting gff3 >> via pred_gff and model_gff to maker, and also didn't call est2genome or >> other predictors. >> >> During maker run for some scaffolds, I receive this error message for >> some chunks, while gathering GFF3 input into hits: >> >> Gathering GFF3 input into hits - chunk:0 >> panic: fold_constants JMPENV_PUSH returned 2 at >> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >> Gathering GFF3 input into hits - chunk:2 >> ... >> >> The index log nevertheless reports these scaffolds as finished and >> annotations are generated. Do I have to be concerned about this message >> because it is related to my cufflinks input? >> >> Thanks >> Olaf >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Olaf Mueller, PhD Duke University Department of Biology, PO Box 90338 369 Biological Sciences Bldg. Science Drive Durham, NC 27708, USA phone: (919) 660-7402 email: olaf.mueller at duke.edu From esther.t.chan at gmail.com Thu Feb 23 10:42:02 2012 From: esther.t.chan at gmail.com (Esther) Date: Thu, 23 Feb 2012 09:42:02 -0800 (PST) Subject: [maker-devel] Error from a malformed gff file Message-ID: Hi, I'm interested in re-annotating gene models with new evidence using MAKER in a first generation genome (budding yeast). I have been able to run it fine in de novo and reference mode as described by Holt and Yandell in the Maize example in their 2011 BMC Bioinformatics paper but I'm having troubles running in re-annotation mode using a gff file with the model_gff parameter. The gff file I'm using is from SGD (http://downloads.yeastgenome.org/curation/chromosomal_feature/ saccharomyces_cerevisiae.gff) which should be GFF3 compliant according to this validator: https://github.com/solgenomics/gff3_validator. I get an error due to a malformed gff file, but without knowledge of which line(s) are offending, it's hard for me to fix the problem. Is there a way to find that information? The error message I get is as follows: Making transcripts Processing transcripts into genes Calculating annotation quality statistics ERROR: The feature being compared appears to be missing some of it's structure. This can happen when you use a malformed GFF3 file as input to one of MAKER's evidence passthrough options. Failed on maker-chrIII-pred_gff_blastx- gene-0.1018-mRNA-1 (from shadow_AED::get_AED) Thanks, Esther From carsonhh at gmail.com Thu Feb 23 10:56:06 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:56:06 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F467A3B.4040002@duke.edu> Message-ID: You should be fine then. It may never even happen again (semi-random), but if it does, you can try reinstalling the Proc::ProcessTable module from CPAN. You can also change line 89 from 'require Proc::ProcessTable' to 'use Proc::ProcessTable', which would load at the start rather than at runtime (safe to do on your system because Proc::ProcessTable is already there). Thanks, Carson On 12-02-23 12:41 PM, "Olaf Mueller" wrote: >Thanks Carson, > >That's good to know. I'm running maker on a single machine (dual Xeon >quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on >this computer without MPICH2 hooked in. > >Best >Olaf > >On 02/23/2012 12:31 PM, Carson Holt wrote: >> The error is caused by a perl module that is loaded at runtime to access >> the system's Process Table. This is an error that sometimes happens in >> cluster environments like SGE. It's not related to the GFF3. It's more >> related to the specific system running MAKER at the time and can be >> semi-random. MAKER has auto-retry on contigs, so it would have done >>it's >> best to recover from any failure. If the master_index_datastore.log >>file >> shows all input contigs as being of status FINISHED, you are fine. >> >> If you are on a cluster and you continually get the error you may need >>to >> install the Proc::ProcessTable locally on that specific node and not >>just >> globally for the cluster. Errors with fold_constants happen when you >> compile on one system and then run on another. The issue can sometimes >>be >> related to floating points being slightly different between the two >> systems. So clusters that have non-identical architectures within the >> same cluster can have these types of errors more often. >> >> Thanks, >> Carson >> >> >> >> On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >> >>> Hi, >>> >>> I've done a preliminary run on an alga genome with maker 2.23beta, >>>using >>> only mRNA-seq tophat/cufflinks input and no additional evidence source. >>> >>> As prerequisite a cufflinks transcripts.gtf (merged from different read >>> sample mappings) has been converted with maker cufflinks2gff3 >>> (strandless transcripts/exons removed). I provided the resulting gff3 >>> via pred_gff and model_gff to maker, and also didn't call est2genome or >>> other predictors. >>> >>> During maker run for some scaffolds, I receive this error message for >>> some chunks, while gathering GFF3 input into hits: >>> >>> Gathering GFF3 input into hits - chunk:0 >>> panic: fold_constants JMPENV_PUSH returned 2 at >>> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >>> Gathering GFF3 input into hits - chunk:2 >>> ... >>> >>> The index log nevertheless reports these scaffolds as finished and >>> annotations are generated. Do I have to be concerned about this message >>> because it is related to my cufflinks input? >>> >>> Thanks >>> Olaf >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > >-- >Olaf Mueller, PhD >Duke University >Department of Biology, PO Box 90338 >369 Biological Sciences Bldg. >Science Drive >Durham, NC 27708, USA > >phone: (919) 660-7402 >email: olaf.mueller at duke.edu > From raramayo at tamu.edu Fri Feb 24 08:43:08 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Fri, 24 Feb 2012 09:43:08 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: *No Good Deed Shall Go Unpunished! *It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software* * Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > >> All MAKER versions after 2.2 use the CPAN forks.pm module rather than >> threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks themselves). >> The place where you get the error suggests the problem is at the C level, >> so the forks.pm 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 >> forks.pm. Don't worry about changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Feb 24 08:49:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 24 Feb 2012 10:49:46 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: I'm glad it is working now. There is nothing harder than tracking down errors in Perl that are really coming from a C compiled source outside of Perl (malloc, folding_constents, etc.). Thanks, Carson From: Rodolfo Aramayo Date: Fri, 24 Feb 2012 09:43:08 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: No Good Deed Shall Go Unpunished! It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: >> All MAKER versions after 2.2 use the CPAN forks.pm module >> rather than threads.pm . forks.pm is >> just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks >> themselves). The place where you get the error suggests the problem is at >> the C level, so the forks.pm 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 forks.pm . Don't worry about >> changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joana.guimaraes at inrb.pt Tue Feb 28 03:25:24 2012 From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=) Date: Tue, 28 Feb 2012 10:25:24 -0000 Subject: [maker-devel] maker run error Message-ID: Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastore_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Feb 28 05:48:09 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 28 Feb 2012 07:48:09 -0500 Subject: [maker-devel] maker run error In-Reply-To: Message-ID: You're using ABBlast. MAKER doesn't support it yet. Maybe now would be a good time to do it though. It would take about 10 hours to implement and test. I could probably look into it this weekend. Thanks, Carson From: "Maria Joana F. B. A. Guimar?es" Date: Tue, 28 Feb 2012 10:25:24 -0000 To: Subject: [maker-devel] maker run error maker run error Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastor e_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb. out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 07:47:32 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 08:47:32 -0600 Subject: [maker-devel] maker-2.23 Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 07:56:55 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 09:56:55 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: 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 Date: Thu, 23 Feb 2012 08:47:32 -0600 To: MAKER 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 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 08:17:36 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 09:17:36 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 08:26:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 10:26:50 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: All MAKER versions after 2.2 use the CPAN forks.pm module rather than threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to the about the module forks.pm and not forks themselves). The place where you get the error suggests the problem is at the C level, so the forks.pm 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 forks.pm. Don't worry about changing the perl installation. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 09:17:36 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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_fi > nal_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_pGMI100 > 0MP.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_fi > nal_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_pGMI100 > 0MP%2Emod.genemark > /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi > nal_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_fi > nal_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/un > iprot_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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 10:00:37 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 11:00:37 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module rather than > threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to > the about the module forks.pm and not forks themselves). The place where > you get the error suggests the problem is at the C level, so the forks.pmmodule 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 forks.pm. > Don't worry about changing the perl installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 10:08:12 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:08:12 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: Does it indicate at any level what the compilation error is? 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. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 11:00:37 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module > rather than threads.pm . forks.pm is > just a drop in replacement for threads.pm 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 forks.pm (I am > referring to the about the module forks.pm and not forks > themselves). The place where you get the error suggests the problem is at the > C level, so the forks.pm 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 forks.pm . Don't worry about changing the perl > installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum%2Emod.genem >> ark >> 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_pGMI10 >> 00MP.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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum_plasmid_pGM >> I1000MP%2Emod.genemark >> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f >> inal_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_50.101 >> 059/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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.0.uniprot_sprot%2Efasta.blastx.temp_di >> r/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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From olaf.mueller at duke.edu Thu Feb 23 10:16:58 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:16:58 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F46748A.8000505@duke.edu> Hi, I've done a preliminary run on an alga genome with maker 2.23beta, using only mRNA-seq tophat/cufflinks input and no additional evidence source. As prerequisite a cufflinks transcripts.gtf (merged from different read sample mappings) has been converted with maker cufflinks2gff3 (strandless transcripts/exons removed). I provided the resulting gff3 via pred_gff and model_gff to maker, and also didn't call est2genome or other predictors. During maker run for some scaffolds, I receive this error message for some chunks, while gathering GFF3 input into hits: Gathering GFF3 input into hits - chunk:0 panic: fold_constants JMPENV_PUSH returned 2 at /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 Gathering GFF3 input into hits - chunk:2 ... The index log nevertheless reports these scaffolds as finished and annotations are generated. Do I have to be concerned about this message because it is related to my cufflinks input? Thanks Olaf From carsonhh at gmail.com Thu Feb 23 10:31:28 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:31:28 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F46748A.8000505@duke.edu> Message-ID: The error is caused by a perl module that is loaded at runtime to access the system's Process Table. This is an error that sometimes happens in cluster environments like SGE. It's not related to the GFF3. It's more related to the specific system running MAKER at the time and can be semi-random. MAKER has auto-retry on contigs, so it would have done it's best to recover from any failure. If the master_index_datastore.log file shows all input contigs as being of status FINISHED, you are fine. If you are on a cluster and you continually get the error you may need to install the Proc::ProcessTable locally on that specific node and not just globally for the cluster. Errors with fold_constants happen when you compile on one system and then run on another. The issue can sometimes be related to floating points being slightly different between the two systems. So clusters that have non-identical architectures within the same cluster can have these types of errors more often. Thanks, Carson On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >Hi, > >I've done a preliminary run on an alga genome with maker 2.23beta, using >only mRNA-seq tophat/cufflinks input and no additional evidence source. > >As prerequisite a cufflinks transcripts.gtf (merged from different read >sample mappings) has been converted with maker cufflinks2gff3 >(strandless transcripts/exons removed). I provided the resulting gff3 >via pred_gff and model_gff to maker, and also didn't call est2genome or >other predictors. > >During maker run for some scaffolds, I receive this error message for >some chunks, while gathering GFF3 input into hits: > >Gathering GFF3 input into hits - chunk:0 >panic: fold_constants JMPENV_PUSH returned 2 at >/home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >Gathering GFF3 input into hits - chunk:2 >... > >The index log nevertheless reports these scaffolds as finished and >annotations are generated. Do I have to be concerned about this message >because it is related to my cufflinks input? > >Thanks >Olaf > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From olaf.mueller at duke.edu Thu Feb 23 10:41:15 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:41:15 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F467A3B.4040002@duke.edu> Thanks Carson, That's good to know. I'm running maker on a single machine (dual Xeon quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on this computer without MPICH2 hooked in. Best Olaf On 02/23/2012 12:31 PM, Carson Holt wrote: > The error is caused by a perl module that is loaded at runtime to access > the system's Process Table. This is an error that sometimes happens in > cluster environments like SGE. It's not related to the GFF3. It's more > related to the specific system running MAKER at the time and can be > semi-random. MAKER has auto-retry on contigs, so it would have done it's > best to recover from any failure. If the master_index_datastore.log file > shows all input contigs as being of status FINISHED, you are fine. > > If you are on a cluster and you continually get the error you may need to > install the Proc::ProcessTable locally on that specific node and not just > globally for the cluster. Errors with fold_constants happen when you > compile on one system and then run on another. The issue can sometimes be > related to floating points being slightly different between the two > systems. So clusters that have non-identical architectures within the > same cluster can have these types of errors more often. > > Thanks, > Carson > > > > On 12-02-23 12:16 PM, "Olaf Mueller" wrote: > >> Hi, >> >> I've done a preliminary run on an alga genome with maker 2.23beta, using >> only mRNA-seq tophat/cufflinks input and no additional evidence source. >> >> As prerequisite a cufflinks transcripts.gtf (merged from different read >> sample mappings) has been converted with maker cufflinks2gff3 >> (strandless transcripts/exons removed). I provided the resulting gff3 >> via pred_gff and model_gff to maker, and also didn't call est2genome or >> other predictors. >> >> During maker run for some scaffolds, I receive this error message for >> some chunks, while gathering GFF3 input into hits: >> >> Gathering GFF3 input into hits - chunk:0 >> panic: fold_constants JMPENV_PUSH returned 2 at >> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >> Gathering GFF3 input into hits - chunk:2 >> ... >> >> The index log nevertheless reports these scaffolds as finished and >> annotations are generated. Do I have to be concerned about this message >> because it is related to my cufflinks input? >> >> Thanks >> Olaf >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Olaf Mueller, PhD Duke University Department of Biology, PO Box 90338 369 Biological Sciences Bldg. Science Drive Durham, NC 27708, USA phone: (919) 660-7402 email: olaf.mueller at duke.edu From esther.t.chan at gmail.com Thu Feb 23 10:42:02 2012 From: esther.t.chan at gmail.com (Esther) Date: Thu, 23 Feb 2012 09:42:02 -0800 (PST) Subject: [maker-devel] Error from a malformed gff file Message-ID: Hi, I'm interested in re-annotating gene models with new evidence using MAKER in a first generation genome (budding yeast). I have been able to run it fine in de novo and reference mode as described by Holt and Yandell in the Maize example in their 2011 BMC Bioinformatics paper but I'm having troubles running in re-annotation mode using a gff file with the model_gff parameter. The gff file I'm using is from SGD (http://downloads.yeastgenome.org/curation/chromosomal_feature/ saccharomyces_cerevisiae.gff) which should be GFF3 compliant according to this validator: https://github.com/solgenomics/gff3_validator. I get an error due to a malformed gff file, but without knowledge of which line(s) are offending, it's hard for me to fix the problem. Is there a way to find that information? The error message I get is as follows: Making transcripts Processing transcripts into genes Calculating annotation quality statistics ERROR: The feature being compared appears to be missing some of it's structure. This can happen when you use a malformed GFF3 file as input to one of MAKER's evidence passthrough options. Failed on maker-chrIII-pred_gff_blastx- gene-0.1018-mRNA-1 (from shadow_AED::get_AED) Thanks, Esther From carsonhh at gmail.com Thu Feb 23 10:56:06 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:56:06 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F467A3B.4040002@duke.edu> Message-ID: You should be fine then. It may never even happen again (semi-random), but if it does, you can try reinstalling the Proc::ProcessTable module from CPAN. You can also change line 89 from 'require Proc::ProcessTable' to 'use Proc::ProcessTable', which would load at the start rather than at runtime (safe to do on your system because Proc::ProcessTable is already there). Thanks, Carson On 12-02-23 12:41 PM, "Olaf Mueller" wrote: >Thanks Carson, > >That's good to know. I'm running maker on a single machine (dual Xeon >quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on >this computer without MPICH2 hooked in. > >Best >Olaf > >On 02/23/2012 12:31 PM, Carson Holt wrote: >> The error is caused by a perl module that is loaded at runtime to access >> the system's Process Table. This is an error that sometimes happens in >> cluster environments like SGE. It's not related to the GFF3. It's more >> related to the specific system running MAKER at the time and can be >> semi-random. MAKER has auto-retry on contigs, so it would have done >>it's >> best to recover from any failure. If the master_index_datastore.log >>file >> shows all input contigs as being of status FINISHED, you are fine. >> >> If you are on a cluster and you continually get the error you may need >>to >> install the Proc::ProcessTable locally on that specific node and not >>just >> globally for the cluster. Errors with fold_constants happen when you >> compile on one system and then run on another. The issue can sometimes >>be >> related to floating points being slightly different between the two >> systems. So clusters that have non-identical architectures within the >> same cluster can have these types of errors more often. >> >> Thanks, >> Carson >> >> >> >> On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >> >>> Hi, >>> >>> I've done a preliminary run on an alga genome with maker 2.23beta, >>>using >>> only mRNA-seq tophat/cufflinks input and no additional evidence source. >>> >>> As prerequisite a cufflinks transcripts.gtf (merged from different read >>> sample mappings) has been converted with maker cufflinks2gff3 >>> (strandless transcripts/exons removed). I provided the resulting gff3 >>> via pred_gff and model_gff to maker, and also didn't call est2genome or >>> other predictors. >>> >>> During maker run for some scaffolds, I receive this error message for >>> some chunks, while gathering GFF3 input into hits: >>> >>> Gathering GFF3 input into hits - chunk:0 >>> panic: fold_constants JMPENV_PUSH returned 2 at >>> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >>> Gathering GFF3 input into hits - chunk:2 >>> ... >>> >>> The index log nevertheless reports these scaffolds as finished and >>> annotations are generated. Do I have to be concerned about this message >>> because it is related to my cufflinks input? >>> >>> Thanks >>> Olaf >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > >-- >Olaf Mueller, PhD >Duke University >Department of Biology, PO Box 90338 >369 Biological Sciences Bldg. >Science Drive >Durham, NC 27708, USA > >phone: (919) 660-7402 >email: olaf.mueller at duke.edu > From raramayo at tamu.edu Fri Feb 24 08:43:08 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Fri, 24 Feb 2012 09:43:08 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: *No Good Deed Shall Go Unpunished! *It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software* * Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > >> All MAKER versions after 2.2 use the CPAN forks.pm module rather than >> threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks themselves). >> The place where you get the error suggests the problem is at the C level, >> so the forks.pm 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 >> forks.pm. Don't worry about changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Feb 24 08:49:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 24 Feb 2012 10:49:46 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: I'm glad it is working now. There is nothing harder than tracking down errors in Perl that are really coming from a C compiled source outside of Perl (malloc, folding_constents, etc.). Thanks, Carson From: Rodolfo Aramayo Date: Fri, 24 Feb 2012 09:43:08 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: No Good Deed Shall Go Unpunished! It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: >> All MAKER versions after 2.2 use the CPAN forks.pm module >> rather than threads.pm . forks.pm is >> just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks >> themselves). The place where you get the error suggests the problem is at >> the C level, so the forks.pm 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 forks.pm . Don't worry about >> changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joana.guimaraes at inrb.pt Tue Feb 28 03:25:24 2012 From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=) Date: Tue, 28 Feb 2012 10:25:24 -0000 Subject: [maker-devel] maker run error Message-ID: Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastore_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Feb 28 05:48:09 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 28 Feb 2012 07:48:09 -0500 Subject: [maker-devel] maker run error In-Reply-To: Message-ID: You're using ABBlast. MAKER doesn't support it yet. Maybe now would be a good time to do it though. It would take about 10 hours to implement and test. I could probably look into it this weekend. Thanks, Carson From: "Maria Joana F. B. A. Guimar?es" Date: Tue, 28 Feb 2012 10:25:24 -0000 To: Subject: [maker-devel] maker run error maker run error Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastor e_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb. out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 07:47:32 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 08:47:32 -0600 Subject: [maker-devel] maker-2.23 Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 07:56:55 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 09:56:55 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: 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 Date: Thu, 23 Feb 2012 08:47:32 -0600 To: MAKER 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 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 08:17:36 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 09:17:36 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 08:26:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 10:26:50 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: All MAKER versions after 2.2 use the CPAN forks.pm module rather than threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to the about the module forks.pm and not forks themselves). The place where you get the error suggests the problem is at the C level, so the forks.pm 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 forks.pm. Don't worry about changing the perl installation. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 09:17:36 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson...please see below On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 > Date: Thu, 23 Feb 2012 08:47:32 -0600 > To: MAKER > 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_fi > nal_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_pGMI100 > 0MP.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_fi > nal_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_pGMI100 > 0MP%2Emod.genemark > /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_fi > nal_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_fi > nal_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/un > iprot_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 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From raramayo at tamu.edu Thu Feb 23 10:00:37 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Thu, 23 Feb 2012 11:00:37 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module rather than > threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am referring to > the about the module forks.pm and not forks themselves). The place where > you get the error suggests the problem is at the C level, so the forks.pmmodule 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 forks.pm. > Don't worry about changing the perl installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Feb 23 10:08:12 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:08:12 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: Does it indicate at any level what the compilation error is? 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. Thanks, Carson From: Rodolfo Aramayo Date: Thu, 23 Feb 2012 11:00:37 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Carson, Reinstalled storable, forks and forks::shared Re-compiled maker Same problem Change from forks/forks::shared to threads/threads::shared in the compiled executable and Running maker gives me: "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to compilation errors." Ideas? Thanks --R On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > All MAKER versions after 2.2 use the CPAN forks.pm module > rather than threads.pm . forks.pm is > just a drop in replacement for threads.pm 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 forks.pm (I am > referring to the about the module forks.pm and not forks > themselves). The place where you get the error suggests the problem is at the > C level, so the forks.pm 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 forks.pm . Don't worry about changing the perl > installation. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 09:17:36 -0600 > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Thanks Carson...please see below > > On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >> Date: Thu, 23 Feb 2012 08:47:32 -0600 >> To: MAKER >> 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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum%2Emod.genem >> ark >> 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_pGMI10 >> 00MP.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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum_plasmid_pGM >> I1000MP%2Emod.genemark >> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f >> inal_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_50.101 >> 059/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_f >> inal_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_50.101 >> 059/NODE_2_length_2929_cov_50%2E101059.0.uniprot_sprot%2Efasta.blastx.temp_di >> r/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 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From olaf.mueller at duke.edu Thu Feb 23 10:16:58 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:16:58 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F46748A.8000505@duke.edu> Hi, I've done a preliminary run on an alga genome with maker 2.23beta, using only mRNA-seq tophat/cufflinks input and no additional evidence source. As prerequisite a cufflinks transcripts.gtf (merged from different read sample mappings) has been converted with maker cufflinks2gff3 (strandless transcripts/exons removed). I provided the resulting gff3 via pred_gff and model_gff to maker, and also didn't call est2genome or other predictors. During maker run for some scaffolds, I receive this error message for some chunks, while gathering GFF3 input into hits: Gathering GFF3 input into hits - chunk:0 panic: fold_constants JMPENV_PUSH returned 2 at /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 Gathering GFF3 input into hits - chunk:2 ... The index log nevertheless reports these scaffolds as finished and annotations are generated. Do I have to be concerned about this message because it is related to my cufflinks input? Thanks Olaf From carsonhh at gmail.com Thu Feb 23 10:31:28 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:31:28 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F46748A.8000505@duke.edu> Message-ID: The error is caused by a perl module that is loaded at runtime to access the system's Process Table. This is an error that sometimes happens in cluster environments like SGE. It's not related to the GFF3. It's more related to the specific system running MAKER at the time and can be semi-random. MAKER has auto-retry on contigs, so it would have done it's best to recover from any failure. If the master_index_datastore.log file shows all input contigs as being of status FINISHED, you are fine. If you are on a cluster and you continually get the error you may need to install the Proc::ProcessTable locally on that specific node and not just globally for the cluster. Errors with fold_constants happen when you compile on one system and then run on another. The issue can sometimes be related to floating points being slightly different between the two systems. So clusters that have non-identical architectures within the same cluster can have these types of errors more often. Thanks, Carson On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >Hi, > >I've done a preliminary run on an alga genome with maker 2.23beta, using >only mRNA-seq tophat/cufflinks input and no additional evidence source. > >As prerequisite a cufflinks transcripts.gtf (merged from different read >sample mappings) has been converted with maker cufflinks2gff3 >(strandless transcripts/exons removed). I provided the resulting gff3 >via pred_gff and model_gff to maker, and also didn't call est2genome or >other predictors. > >During maker run for some scaffolds, I receive this error message for >some chunks, while gathering GFF3 input into hits: > >Gathering GFF3 input into hits - chunk:0 >panic: fold_constants JMPENV_PUSH returned 2 at >/home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >Gathering GFF3 input into hits - chunk:2 >... > >The index log nevertheless reports these scaffolds as finished and >annotations are generated. Do I have to be concerned about this message >because it is related to my cufflinks input? > >Thanks >Olaf > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From olaf.mueller at duke.edu Thu Feb 23 10:41:15 2012 From: olaf.mueller at duke.edu (Olaf Mueller) Date: Thu, 23 Feb 2012 12:41:15 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: References: Message-ID: <4F467A3B.4040002@duke.edu> Thanks Carson, That's good to know. I'm running maker on a single machine (dual Xeon quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on this computer without MPICH2 hooked in. Best Olaf On 02/23/2012 12:31 PM, Carson Holt wrote: > The error is caused by a perl module that is loaded at runtime to access > the system's Process Table. This is an error that sometimes happens in > cluster environments like SGE. It's not related to the GFF3. It's more > related to the specific system running MAKER at the time and can be > semi-random. MAKER has auto-retry on contigs, so it would have done it's > best to recover from any failure. If the master_index_datastore.log file > shows all input contigs as being of status FINISHED, you are fine. > > If you are on a cluster and you continually get the error you may need to > install the Proc::ProcessTable locally on that specific node and not just > globally for the cluster. Errors with fold_constants happen when you > compile on one system and then run on another. The issue can sometimes be > related to floating points being slightly different between the two > systems. So clusters that have non-identical architectures within the > same cluster can have these types of errors more often. > > Thanks, > Carson > > > > On 12-02-23 12:16 PM, "Olaf Mueller" wrote: > >> Hi, >> >> I've done a preliminary run on an alga genome with maker 2.23beta, using >> only mRNA-seq tophat/cufflinks input and no additional evidence source. >> >> As prerequisite a cufflinks transcripts.gtf (merged from different read >> sample mappings) has been converted with maker cufflinks2gff3 >> (strandless transcripts/exons removed). I provided the resulting gff3 >> via pred_gff and model_gff to maker, and also didn't call est2genome or >> other predictors. >> >> During maker run for some scaffolds, I receive this error message for >> some chunks, while gathering GFF3 input into hits: >> >> Gathering GFF3 input into hits - chunk:0 >> panic: fold_constants JMPENV_PUSH returned 2 at >> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >> Gathering GFF3 input into hits - chunk:2 >> ... >> >> The index log nevertheless reports these scaffolds as finished and >> annotations are generated. Do I have to be concerned about this message >> because it is related to my cufflinks input? >> >> Thanks >> Olaf >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Olaf Mueller, PhD Duke University Department of Biology, PO Box 90338 369 Biological Sciences Bldg. Science Drive Durham, NC 27708, USA phone: (919) 660-7402 email: olaf.mueller at duke.edu From esther.t.chan at gmail.com Thu Feb 23 10:42:02 2012 From: esther.t.chan at gmail.com (Esther) Date: Thu, 23 Feb 2012 09:42:02 -0800 (PST) Subject: [maker-devel] Error from a malformed gff file Message-ID: Hi, I'm interested in re-annotating gene models with new evidence using MAKER in a first generation genome (budding yeast). I have been able to run it fine in de novo and reference mode as described by Holt and Yandell in the Maize example in their 2011 BMC Bioinformatics paper but I'm having troubles running in re-annotation mode using a gff file with the model_gff parameter. The gff file I'm using is from SGD (http://downloads.yeastgenome.org/curation/chromosomal_feature/ saccharomyces_cerevisiae.gff) which should be GFF3 compliant according to this validator: https://github.com/solgenomics/gff3_validator. I get an error due to a malformed gff file, but without knowledge of which line(s) are offending, it's hard for me to fix the problem. Is there a way to find that information? The error message I get is as follows: Making transcripts Processing transcripts into genes Calculating annotation quality statistics ERROR: The feature being compared appears to be missing some of it's structure. This can happen when you use a malformed GFF3 file as input to one of MAKER's evidence passthrough options. Failed on maker-chrIII-pred_gff_blastx- gene-0.1018-mRNA-1 (from shadow_AED::get_AED) Thanks, Esther From carsonhh at gmail.com Thu Feb 23 10:56:06 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 Feb 2012 12:56:06 -0500 Subject: [maker-devel] maker-2.23 with tophat / cufflinks input In-Reply-To: <4F467A3B.4040002@duke.edu> Message-ID: You should be fine then. It may never even happen again (semi-random), but if it does, you can try reinstalling the Proc::ProcessTable module from CPAN. You can also change line 89 from 'require Proc::ProcessTable' to 'use Proc::ProcessTable', which would load at the start rather than at runtime (safe to do on your system because Proc::ProcessTable is already there). Thanks, Carson On 12-02-23 12:41 PM, "Olaf Mueller" wrote: >Thanks Carson, > >That's good to know. I'm running maker on a single machine (dual Xeon >quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on >this computer without MPICH2 hooked in. > >Best >Olaf > >On 02/23/2012 12:31 PM, Carson Holt wrote: >> The error is caused by a perl module that is loaded at runtime to access >> the system's Process Table. This is an error that sometimes happens in >> cluster environments like SGE. It's not related to the GFF3. It's more >> related to the specific system running MAKER at the time and can be >> semi-random. MAKER has auto-retry on contigs, so it would have done >>it's >> best to recover from any failure. If the master_index_datastore.log >>file >> shows all input contigs as being of status FINISHED, you are fine. >> >> If you are on a cluster and you continually get the error you may need >>to >> install the Proc::ProcessTable locally on that specific node and not >>just >> globally for the cluster. Errors with fold_constants happen when you >> compile on one system and then run on another. The issue can sometimes >>be >> related to floating points being slightly different between the two >> systems. So clusters that have non-identical architectures within the >> same cluster can have these types of errors more often. >> >> Thanks, >> Carson >> >> >> >> On 12-02-23 12:16 PM, "Olaf Mueller" wrote: >> >>> Hi, >>> >>> I've done a preliminary run on an alga genome with maker 2.23beta, >>>using >>> only mRNA-seq tophat/cufflinks input and no additional evidence source. >>> >>> As prerequisite a cufflinks transcripts.gtf (merged from different read >>> sample mappings) has been converted with maker cufflinks2gff3 >>> (strandless transcripts/exons removed). I provided the resulting gff3 >>> via pred_gff and model_gff to maker, and also didn't call est2genome or >>> other predictors. >>> >>> During maker run for some scaffolds, I receive this error message for >>> some chunks, while gathering GFF3 input into hits: >>> >>> Gathering GFF3 input into hits - chunk:0 >>> panic: fold_constants JMPENV_PUSH returned 2 at >>> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89 >>> Gathering GFF3 input into hits - chunk:2 >>> ... >>> >>> The index log nevertheless reports these scaffolds as finished and >>> annotations are generated. Do I have to be concerned about this message >>> because it is related to my cufflinks input? >>> >>> Thanks >>> Olaf >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > >-- >Olaf Mueller, PhD >Duke University >Department of Biology, PO Box 90338 >369 Biological Sciences Bldg. >Science Drive >Durham, NC 27708, USA > >phone: (919) 660-7402 >email: olaf.mueller at duke.edu > From raramayo at tamu.edu Fri Feb 24 08:43:08 2012 From: raramayo at tamu.edu (Rodolfo Aramayo) Date: Fri, 24 Feb 2012 09:43:08 -0600 Subject: [maker-devel] maker-2.23 In-Reply-To: References: Message-ID: Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: *No Good Deed Shall Go Unpunished! *It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software* * Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: > >> All MAKER versions after 2.2 use the CPAN forks.pm module rather than >> threads.pm. forks.pm is just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks themselves). >> The place where you get the error suggests the problem is at the C level, >> so the forks.pm 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 >> forks.pm. Don't worry about changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Feb 24 08:49:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 24 Feb 2012 10:49:46 -0500 Subject: [maker-devel] maker-2.23 In-Reply-To: Message-ID: I'm glad it is working now. There is nothing harder than tracking down errors in Perl that are really coming from a C compiled source outside of Perl (malloc, folding_constents, etc.). Thanks, Carson From: Rodolfo Aramayo Date: Fri, 24 Feb 2012 09:43:08 -0600 To: Carson Holt Cc: MAKER Subject: Re: [maker-devel] maker-2.23 Thanks Carson, So I did the following: Deleted the Maker installation Re-configure, re-compiled and re-installed mpich2 Re-installed CPAN and all the CPAN-modules required by Maker Re-compiled and re-installed Maker Re-installed Genemark and now things work! The question remains, why did this failed? 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?? 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 Like they say: No Good Deed Shall Go Unpunished! It is like I had to pay the Gods their tribute in pain over the fact that I dared to upgrade the software Thanks for your help --Rodolfo On Thu, Feb 23, 2012 at 11:08, Carson Holt wrote: > Does it indicate at any level what the compilation error is? > > 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. > > Thanks, > Carson > > From: Rodolfo Aramayo > Date: Thu, 23 Feb 2012 11:00:37 -0600 > > To: Carson Holt > Cc: MAKER > Subject: Re: [maker-devel] maker-2.23 > > Carson, > > Reinstalled storable, forks and forks::shared > Re-compiled maker > Same problem > > Change from forks/forks::shared to threads/threads::shared in the compiled > executable and > Running maker gives me: > > "Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to > compilation errors." > > Ideas? > > Thanks > > --R > > > > > > On Thu, Feb 23, 2012 at 09:26, Carson Holt wrote: >> All MAKER versions after 2.2 use the CPAN forks.pm module >> rather than threads.pm . forks.pm is >> just a drop in replacement for threads.pm 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 forks.pm (I am >> referring to the about the module forks.pm and not forks >> themselves). The place where you get the error suggests the problem is at >> the C level, so the forks.pm 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 forks.pm . Don't worry about >> changing the perl installation. >> >> Thanks, >> Carson >> >> From: Rodolfo Aramayo >> Date: Thu, 23 Feb 2012 09:17:36 -0600 >> To: Carson Holt >> Cc: MAKER >> Subject: Re: [maker-devel] maker-2.23 >> >> Thanks Carson...please see below >> >> On Thu, Feb 23, 2012 at 08:56, Carson Holt 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 >>> Date: Thu, 23 Feb 2012 08:47:32 -0600 >>> To: MAKER >>> 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 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joana.guimaraes at inrb.pt Tue Feb 28 03:25:24 2012 From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=) Date: Tue, 28 Feb 2012 10:25:24 -0000 Subject: [maker-devel] maker run error Message-ID: Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastore_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Feb 28 05:48:09 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 28 Feb 2012 07:48:09 -0500 Subject: [maker-devel] maker run error In-Reply-To: Message-ID: You're using ABBlast. MAKER doesn't support it yet. Maybe now would be a good time to do it though. It would take about 10 hours to implement and test. I could probably look into it this weekend. Thanks, Carson From: "Maria Joana F. B. A. Guimar?es" Date: Tue, 28 Feb 2012 10:25:24 -0000 To: Subject: [maker-devel] maker run error maker run error Hi I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error: bioinf at linux-hdoc:~/Desktop/TEMP> maker STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore To access files for individual sequences use the datastore index: /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastor e_index.log STATUS: Now running MAKER... --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: contig-dpp-500-500 Length: 32156 #--------------------------------------------------------------------- running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1 #-------------------------------# processing output: cycle 1 cycle 2 cycle 3 cycle 4 cycle 5 cycle 6 cycle 7 cycle 8 cycle 9 cycle 10 Generating output... masking done formating database... #--------- command -------------# Widget::formater: /home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now retrying the contig!! SeqID: contig-dpp-500-500 Length: 32156 Tries: 2!! #--------------------------------------------------------------------- re reading repeat masker report. /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb. out running blast search. #--------- command -------------# Widget::blastx: /home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F /contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner #-------------------------------# FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 FATAL: Argument 1 ("-db") is not recognized or is improperly formed. EXIT CODE 5 ERROR: BLASTX failed ERROR: Failed while doing blastx repeats ERROR: Chunk failed at level:1, tier_type:1 FAILED CONTIG:contig-dpp-500-500 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:contig-dpp-500-500 --Next Contig-- Processing run.log file... MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner did not finish on the last run and must be erased Maker is now finished!!! bioinf at linux-hdoc:~/Desktop/TEMP> Can you please help me? Thanks Joana _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: