[maker-devel] maker 2.10 Segmentation fault
Alvin Chen
alvinchen2002 at gmail.com
Tue Jun 19 21:57:33 MDT 2012
Hey Carson and Gowthaman,
Thanks for your replies! You are right, Carson, the problem caused by "Proc::Signal::reap_children_by_name(9, 'maintain.pl');". dpp_contig_master_datastore_index.log shows that the job has finished. I have installed the newest version of forks and forks::shared. but the version is 0.34 not 2.25, is that correct? The bad news is that the program still crashed at last, but it won't hurt. I have tried the dpp and hsap data in data folder, and I have got 6 genes for hsap and 3 genes for dpp, is this number correct? I just want make sure everything works fine and I will begin to use it with my data. Thanks!
Best,
Alvin
On Jun 19, 2012, at 11:39 AM, Carson Holt wrote:
> The "Maker is now finished" message occurs before the Segmentation fault
> so it is finished. The Segmentation fault is probably an issue with your
> system reaping the perl threads on completion. You can try reinstalling
> the forks and forks::shared from CPAN. Also make sure you are using the
> 2.25 version and no 2.10. But your job is finished anyways, so it's
> really not affecting the output. MAKER puts the results for each contig
> in a separate folder because some downstream programs like Apollo can only
> handle one contig at a time. Use the
> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_d
> atastore_index.log file to see where each contigs output is stored.
>
>
> If you want a merged output file for everything, use the merge_gff script
> in maker and give it the
> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_d
> atastore_index.log file and it will assemble a merged output file for you.
> There are two type of output GFF3 which gives detailed annotation
> information and fasta which just produces sequence for each transcript.
> Use fasta_merge to get a merged fasta file for all contigs (giving it the
> same
> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_d
> atastore_index.log file). The fiel you are interested will be the
> maker.pteins.fasta and maker.transcripts.fasta file.
>
> More information on MAKER's output here -->
> http://gmod.org/wiki/MAKER_Tutorial#MAKER.27s_Output
>
> Thanks,
> Carson
>
>
> On 12-06-18 2:16 PM, "Gowthaman Ramasamy"
> <gowthaman.ramasamy at seattlebiomed.org> wrote:
>
>> Hi Alvin,
>> I am a relatively new user too. I too get "seg fault" even though, maker
>> did finish making the gff file successfully.
>>
>> GFFs are actually buried deep down. One possibility is that you were
>> looking only in parent folders.
>> If you have not done already, you might want to check for gffs at:
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/*/*/*. ie, three levels down your data store.
>>
>> what does "dpp_contig_master_datastore_index.log" says? Failed/Finsihed ?
>>
>> Gowthaman
>> ________________________________________
>> From: maker-devel-bounces at yandell-lab.org
>> [maker-devel-bounces at yandell-lab.org] On Behalf Of Alvin Chen
>> [alvinchen2002 at gmail.com]
>> Sent: Friday, June 15, 2012 12:41 PM
>> To: maker-devel at yandell-lab.org
>> Subject: [maker-devel] maker 2.10 Segmentation fault
>>
>> Hi,
>>
>> This is my first time to use maker. I have installed everything
>> that required by maker, and use the data in "data" folder to test this
>> program. But I got a "Segmentation fault" message after "Maker is now
>> finished!!!". And I can't find gff file anywhere. Does anyone have a clue
>> of this?
>>
>> Thanks,
>> Alvin
>>
>> Here is the output of the program:
>>
>> [yc136 at mmrl-n01 data]$ maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl
>> WARNING: blast_type is set to 'wublast' but executables cannot be located
>> The blast_type 'ncbi' will be used instead.
>>
>> A data structure will be created for you at:
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re
>>
>> To access files for individual sequences use the datastore index:
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_
>> datastore_index.log
>>
>>
>>
>>
>> --Next Contig--
>>
>> #---------------------------------------------------------------------
>> Now starting the contig!!
>> SeqID: contig-dpp-500-500
>> Length: 32156
>> #---------------------------------------------------------------------
>>
>>
>> running repeat masker.
>> #--------- command -------------#
>> Widget::RepeatMasker:
>> /home/mmrl/yc136/bin/RepeatMasker/RepeatMasker
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .0.all.rb -species all -dir
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.0
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.0 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.1
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.1 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.1.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.2
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.2 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.2.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.3
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.3 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.3.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.4
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.4 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.4.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.5
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.5 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.5.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.6
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.6 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.6.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.7
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.7 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.7.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.8
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.8 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.8.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.9
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.9 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/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.10.9.
>> repeatrunner
>> #-------------------------------#
>> deleted:0 hits
>> in cluster:shadow cluster...
>> i_size:5 j_size:3
>> sorting hits in shadow cluster...
>> ... finished.
>> i_size:5 current i:0
>> i_size:5 current i:1
>> i_size:5 current i:2
>> i_size:5 current i:3
>> i_size:5 current i:4
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p F -i /tmp/maker_MsJuiW/dpp_est%2Efasta.mpi.1.0
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastn:
>> /usr/bin/blastall -p blastn -d /tmp/maker_MsJuiW/dpp_est%2Efasta.mpi.1.0
>> -i /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e
>> 1e-10 -E 3 -W 15 -r 1 -q -3 -G 3 -z 1000 -Y 500000000 -a 1 -U -F T -I T
>> -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .0.dpp_est%2Efasta.blastn.temp_dir/dpp_est%2Efasta.mpi.1.0.blastn
>> #-------------------------------#
>> deleted:-1 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/dpp_protein%2Efasta.mpi.1.0
>> #-------------------------------#
>> running blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/bin/blastall -p blastx -d
>> /tmp/maker_MsJuiW/dpp_protein%2Efasta.mpi.1.0 -i
>> /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>> -z 300 -Y 500000000 -a 1 -U -F T -I T -o
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .0.dpp_protein%2Efasta.blastx.temp_dir/dpp_protein%2Efasta.mpi.1.0.blastx
>> #-------------------------------#
>> deleted:0 hits
>> running est2genome search.
>> #--------- command -------------#
>> Widget::exonerate::est2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-5.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26586-31847.fasta -Q dna -T dna --model est2genome --minintron 20
>> --showcigar --percent 20 >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26586-31847.dpp-mRNA-5.est_exonerate
>> #-------------------------------#
>> running est2genome search.
>> #--------- command -------------#
>> Widget::exonerate::est2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-4.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .23089-31847.fasta -Q dna -T dna --model est2genome --minintron 20
>> --showcigar --percent 20 >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .23089-31847.dpp-mRNA-4.est_exonerate
>> #-------------------------------#
>> running est2genome search.
>> #--------- command -------------#
>> Widget::exonerate::est2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-3.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .22854-31847.fasta -Q dna -T dna --model est2genome --minintron 20
>> --showcigar --percent 20 >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .22854-31847.dpp-mRNA-3.est_exonerate
>> #-------------------------------#
>> running est2genome search.
>> #--------- command -------------#
>> Widget::exonerate::est2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-2.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .20908-31847.fasta -Q dna -T dna --model est2genome --minintron 20
>> --showcigar --percent 20 >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .20908-31847.dpp-mRNA-2.est_exonerate
>> #-------------------------------#
>> running est2genome search.
>> #--------- command -------------#
>> Widget::exonerate::est2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-1.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26901-31847.fasta -Q dna -T dna --model est2genome --minintron 20
>> --showcigar --percent 20 >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26901-31847.dpp-mRNA-1.est_exonerate
>> #-------------------------------#
>> cleaning blastn...
>> cleaning tblastx...
>> running exonerate search.
>> #--------- command -------------#
>> Widget::exonerate::protein2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-5.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>> --percent 20 --showcigar >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.dpp-CDS-5.p_exonerate
>> #-------------------------------#
>> running exonerate search.
>> #--------- command -------------#
>> Widget::exonerate::protein2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-4.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>> --percent 20 --showcigar >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.dpp-CDS-4.p_exonerate
>> #-------------------------------#
>> running exonerate search.
>> #--------- command -------------#
>> Widget::exonerate::protein2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-3.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>> --percent 20 --showcigar >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.dpp-CDS-3.p_exonerate
>> #-------------------------------#
>> running exonerate search.
>> #--------- command -------------#
>> Widget::exonerate::protein2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-2.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>> --percent 20 --showcigar >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.dpp-CDS-2.p_exonerate
>> #-------------------------------#
>> running exonerate search.
>> #--------- command -------------#
>> Widget::exonerate::protein2genome:
>> /home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-1.fasta
>> -t
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>> --percent 20 --showcigar >
>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>> .26918-30804.dpp-CDS-1.p_exonerate
>> #-------------------------------#
>> cleaning blastx...
>> Preparing evidence for hint based annotation
>> in cluster:shadow cluster...
>> i_size:15 j_size:1
>> sorting hits in shadow cluster...
>> ... finished.
>> i_size:15 current i:0
>> i_size:15 current i:1
>> i_size:15 current i:2
>> i_size:15 current i:3
>> i_size:15 current i:4
>> i_size:15 current i:5
>> i_size:15 current i:6
>> i_size:15 current i:7
>> i_size:15 current i:8
>> i_size:15 current i:9
>> i_size:15 current i:10
>> i_size:15 current i:11
>> i_size:15 current i:12
>> i_size:15 current i:13
>> i_size:15 current i:14
>> in cluster:shadow cluster...
>> i_size:0 j_size:0
>> sorting hits in shadow cluster...
>> ... finished.
>> ...processing 0 of 5
>> ...processing 1 of 5
>> ...processing 2 of 5
>> ...processing 3 of 5
>> Making transcripts
>> Processing transcripts into genes
>> in cluster:shadow cluster...
>> i_size:3 j_size:1
>> sorting hits in shadow cluster...
>> ... finished.
>> i_size:3 current i:0
>> i_size:3 current i:1
>> i_size:3 current i:2
>> in cluster:shadow cluster...
>> i_size:0 j_size:0
>> sorting hits in shadow cluster...
>> ... finished.
>> now careful_clustering....
>> getting Pairs
>> doing single linkage clustering
>> ...processing 0 of 3
>> ...processing 1 of 3
>> Calculating annotation quality statistics
>> Choosing best annotations
>>
>>
>> Maker is now finished!!!
>>
>> Segmentation fault
>>
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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