[maker-devel] maker 2.10 Segmentation fault
Alvin Chen
alvinchen2002 at gmail.com
Tue Jun 19 23:15:24 MDT 2012
Hey Carson,
I am still using 2.10, because 2.25 get crashed at the beginning. I think it may be caused by these codes:
Proc::Signal::reap_children_by_name(15, 'maintain.pl'); #clean up maintainers
Proc::Signal::reap_children_by_name(9, 'maintain.pl'); #clean up maintainers"
You have added them at the top of the scripts in the new version.
Alvin
On Jun 20, 2012, at 1:03 AM, Carson Holt wrote:
> Yes. dpp_contig should produce 3 transcripts for 1 gene. I meant MAKER
> version 2.25 (type maker -v to see the version you are using). The
> reap_children_by_name(9, 'maintain.pl') is basically a fallback if the
> process fails to respond to signals upstream in the code. The 2.25
> version of MAKER does some extra things that should even further avoid the
> need for the call compared to MAKER 2.10.
>
> Thanks,
> Carson
>
>
>
>
>
>
> On 12-06-19 8:57 PM, "Alvin Chen" <alvinchen2002 at gmail.com> wrote:
>
>> 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_datas
>>>> to
>>>> 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_datas
>>>> to
>>>> re
>>>>
>>>> To access files for individual sequences use the datastore index:
>>>>
>>>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_maste
>>>> r_
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .0.all.rb -species all -dir
>>>>
>>>> /home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datas
>>>> to
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>>
>>>> .0.dpp_protein%2Efasta.blastx.temp_dir/dpp_protein%2Efasta.mpi.1.0.blast
>>>> x
>>>> #-------------------------------#
>>>> 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_datas
>>>> to
>>>>
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>> 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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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_datas
>>>> to
>>>>
>>>> re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-5
>>>> 00
>>>> .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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