[maker-devel] maker 2.10 Segmentation fault
Carson Holt
carsonhh at gmail.com
Tue Jun 19 23:21:22 MDT 2012
Those are wrapped in an END block so they only run when perl exits (I.e.
post completion or failure). If 2.25 is failing it would likely be for
another reason. Can you run 2.25 with the -debug flag set I.e. (maker
-debug). Does it produce any output before failure?
Thanks,
Carson
On 12-06-19 10:15 PM, "Alvin Chen" <alvinchen2002 at gmail.com> wrote:
>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_mast
>>>>er
>>>> _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_mast
>>>>er
>>>> _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_mast
>>>>er
>>>> _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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>> re
>>>>>
>>>>> To access files for individual sequences use the datastore index:
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_mas
>>>>>te
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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.1
>>>>>0.
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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.bla
>>>>>st
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-5.fas
>>>>>ta
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-4.fas
>>>>>ta
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-3.fas
>>>>>ta
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-2.fas
>>>>>ta
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-1.fas
>>>>>ta
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-5.fast
>>>>>a
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-4.fast
>>>>>a
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-3.fast
>>>>>a
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-2.fast
>>>>>a
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> to
>>>>>
>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-1.fast
>>>>>a
>>>>> -t
>>>>>
>>>>>
>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_dat
>>>>>as
>>>>> 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_dat
>>>>>as
>>>>> 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.or
>>>>>g
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>
>>>>
>>>
>>
>>
>
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