[maker-devel] maker 2.10 Segmentation fault
Alvin Chen
alvinchen2002 at gmail.com
Tue Jun 19 23:48:10 MDT 2012
Hey Carson,
It seems like there is a bug in Proc-ProcessTable 0.45. I solved the problem by downgraded Proc-ProcessTable from 0.45 to 0.44. I can run 2.25 without any problems now.
Cheers,
Alvin
On Jun 20, 2012, at 1:21 AM, Carson Holt wrote:
> 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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