[maker-devel] maker 2.10 Segmentation fault
Carson Holt
carsonhh at gmail.com
Tue Jun 19 23:50:03 MDT 2012
Perfect. And good to know.
Thanks,
Carson
On 12-06-19 10:48 PM, "Alvin Chen" <alvinchen2002 at gmail.com> wrote:
>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_ma
>>>>>>st
>>>>>> 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_ma
>>>>>>st
>>>>>> 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_ma
>>>>>>st
>>>>>> 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_d
>>>>>>>at
>>>>>>> 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_d
>>>>>>>at
>>>>>>> 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_m
>>>>>>>as
>>>>>>> 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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -5
>>>>>>> 00
>>>>>>> .0.all.rb -species all -dir
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> 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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -5
>>>>>>> 00
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>.0.dpp_protein%2Efasta.blastx.temp_dir/dpp_protein%2Efasta.mpi.1.0.b
>>>>>>>la
>>>>>>> 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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-5.f
>>>>>>>as
>>>>>>> ta
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-4.f
>>>>>>>as
>>>>>>> ta
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-3.f
>>>>>>>as
>>>>>>> ta
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-2.f
>>>>>>>as
>>>>>>> ta
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-1.f
>>>>>>>as
>>>>>>> ta
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-5.fa
>>>>>>>st
>>>>>>> a
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-4.fa
>>>>>>>st
>>>>>>> a
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-3.fa
>>>>>>>st
>>>>>>> a
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-2.fa
>>>>>>>st
>>>>>>> a
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-1.fa
>>>>>>>st
>>>>>>> a
>>>>>>> -t
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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_d
>>>>>>>at
>>>>>>> as
>>>>>>> to
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-5
>>>>>>>00
>>>>>>> -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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