[maker-devel] maker 2.10 Segmentation fault

Tue Jun 19 09:39:55 MDT 2012

The "Maker is now finished" message occurs before the Segmentation fault
so it is finished.  The Segmentation fault is probably an issue with your
system reaping the perl threads on completion.  You can try reinstalling
the forks and forks::shared from CPAN.  Also make sure you are using the
2.25 version and no 2.10.  But your job is finished anyways, so it's
really not affecting the output.  MAKER puts the results for each contig
in a separate folder because some downstream programs like Apollo can only
handle one contig at a time.  Use the
/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_d
atastore_index.log file to see where each contigs output is stored.

If you want a merged output file for everything, use the merge_gff script
in maker and give it the
/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_d
atastore_index.log file and it will assemble a merged output file for you.
 There are two type of output GFF3 which gives detailed annotation
information and fasta which just produces sequence for each transcript.
Use fasta_merge to get a merged fasta file for all contigs (giving it the
same 
/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_d
atastore_index.log file).  The fiel you are interested will be the
maker.pteins.fasta and maker.transcripts.fasta file.

More information on MAKER's output here -->
http://gmod.org/wiki/MAKER_Tutorial#MAKER.27s_Output

Thanks,
Carson

On 12-06-18 2:16 PM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>Hi Alvin,
>I am a relatively new user too. I too get "seg fault" even though, maker
>did finish making the gff file successfully.
>
>GFFs are actually buried deep down. One possibility is that you were
>looking only in parent folders.
>If you have not done already,  you might want to check for gffs at:
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/*/*/*. ie, three levels down your data store.
>
>what does "dpp_contig_master_datastore_index.log" says? Failed/Finsihed ?
>
>Gowthaman
>________________________________________
>From: maker-devel-bounces at yandell-lab.org
>[maker-devel-bounces at yandell-lab.org] On Behalf Of Alvin Chen
>[alvinchen2002 at gmail.com]
>Sent: Friday, June 15, 2012 12:41 PM
>To: maker-devel at yandell-lab.org
>Subject: [maker-devel] maker 2.10 Segmentation fault
>
>Hi,
>
>        This is my first time to use maker. I have installed everything
>that required by maker, and use the data in "data" folder to test this
>program. But I got a "Segmentation fault" message after "Maker is now
>finished!!!". And I can't find gff file anywhere. Does anyone have a clue
>of this?
>
>Thanks,
>Alvin
>
>Here is the output of the program:
>
>[yc136 at mmrl-n01 data]$ maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl
>WARNING: blast_type is set to 'wublast' but executables cannot be located
>The blast_type 'ncbi' will be used instead.
>
>A data structure will be created for you at:
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re
>
>To access files for individual sequences use the datastore index:
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_master_
>datastore_index.log
>
>
>
>
>--Next Contig--
>
>#---------------------------------------------------------------------
>Now starting the contig!!
>SeqID: contig-dpp-500-500
>Length: 32156
>#---------------------------------------------------------------------
>
>
>running  repeat masker.
>#--------- command -------------#
>Widget::RepeatMasker:
>/home/mmrl/yc136/bin/RepeatMasker/RepeatMasker
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.all.rb -species all -dir
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1
>#-------------------------------#
>processing output:
>cycle 1
>cycle 2
>cycle 3
>cycle 4
>cycle 5
>cycle 6
>cycle 7
>cycle 8
>cycle 9
>cycle 10
>Generating output...
>masking
>done
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.0
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.0 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.1
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.1 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.2
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.2 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.3
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.3 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.4
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.4 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.5
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.5 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.6
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.6 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.7
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.7 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.8
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.8 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.9
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/te_proteins%2Efasta.mpi.10.9 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.
>repeatrunner
>#-------------------------------#
>deleted:0 hits
> in cluster:shadow cluster...
>    i_size:5 j_size:3
> sorting hits in shadow cluster...
>... finished.
> i_size:5   current i:0
> i_size:5   current i:1
> i_size:5   current i:2
> i_size:5   current i:3
> i_size:5   current i:4
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p F -i /tmp/maker_MsJuiW/dpp_est%2Efasta.mpi.1.0
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastn:
>/usr/bin/blastall -p blastn -d /tmp/maker_MsJuiW/dpp_est%2Efasta.mpi.1.0
>-i /tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e
>1e-10 -E 3 -W 15 -r 1 -q -3 -G 3 -z 1000 -Y 500000000 -a 1 -U -F T -I T
>-o 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.dpp_est%2Efasta.blastn.temp_dir/dpp_est%2Efasta.mpi.1.0.blastn
>#-------------------------------#
>deleted:-1 hits
>formating database...
>#--------- command -------------#
>Widget::formater:
>/usr/bin/formatdb -p T -i /tmp/maker_MsJuiW/dpp_protein%2Efasta.mpi.1.0
>#-------------------------------#
>running  blast search.
>#--------- command -------------#
>Widget::blastx:
>/usr/bin/blastall -p blastx -d
>/tmp/maker_MsJuiW/dpp_protein%2Efasta.mpi.1.0 -i
>/tmp/maker_MsJuiW/rank0/contig-dpp-500-500.0 -b 100000 -v 100000 -e 1e-06
>-z 300 -Y 500000000 -a 1 -U -F T -I T -o
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.0.dpp_protein%2Efasta.blastx.temp_dir/dpp_protein%2Efasta.mpi.1.0.blastx
>#-------------------------------#
>deleted:0 hits
>running  est2genome search.
>#--------- command -------------#
>Widget::exonerate::est2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate  -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-5.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26586-31847.fasta -Q dna -T dna --model est2genome  --minintron 20
>--showcigar --percent 20 >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26586-31847.dpp-mRNA-5.est_exonerate
>#-------------------------------#
>running  est2genome search.
>#--------- command -------------#
>Widget::exonerate::est2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate  -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-4.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.23089-31847.fasta -Q dna -T dna --model est2genome  --minintron 20
>--showcigar --percent 20 >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.23089-31847.dpp-mRNA-4.est_exonerate
>#-------------------------------#
>running  est2genome search.
>#--------- command -------------#
>Widget::exonerate::est2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate  -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-3.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.22854-31847.fasta -Q dna -T dna --model est2genome  --minintron 20
>--showcigar --percent 20 >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.22854-31847.dpp-mRNA-3.est_exonerate
>#-------------------------------#
>running  est2genome search.
>#--------- command -------------#
>Widget::exonerate::est2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate  -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-2.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.20908-31847.fasta -Q dna -T dna --model est2genome  --minintron 20
>--showcigar --percent 20 >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.20908-31847.dpp-mRNA-2.est_exonerate
>#-------------------------------#
>running  est2genome search.
>#--------- command -------------#
>Widget::exonerate::est2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate  -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-mRNA-1.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26901-31847.fasta -Q dna -T dna --model est2genome  --minintron 20
>--showcigar --percent 20 >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26901-31847.dpp-mRNA-1.est_exonerate
>#-------------------------------#
>cleaning blastn...
>cleaning tblastx...
>running  exonerate search.
>#--------- command -------------#
>Widget::exonerate::protein2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-5.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>--percent 20 --showcigar  >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.dpp-CDS-5.p_exonerate
>#-------------------------------#
>running  exonerate search.
>#--------- command -------------#
>Widget::exonerate::protein2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-4.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>--percent 20 --showcigar  >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.dpp-CDS-4.p_exonerate
>#-------------------------------#
>running  exonerate search.
>#--------- command -------------#
>Widget::exonerate::protein2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-3.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>--percent 20 --showcigar  >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.dpp-CDS-3.p_exonerate
>#-------------------------------#
>running  exonerate search.
>#--------- command -------------#
>Widget::exonerate::protein2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-2.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>--percent 20 --showcigar  >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.dpp-CDS-2.p_exonerate
>#-------------------------------#
>running  exonerate search.
>#--------- command -------------#
>Widget::exonerate::protein2genome:
>/home/mmrl/yc136/bin/exonerate-2.2.0-x86_64/bin/exonerate -q
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/dpp-CDS-1.fasta
>-t 
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.fasta -Q protein -T dna -m protein2genome --softmasktarget
>--percent 20 --showcigar  >
>/home/mmrl/yc136/bin/maker/data/dpp_contig.maker.output/dpp_contig_datasto
>re/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500
>.26918-30804.dpp-CDS-1.p_exonerate
>#-------------------------------#
>cleaning blastx...
>Preparing evidence for hint based annotation
> in cluster:shadow cluster...
>    i_size:15 j_size:1
> sorting hits in shadow cluster...
>... finished.
> i_size:15   current i:0
> i_size:15   current i:1
> i_size:15   current i:2
> i_size:15   current i:3
> i_size:15   current i:4
> i_size:15   current i:5
> i_size:15   current i:6
> i_size:15   current i:7
> i_size:15   current i:8
> i_size:15   current i:9
> i_size:15   current i:10
> i_size:15   current i:11
> i_size:15   current i:12
> i_size:15   current i:13
> i_size:15   current i:14
> in cluster:shadow cluster...
>    i_size:0 j_size:0
> sorting hits in shadow cluster...
>... finished.
> ...processing 0 of 5
> ...processing 1 of 5
> ...processing 2 of 5
> ...processing 3 of 5
>Making transcripts
>Processing transcripts into genes
> in cluster:shadow cluster...
>    i_size:3 j_size:1
> sorting hits in shadow cluster...
>... finished.
> i_size:3   current i:0
> i_size:3   current i:1
> i_size:3   current i:2
> in cluster:shadow cluster...
>    i_size:0 j_size:0
> sorting hits in shadow cluster...
>... finished.
>now careful_clustering....
>getting Pairs
>doing single linkage clustering
> ...processing 0 of 3
> ...processing 1 of 3
>Calculating annotation quality statistics
>Choosing best annotations
>
>
>Maker is now finished!!!
>
>Segmentation fault
>
>
>
>
>_______________________________________________
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>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org