[maker-devel] maker 2.10 Segmentation fault
Gowthaman Ramasamy
gowthaman.ramasamy at seattlebiomed.org
Mon Jun 18 12:16:00 MDT 2012
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_datastore/*/*/*. 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_datastore
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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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_datastore/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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