[maker-devel] maker 2.10 Segmentation fault
Alvin Chen
alvinchen2002 at gmail.com
Fri Jun 15 13:41:52 MDT 2012
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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