Segmentation fault in start_site_curation

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Segmentation fault in start_site_curation

Paul Li
Hi Ergatis users,

I am trying to run prokaryotic annotation pipeline with a 5.2MB fasta file that contains a single sequence. But I am getting segmentation fault at start_site_curation step. When I trimmed the same fasta file into smaller sizes (1MB, 2MB) then run the pipeline respectively, they both passed. I ran in debug mode; It seems successfully parsing input BSML file in subroutine parse_input_bsml. But segfault appears while exiting subroutine parse_input_bsml.

/opt/ergatis/bin/start_site_curation --input_file="" --input_list="/usr/local/projects/paul/output_repository/overlap_analysis/179_default/overlap_analysis.bsml.list" --output_directory=/usr/local/projects/paul/output_repository/start_site_curation/179_default --evidence=/usr/local/projects/paul/output_repository/ber/179_pre_overlap_analysis/ber.bsml.list --ber_extension=300 --char_db='/usr/local/db/lookups/uniref100_lookup.db' --hmm_coding_db=/usr/local/db/lookups/coding_hmm.lib.h2.db --username='' --password='' --percent_identity_cutoff=60 --p_value_cutoff=1e-30 --characterized_vote_bonus=4 --min_vote_cutoff=2 --rbs_sliding_window_size=6 --rbs_ag_percent_cutoff=75 --log=/usr/local/projects/paul/output_repository/start_site_curation/179_default/start_site_curation.log --debug=5

return value: 139
message: Error executing script exit value: 139/opt/ergatis/bin/start_site_curation: line 34: 16161 Segmentation fault /usr/bin/perl /opt/ergatis/bin/ "$@"

Has anyone seen the similar problem?
Any suggestions would be appreciated.

Thank you so much.

Paul Li
Bioscience Division
Los Alamos National Laboratory
Phone:(505) 664-0943

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