parse_evidence error

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parse_evidence error

gary_xie
Anyone has insight on this?
Thanks,
Gary

>
> The 'parse_evidence' is failing, and I'm sure it's misconfiguration  
> of my TIGRFAMs stuff, but I think I have everything it needs, and I  
> can find TIGR03654. in the TIGRFAMS directory. But I'm not clear  
> enough on what it's trying to do to debug:
>
> [WIN+117163@seed bin]$ /opt/ergatis/bin/parse_evidence --input_list=/
> usr/local/projects/rox/output_repository/hmmpfam/
> 90_pre_overlap_analysis/hmmpfam.bsml.list --output=/usr/local/
> projects/rox/output_repository/parse_evidence/93_hmmpfam_pre/
> parse_evidence.HMM.tab --evidence_type=HMM --
> bsml_feature_lookup_list=/usr/local/projects/rox/output_repository/
> start_site_curation/90_default/start_site_curation.bsml.list --
> annotate_on=transcript --other_options='hmm_info=/usr/local/db/
> lookups/coding_hmm.lib.h2.db tigr_roles_db_dir=/usr/local/db/lookups  
> tigrfams_dir=/usr/local/db/TIGRFAMS'
> $parser = new PFunc::EvidenceParser::HMMParser( hmm_info => "/usr/
> local/db/lookups/coding_hmm.lib.h2.db", tigr_roles_db_dir => "/usr/
> local/db/lookups", tigrfams_dir => "/usr/local/db/TIGRFAMS" )
> Parsing bsml feature lookup
> Pre parse
> starting evidence parse
> 11/41Could not find hmm TIGR03654 in lookup at /opt/ergatis/lib/
> perl5//PFunc/EvidenceParser/HMMParser.pm line 238.
> at /opt/ergatis/lib/perl5//PFunc/EvidenceParser/HMMParser.pm line 117
> [WIN+117163@seed bin]$
>


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