ID h45
TITLE Zero length sequences crash hmmscan
STATUS CLOSED in 3.0a2
XREF J4/112 2009/0310-bug-h45
REPORTED_BY Ryan Richt ryan_richt@cofactorgenomics.com
OPENED_DATE SRE, Tue Mar 10 13:28:00 2009
CLOSED_DATE SRE, Tue Mar 10 14:48:40 2009
DESCRIPTION
Searching a sequence of length 0 crashes:
% hmmscan tutorial/minifam test.fa
...
Fatal exception (source file fwdback.c, line 140):
Forward implementation makes assumptions that only work for local alignment
Abort
or for hmmsearch:
Fatal exception (source file fwdback.c, line 461):
forward score underflow (is 0.0)
Abort
Need to skip targets of length 0 in p7_Pipeline() because models
can't be set to a length model of 0; they'll look like global models
and trigger an exception in Forward() implementation.
Need to ignore queries of length 0 (phmmer, jackhmmer) because length 0
models can't be calibrated (crash in p7_Tau).
ID h45 TITLE Zero length sequences crash hmmscan STATUS CLOSED in 3.0a2 XREF J4/112 2009/0310-bug-h45 REPORTED_BY Ryan Richt ryan_richt@cofactorgenomics.com OPENED_DATE SRE, Tue Mar 10 13:28:00 2009 CLOSED_DATE SRE, Tue Mar 10 14:48:40 2009 DESCRIPTION
Searching a sequence of length 0 crashes: % hmmscan tutorial/minifam test.fa ... Fatal exception (source file fwdback.c, line 140): Forward implementation makes assumptions that only work for local alignment Abort or for hmmsearch: Fatal exception (source file fwdback.c, line 461): forward score underflow (is 0.0) Abort
Need to skip targets of length 0 in p7_Pipeline() because models can't be set to a length model of 0; they'll look like global models and trigger an exception in Forward() implementation.
Need to ignore queries of length 0 (phmmer, jackhmmer) because length 0 models can't be calibrated (crash in p7_Tau).