Assertion `xa>0' failed

[GoogleCodeExporter]

What steps will reproduce the problem?
1. prank -d=EOG78Q418.fa -o=EOG78Q418
2. Same problem whether using prank compiled from source or pre-made binary
3. prank works well for the vast majority of sequences, but chokes on a few

What is the expected output? What do you see instead?

Expected to produce alignments, but got this:

-----------------
 PRANK v.140603:
-----------------

Input for the analysis
 - aligning sequences in '../../data/ants/orthoDB/alignments/EOG78Q418.fa'
 - using inferred alignment guide tree
 - option '+F' is not used; it can be enabled with '+F'
 - external tools available:
    MAFFT for initial alignment
    Exonerate for alignment anchoring

prank: flmatrix.cpp:43: FlMatrix::FlMatrix(int, int, std::string): Assertion 
`xa>0' failed.
sh: line 1: 19420 Aborted                 (core dumped) prank 
-d=../../data/ants/orthoDB/alignments/EOG78Q418.fa 
-o=../../data/ants/orthoDB/alignments/EOG78Q418


What version of the product are you using? On what operating system?
prank v.140603 on Red Hat Linux

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 21 Aug 2014 at 12:55

Attachments:

• EOG78Q418.fa