hirschberg initialisation: impossible bwd state '-1' terminate called after throwing an instance of 'std::out_of_range'

[eric-jm-lang]

Hi, I have been using PRANK without any problems for several alignements but for a particular one, PRANK keep crashing with the following error:

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

Input for the analysis
 - aligning sequences in 'New_type1beta_main1_1_tax_90_cur.fasta'
 - using inferred alignment guide tree
 - external tools available:
    MAFFT for initial alignment
    Exonerate for alignment anchoring
    BppAncestor for ancestral state reconstruction

Warning: sequence names changed.

Generating multiple alignment: iteration 1.
#633#(633/633): 9% aligned                    hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
hirschberg initialisation: impossible bwd state '-1'
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check
Aborted (core dumped)

Could you please let me know what this error corresponds to and how to fix it?

Many thanks in advance.

Eric

[Van-Doorslaer]

any updates on this?

[jeffmatskin]

I've had this error come up as well.

[AdeFouchier]

Hi,

I'm having this error as well. On gywin PRANK 170427

Any idea on the source of this error ? And how to fix it ?

[ReverendCasy]

In my case, the error stemmed from PRANK erroneously detecting the amino acid input sequence as DNA; explicitly setting -protein flag solved the problem.