Prank segmentation fault

[francicco]

Dear Dr Loytynoja,

This is Francesco from the university of Innsbruck. I'm trying to use prank to align coding mtDNA sequences, but prank is giving me bad jokes. The program works perfectly with the default settings but when I try to run it with -codon, -translate or the more suitable -mttranslate it crashes:

-----------------
 PRANK v.150803:
-----------------

Input for the analysis
 - aligning sequences in '/global/lv70640/c7701100/Projects/AntMitogenomeBproject/Alignments/atp8.GUIDANCE/Seqs.numberd.fas'
 - 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
    BppAncestor for ancestral state reconstruction

Correcting (arbitrarily) for multifurcating nodes.
Correcting (arbitrarily) for multifurcating nodes.

Generating multiple alignment: iteration 1.
#7#(7/7): 0% aligned                    Segmentation fault

I can't see the problem.
I tried using the compiled version and source version compiled by myself, and both available versions. The input is ok, I tried webPRANK and it works.
What to do?

Best
Francesco

[RAWWiberg]

Hi,
I am having a similar problem even with a newer version of prank (PRANK v.170427). I downloaded the binaries for this version because an earlier version was also giving this problem. I have not tried compiling from source. A nucleotide alignment works fine but if I use the -translate option the program will run for a while and then produce a segmentation fault.
Cheers,
Axel

[isabelschober]

I have the same problem trying to do a codon alignment.

[Neo-xbx-00]

If you get this type of error, please set "ulimit -c unlimited" before you run the prank command. Good luck to you~

[yzliu01]

@ariloytynoja I got the same issue when using prank -d=input.fa -o=out.prank_translated.fa -translate -F, which has been there for a few years: Segmentation fault (core dumped). I have tried ulimit -c unlimited but no luck.
I appreciate it very much if you can give any hints to get it worked.