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Bug report
Prank -- segmentation fault
ID: 1298Status: resolvedVersion: N/AReport Date: July 4, 2016Product: Prank

Hello, I was trying to align 1,311 orthologous sequences and I got a Segfault error. The sequences do not contain strange characters (characters: A, T, G, C, N). I was capable to correctly align hundreds of files like the one listed below. Can you help me understanding why I get this error?

lfreschi@manitou:~/tasks/pseudo_all/analyses/analyses_paper/tree/alignment> prank -d=../core11_genes/line_33908.fasta -o=line_33908.aln -codon -F

PRANK v.150803:

Input for the analysis
– aligning sequences in '../core11_genes/line_33908.fasta'
– using inferred alignment guide tree
– external tools available:
MAFFT for initial alignment
Exonerate for alignment anchoring

Warning: Unknown codons replaced with 'NNN'.
Correcting (arbitrarily) for multifurcating nodes.
Correcting (arbitrarily) for multifurcating nodes.

Generating multiple alignment: iteration 1.
#1310#(1310/1310): 72% aligned
Alignment score: 7555
Correcting (arbitrarily) for multifurcating nodes.

Generating multiple alignment: iteration 2. #13#(547/1310): 88% computed seqvec 112 0 0 0
P_right_codon 0 0 808464428 0
Segmentation fault

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One comment on “Prank — segmentation fault
  1. Ari says:

    Prank is not the right program for sequences that are very similar to each other. It shouldn’t crash, though, and it should produce a good alignment but it takes a very long time.

    I suggest that you compute an alignment with Pagan:

    pagan -q line_33908.fasta –pileup –translate

    The tree-parsing code will be fixed for the next release of Prank.

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