Segmentation fault (core dumped) when ffindex_from_fasta

[zhaoxvwahaha]

Hi,

ffindex_from_fasta broken off because of the following error, the output looks like imcomplete, anyone konw the reason and solution:

$ffindex_from_fasta -s segment_fas.ff{data,index} combine.segment.faa data file: segment_fas.ffdata index file: segment_fas.ffindex fasta file: combine.segment.faa Segmentation fault (core dumped)

[apcamargo]

Do you have sequences longer than 100,000 bp? I had a similar problem (https://github.com/soedinglab/hh-suite/issues/262) and I could fix it by modifying the sequence length limit in ffindex_from_fasta.

[milot-mirdita]

That is probably the issue, i'd recommend either @apcamargo fix or using mmseqs createdb as mentioned in the other thread (https://github.com/soedinglab/hh-suite/issues/262#issuecomment-831439909).

[zhaoxvwahaha]

@apcamargo Thank you for reply, my longest length is 4403 bp; And how to modifying the limit, I don't find parameter introduction when I execute ffindex_from_fasta -h or ffindex_from_fasta --help

[apcamargo]

Hey @zhaoxvwahaha

You'll have to clone the repository, change this line, and then compile HH-Suite anew.

Otherwise you could try Milot's suggestion above.

[ahcm]

This code diverges far from mainline and violates the license that asks to add ones name if one distributes modified versions.

Mainline is: https://github.com/ahcm/ffindex

Unlike mainline they allocate this on the stack for whatever reason: char entry[MAX_ENTRY_LENGTH];

If you make this larger than your stacksize the executable will not start.

This is also introduces a severe security bug.