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I got segmentation fault (core dumped) error when I try read SCF file.

I'm using Bio::SCF module in perl and just followed the example from "https://metacpan.org/pod/Bio::SCF".

The code is as below ...

#!/usr/bin/perl
use warnings;
use Bio::SCF;

my $scf = Bio::SCF->new('filename.scf'); # line A
or 
tie %scf, 'Bio::SCF', "filename.scf"; # line B

I hoped one of the lines read the scf file but, neither worked and just sending the "segmentation fault (core dumped" message.

What can I do? Could anyone help with this?

Yushin Jung
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  • Please provide the input file, the output of `perl -V`, the version of the `io_lib`/`staden-read` library. – daxim Oct 08 '19 at 07:30
  • Thanks for your attention, I want to provide output of "perl -V" but seems too long. Anyway, the version of perl is v5.28.1. if you need more information please let me know. The version of "io_lib" is 1.14.8 and "staden" is 2.0.0b11-2016. Also I don't know how to provide scf file to you. It's just normal sanger sequencing data, which opens well at software "UGENE". Thanks – Yushin Jung Oct 10 '19 at 00:32
  • I'm sure you can figure out a way to give us the info we need [so we can reproduce the problem](https://stackoverflow.com/help/mcve#Reproducible). Maybe ask your colleagues for help. – daxim Oct 11 '19 at 07:41

1 Answers1

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(This is not really an answer, since you didn't provide much information, but it's the best I can do presently...)

Bio::SCF is a compiled library (notice the .xs file), so it could have easily broken if something changed in your perl install and BIO::SCF wasn't recompiled. I would suggest, as a first step, to reinstall BIO::SCF and make sure that its tests pass (check the log for the cpan client you are using).

Ether
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