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incertae-sedis / lagan

LAGAN: large-scale multiple alignment of genomic DNA
GNU General Public License v2.0
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Segmentation fault triggered by the Glue binary file under LAGAN_DIR/utils #4

Open yjx1217 opened 6 years ago

yjx1217 commented 6 years ago

Hi @arendsee ,

I encountered the following error when running the xmfa2mfa.pl script provided by the lagan package. It seems that the Glue binary compiled by lagan is not working properly.

sh: line 1: 80101 Segmentation fault (core dumped) /home/jxyue/Programs/lagan/utils/Glue tmp.xmfa > glue.out 2> glue.err

The commands that I used are as follows: $lagan_dir/slagan.pl seq1.fa seq2.fa -out test.xmfa # this one works fine $lagan_dir/xmfa2mfa.pl 1 < test.xmfa >test.mfa # this one triggered the error

Alternatively, you can also run the slagan-mfa.pl wrapper provided by the lagan package to replicate the same error: $lagan_dir/slagan-mfa.pl seq1.fa seq2.fa

I further attach the two sequences that I want to align for this example. You can gunzip them to run the test.

Thanks in advance!

Best, Jia-Xing

seq1.fa.gz seq2.fa.gz

arendsee commented 6 years ago

@yjx1217 Thanks for submitting the bug report! I'll look into it.