#3 segmentation fault

[Joaquim Martins Jr]

I am try to run mugsy and after few seconds it starts an error message appears and the program ends.

The error is: segmentation fault in .stderr file.

12 genomes
Starting Nucmer: Sáb Dez 3 09:41:52 BRST 2011
...........
Finished Nucmer Sáb Dez 3 09:45:14 BRST 2011
Starting MUGSYWGA: Sáb Dez 3 09:45:14 BRST 2011
system /opt/mugsy/mugsy_x86-64-v1r2.2/mugsyWGA --outfile /home/joaquim/Documentos/Pos_Doc/genomas_xylella/mf/output_mugsy/XfGenomeMf --seq /home/joaquim/Documentos/Pos_Doc/genomas_xylella/mf/output_mugsy/XfGenomeMf.all.fsa --aln /home/joaquim/Documentos/Pos_Doc/genomas_xylella/mf/output_mugsy/XfGenomeMf.xmfa --distance 1000 --minlength 30 --unique true > /home/joaquim/Documentos/Pos_Doc/genomas_xylella/mf/output_mugsy/XfGenomeMf.mugsywga.out 2> /home/joaquim/Documentos/Pos_Doc/genomas_xylella/mf/output_mugsy/XfGenomeMf.mugsywga.stderr failed: 35584: at /opt/mugsy/mugsy_x86-64-v1r2.2/mugsy line 906.

Line 906 is like this:

904 #Cleanup and return
905 if($ret !=0){
906 die "system $runmugsywgacmd failed: $?:$!";
907 }
908 else{
909 if(!$options{'debug'}){
unlink "$absprefix.mugsywga.out" if(! defined $options{'keeptmpfiles'});
unlink "$absprefix.mugsywga.stderr" if(! defined $options{'keeptmpfiles'});
}
}
unlink "$pwfasta" if(! defined $options{'keeptmpfiles'});
unlink "$pwdupsfasta" if(defined $options{'duplications'} && ! defined $options{'keeptmpfiles'});
return "$outputfile";
}

[Rintze Zelle]

I'm running into the same problem with a freshly compiled checkout of the SVN on OS X 10.10:

--
bash-3.2$ perl mugsy --prefix m1wga ./MSA/M1.fasta ./MSA/M2.fasta ./MSA/M3.fasta ./MSA/M4.fasta ./MSA/M5.fasta
Parsing sequences for M1 num_seqs:42
Parsing sequences for M2 num_seqs:52
Parsing sequences for M3 num_seqs:45
Parsing sequences for M4 num_seqs:34
Parsing sequences for M5 num_seqs:44
5 genomes
Starting Nucmer: Tue Mar 24 12:23:28 EDT 2015
....
Finished Nucmer Tue Mar 24 12:28:01 EDT 2015
Starting MUGSYWGA: Tue Mar 24 12:28:01 EDT 2015
system /Users/rz/Documents/mas/mugsy_trunk/trunk/mugsyWGA --outfile /tmp/m1wga --seq /tmp/m1wga.all.fsa --aln /tmp/m1wga.xmfa --distance 1000 --minlength 30 --unique true > /tmp/m1wga.mugsywga.out 2> /tmp/m1wga.mugsywga.stderr failed: 32256: at mugsy line 933.
--

Joaquim Martins Jr, were you ever able to figure this out?