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sanger-pathogens / mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST
http://sanger-pathogens.github.io/mlst_check/
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Issue with running get_sequence_type #65

Closed BioMEC closed 7 years ago

BioMEC commented 8 years ago

I get this error when running get_sequence type after installing mlst_check using 'cpan Bio::MLST::Check' on two different Linux machines. Is this a fixable error or something of my wrongdoing?

Thank you in advance, Matt

get_sequence_type -s "Clostridium difficile" -d 8 *.fa Smartmatch is experimental at /home/matthew/perl5/lib/perl5/Bio/MLST/FilterAlleles.pm line 28. readdir() attempted on invalid dirhandle $dh at /home/matthew/perl5/lib/perl5/Bio/MLST/SearchForFiles.pm line 26. rewinddir() attempted on invalid dirhandle $dh at /home/matthew/perl5/lib/perl5/Bio/MLST/SearchForFiles.pm line 31. readdir() attempted on invalid dirhandle $dh at /home/matthew/perl5/lib/perl5/Bio/MLST/SearchForFiles.pm line 32. Nothing found for species: Clostridium difficile

andrewjpage commented 7 years ago

Hi, Please install the latest version which should fix these issues. Please also take care to read the installation instructions as there are dependancies not installed by CPAN Andrew