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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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New Scheme error #80

Closed Merguerrero closed 4 years ago

Merguerrero commented 5 years ago

I'm not able to create a new scheme, when mlst --longlist | grep pj got this error: 

readline() on closed filehandle $fh at ~/mlst/bin/../perl5/MLST/Scheme.pm line 38.
Use of uninitialized value $header in scalar chomp at ~/mlst/bin/../perl5/MLST/Scheme.pm line 39.
Use of uninitialized value $header in split at ~/mlst/bin/../perl5/MLST/Scheme.pm line 40.

Any clue?

Thanks in advance!

tseemann commented 5 years ago
  1. what do you mean "create new scheme" ?
  2. how did you install mlst?
  3. what does mlst --version say?
Merguerrero commented 5 years ago
  1. what do you mean "create new scheme" ? I would like to add a new scheme, and I followed the guidelines in Adding a new scheme secion
  2. how did you install mlst? I cloned from git hub.
  3. what does mlst --version say? mlst 2.16.2
tseemann commented 5 years ago

please can you tell me what this command says

ls -lsa /path/to/mlst/db/pubmlst/yourscheme/
eneasdecarvalho commented 4 years ago

Hi. It happened to me. I just fixed it renaming the .txt scheme file (which I had named as DownloadedScheme_organism.txt) to the same name of the scheme (then just scheme.txt)

Although, in the guidelines, the filename has the same name of the scheme, this is not highlighted as essencial, and I did not notice it. Maybe it could be highlighted in the guidelines.

tseemann commented 4 years ago

@eneasdecarvalho thank you - i have updated the documentation to make it clear that SCHEME (folder) must match (SCHEME.txt) filename.