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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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Cannot open reference file ! #73

Closed lanlan0210 closed 4 years ago

lanlan0210 commented 4 years ago

Hi~ I just installed parsnp and reported an error while running the program. The genome I used is the example you used: 49 MERS Coronavirus. The reported error is shown below:

Cannot open reference file !

Looking forward to your reply. Thank you very much

bkille commented 4 years ago

Hi, that example contained hidden MacOS files w/ the prefix ._, you can delete them via rm mers49/._* or redownload the zip file (it has been updated)