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arvestad / jprime

Probabilistic Inference of Molecular Evolution
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Couldn't reading the example fasta correctly #29

Closed yongzhiyang2012 closed 5 years ago

yongzhiyang2012 commented 5 years ago

Hello, I am testing the example data, but it couldn't read the fasta correctly with the following warnings.

java -jar ../../jprime-0.3.7.jar DLRS dlrs_example_1.stree dlrs_example_1.fa dlrs_example_1.map

16:13:03.375 [main] WARN  o.b.n.core.sequence.io.FastaReader - Sequence with header 'Canis_lupus_1' has unrecognised compounds (Cannot find compound for: L), it will be ign
ored                                                           
16:13:03.377 [main] WARN  o.b.n.core.sequence.io.FastaReader - Sequence with header 'Cavia_porcellus_1' has unrecognised compounds (Cannot find compound for: V), it will be
 ignored                                                             
16:13:03.377 [main] WARN  o.b.n.core.sequence.io.FastaReader - Sequence with header 'Cavia_porcellus_2' has unrecognised compounds (Cannot find compound for: L), it will be
 ignored                                                                                                                                                                   
...
ERROR: Cannot create sequence data without any sequences.
arvestad commented 5 years ago

The error could be more clear here. The example contains protein sequences and the default model (and then: assumed sequence type) is DNA. If you add the option "-sm JTT" (for example), then it should work.