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institut-de-genomique / MaGuS

MaGuS (Map-Guided Scaffolding) is a map-guided scaffolder and a reference-free assembly quality evaluator.
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Magus: Can't exec "getseq" at PATH/Magus/Magus.pm line 64 #2

Closed HmuSong closed 6 years ago

HmuSong commented 7 years ago

Hello, when I used the Magus pairs2links function to estimate the gaps size between two scaffold, I have encounted this problem that Can't exec "getseq": at PATH/Magus/Magus.pm line 64 [ERROR] :: fill :: Cannot use getseq : . I have searched the entire file but could not find the sub function "getseq". Could you tell me the reason why this error occured? Thank very much!

cdossat commented 7 years ago

Hello, getseq is not a sub function, it's a stand-alone program which is provided in bin/ directory. Have you added MaGuS binaries in $PATH ?

HmuSong commented 7 years ago

Hello, I have checked my $PATH, the problem just like you said. The issue have been solved and MaGus works well now. Thanks a lot for your help. I got the results of pairs2links now, but I can't understand the meaning of each column of the "***.de" file.

leo-dagata commented 7 years ago

Hello, The format of .de file belongs to SGA program that you can find in the following link: https://github.com/jts/sga Fortunatly, you can learn more about .de format by reading this google group: https://groups.google.com/forum/#!topic/sga-users/7a01mz_ObTE

HmuSong commented 7 years ago

Thank you very much for your guide.