readpb_mpi error - Githubissues

bailliecharles commented 6 years ago

Getting the following half way though running: mpirun -np 100 /SOFTWARE/pbmpi/data/readpb_mpi -x 2000 -div CHAIN1

.............................................in tree: null string

Any ideas/ Thanks C

bayesiancook commented 6 years ago

apparently, this sometimes happens when the .chain is corrupted.

gerthmicha commented 5 years ago

Hi, could you provide some more information on this please? I have also encountered the error in tree: null string multiple times but don't understand how the .chain file can become corrupted or how to avoid this. Is there a way to 'repair' the chain file? Any ideas would be really helpful, thanks!

nicrodrigue commented 5 years ago

I suspect that some taxa names are entirely numerical in your data set. If this is the case, the parsing of trees produced by the software will run into the problems, with a confusion between branch lengths and taxa names.

In the future, try adding a letter to your taxa names to avoid the confusion.

Regards,

Nic

From: Michael Gerth notifications@github.com Sent: Monday, January 7, 2019 7:52:56 AM To: bayesiancook/pbmpi Cc: Subscribed Subject: Re: [bayesiancook/pbmpi] readpb_mpi error (#5)

Hi, could you provide some more information on this please? I have also encountered the error in tree: null string multiple times but don't understand how the .chain file can become corrupted or how to avoid this. Is there a way to 'repair' the chain file? Any ideas would be really helpful, thanks!

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gerthmicha commented 5 years ago

Hi Nic, thanks for the feedback. Non of the taxa in my dataset are entirely numerical. I did stop the runs though, performed some posterior predictive tests (which worked out fine), then continued the runs and stopped them again after some more iterations. After this, the error occurs. Cheers, Michael

bayesiancook / pbmpi

readpb_mpi error #5