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NBISweden / MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
http://NBISweden.github.io/MrBayes/
GNU General Public License v3.0
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WARNING: Reallocation of zero size attempted. This is probably a bug. Problems may follow #215

Open 473021677 opened 4 years ago

473021677 commented 4 years ago

Hello I am using MrBayes v3.2.7a to conduct bayesian inference analysis but the program aborted abnormally. It showed the errors "Setting number of generations to 2000000 WARNING: Reallocation of zero size attempted. This is probably a bug. Problems may follow. WARNING: Reallocation of zero size attempted. This is probably a bug. Problems may follow. Setting number of runs to 4 WARNING: Allocation of zero size attempted. This is probably a bug; problems may follow.

 =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
 =   PID 17616 RUNNING AT localhost.localdomain
 =   EXIT CODE: 9
 =   CLEANING UP REMAINING PROCESSES
 =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
 ===================================================================================
 YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
 This typically refers to a problem with your application.
 Please see the FAQ page for debugging suggestions".
 The commands were "execute /home/lianzh/yuanyang/50.concatenated-v2.nex
                                 prset aamodelpr=fixed(lg)
                                 lset rates=invgamma ngammacat=8
                                 mcmc ngen=2000000 nruns=4 nchains=8 samplefreq=2000 printfreq=2000 diagnfreq=2000 relburnin=yes                                                           burninfrac=0.25 Temp=0.15
                                 yes
                                 sump
                                 sumt".
 I have searched the website “https://github.com/NBISweden/MrBayes/issues/70” and found that someone have encountered similar problems. However, I don't know how to solve it. I will be eager to get your guidance. I have appended the files. Thanks very much.

Best regards 50.concatenated-v2.nex.txt nohup.out.txt

zhangchicool commented 4 years ago

This issue has been fixed, see #70 #28, but hasn't been released yet. I think the new release is coming soon. The program termination is not expected. Normally the program will continue running without error, not sure if there is another bug causing the termination.

473021677 commented 4 years ago

Thanks for your comment. The program aborted for the nex file of 50 concatenated proteins. However, when I using the nex file of 16 concatenated ribosomal proteins, the result tree file could be generated, despite the same warning "WARNING: Reallocation of zero size attempted. This is probably a bug. Problems may follow.". I suspected if there were some wrong with the nex file of 50 concatenated proteins. I have appended the two nex files. Could you help me check the files? Thanks very much.

Best regards 16rp.concatenated.nex.txt 50.concatenated-v2.nex.txt