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lliu1871 / mp-est

MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function
GNU General Public License v3.0
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Error running mp-est 2.0 #1

Open tanhuizhen opened 4 years ago

tanhuizhen commented 4 years ago

Hello,

I am facing errors using mp-est 2.0, both at the compilation step and also if I opt to use the provided binary.

My computer runs macOS Sierra 10.12.6 and the following are my steps for respective errors:

Error 1: compilation

  1. Download source files from github
  2. Go into folder with makefile, ensure that Architecture is 'mac' 
    make: *** No rule to make target '-lm', needed by 'mpest'. Stop.

    Do you have any advice for the lines in the makefile that should be inspected to allow for compilation?

Error 2: use provided binary

As compilation was unsuccessful, I tried using the given binary file in the 'mac' folder. It worked on the test dataset. When I run my dataset (546 gene trees, 67 samples, 10 species) however, I run into a segmentation error.

Segmentation fault: 11

I have tried multiple solutions but have yet to resolve either of the issues. In the second issue for example, I tried to increase the stack memory limit but it did not improve the situation. I was unable to find solutions specific to mp-est and would like to check in with you to see if you have alternative suggestions.

Thank you in advance for any advice regarding these errors, should it be version incompatibility or otherwise.

Best, Hui Zhen

lliu1871 commented 4 years ago

The gene trees must be rooted binary trees. How did you estimate the gene trees, using RAxML? If so, the estimated gene trees must be rooted before building the mp-est tree.

Liang

Liang Liu Graduate Advisor Department of Statistics University of Georgia www.stat.uga.edu/~lliu

From: Hui Zhen Tan notifications@github.com Sent: Monday, August 24, 2020 5:52 AM To: lliu1871/mp-est mp-est@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [lliu1871/mp-est] Error running mp-est 2.0 (#1)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hello,

I am facing errors using mp-est 2.0, both at the compilation step and also if I opt to use the provided binary.

My computer runs macOS Sierra 10.12.6 and the following are my steps for respective errors:

Error 1: compilation

  1. Download source files from github
  2. Go into folder with makefile, ensure that Architecture is 'mac'

make: *** No rule to make target '-lm', needed by 'mpest'. Stop.

Do you have any advice for the lines in the makefile that should be inspected to allow for compilation?

Error 2: use provided binary

As compilation was unsuccessful, I tried using the given binary file in the 'mac' folder. It worked on the test dataset. When I run my dataset (546 gene trees, 67 samples, 10 species) however, I run into a segmentation error.

Segmentation fault: 11

I have tried multiple solutions but have yet to resolve either of the issues. In the second issue for example, I tried to increase the stack memory limit but it did not improve the situation. I was unable to find solutions specific to mp-est and would like to check in with you to see if you have alternative suggestions.

Thank you in advance for any advice regarding these errors, should it be version incompatibility or otherwise.

Best, Hui Zhen

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/lliu1871/mp-est/issues/1, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACZITQXSLWSEKU22D5GDHY3SCIZ4ZANCNFSM4QJJ7ZSA.

tanhuizhen commented 4 years ago

Hi Liang,

Thank you for the prompt reply.

The gene trees were estimated in PhyML and rooted with Newick Utilities. The same dataset which failed to run in version 2.0 runs successfully in older versions of mp-est, including version 1.6.

Best, Hui Zhen

lliu1871 commented 4 years ago

If you can send me the gene trees and teh control file, I can figure out what caused the error.

Liang

Liang Liu Graduate Advisor Department of Statistics University of Georgia www.stat.uga.edu/~lliu

From: Hui Zhen Tan notifications@github.com Sent: Tuesday, August 25, 2020 10:32 PM To: lliu1871/mp-est mp-est@noreply.github.com Cc: Liang Liu lliu@uga.edu; Comment comment@noreply.github.com Subject: Re: [lliu1871/mp-est] Error running mp-est 2.0 (#1)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Liang,

Thank you for the prompt reply.

The gene trees were estimated in PhyML and rooted with Newick Utilities. The same dataset which failed to run in version 2.0 runs successfully in older versions of mp-est, including version 1.6.

Best, Hui Zhen

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/lliu1871/mp-est/issues/1#issuecomment-680423775, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACZITQQDGBSNVW2BAZ2WLXTSCRX3XANCNFSM4QJJ7ZSA.

tanhuizhen commented 4 years ago

Hi Liang,

Thank you for the kind offer and I will consider sending the files to you. In the meantime, I have decided to use mp-est version 1.6 for my purposes.

Best, Hui Zhen

tanhuizhen commented 3 years ago

Hi Liang,

Thanks very much for your previous help in running mp-est.

I am writing today regarding another question about deriving the population size estimator theta from the species tree. For example, I understand that the internal branch lengths are calculated with theta. May I know if there is a way to work backwards to extract theta and would that represent effective population size for that ancestral branch?

As this question is not related to the original issue topic. Please let me know if I should open a separate issue.

Thank you.

Best, Hui Zhen

lliu1871 commented 3 years ago

Huizhen,

The branch length of the mp-est tree is in coalescent units, i.e., brlen = tau/theta. It is impossible to get theta unless tau is given (tau=mu*t).

Liang

Liang Liu Graduate Advisor Department of Statistics University of Georgia www.stat.uga.edu/~lliu

From: Hui Zhen Tan notifications@github.com Sent: Thursday, October 1, 2020 4:51 AM To: lliu1871/mp-est mp-est@noreply.github.com Cc: Liang Liu lliu@uga.edu; Comment comment@noreply.github.com Subject: Re: [lliu1871/mp-est] Error running mp-est 2.0 (#1)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Liang,

Thanks very much for your previous help in running mp-est.

I am writing today regarding another question about deriving the population size estimator theta from the species tree. For example, I understand that the internal branch lengths are calculated with theta. May I know if there is a way to work backwards to extract theta and would that represent effective population size for that ancestral branch?

As this question is not related to the original issue topic. Please let me know if I should open a separate issue.

Thank you.

Best, Hui Zhen

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/lliu1871/mp-est/issues/1#issuecomment-701990097, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACZITQS7BODAFGHFXXOSSNDSIQ7INANCNFSM4QJJ7ZSA.

tanhuizhen commented 3 years ago

Hi Liang,

Noted and thank you again for your help.

Best, Hui Zhen