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millanek / fineRADstructure

A package for population structure inference from RAD-seq data
https://www.milan-malinsky.org/fineradstructure
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cannot get tree building to work #3

Closed bnsacks closed 5 years ago

bnsacks commented 6 years ago

I can successfully run radpainter to make a coancestry matrix and then fineradstructure to make an mcmc.xml file, but I cannot seem to get the tree model to work. Here is my command:

finestructure -m T -x 10000 abbrev.populations.haps_chunks.out fineRADstru4.mcmc.xml fineRADstruoutput4.tree.xml

A tree file is produced but with no data in it. The slurm message is:

0%^H^H^H^H# 2%^H^H^H^H# 4%^H^H^H^H# 6%^H^H^H^H# 8%^H^H^H^H# 10%^H^H^H^H# 12%^H^H^H^H# 14%^H^H^H^H# 16%^H^H^H^H# 18%^H^H^H^H# 20%^H^H^H^H# 22%^H^H^H^H# 24%^H^H^H^H# 26%^H^H^H^H# 28%^H^H^H^H#$

Lgamma error: z=-6.99672e+08 terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >' /var/spool/slurmd/job5454124/slurm_script: line 7: 6780 Aborted finestructure -m T -x 10000 abbrev.populations.haps...

lneaves commented 5 years ago

I have the same issue and it still gave this error when I tried to run old input files that had run successfully on an older version (about a year ago).

janxkoci commented 5 years ago

I worked around this issue by using the original finestructure for tree-building step:

  1. I installed finestructure (v2) using this conda package from Bioconda channel.
  2. I then replaced ./finestructure (the fineRADstructure version) with fs fs (the finestructure version)
  3. It finished successfully and I could load the data into R to make plots.

I'm considering to re-run the second MCMC step in original fs just to see if it makes any difference.

I've also found finestructure v4 in other channels, if somebody wants to test it out (there is no need to add the channels permanently).

Moreover there is a fork repo of fineRADstructure made by the original author of finestructure, with some fixes in the program - it could solve the problems, but it requires GSL 2.5 that I just couldn't make working.

Hope this helps

Jan

bnsacks commented 5 years ago

Hi Jan, Thanks very much for passing this information on. I will give it a try. Best wishes, Ben

From: janxkoci notifications@github.com Sent: Tuesday, June 04, 2019 5:08 AM To: millanek/fineRADstructure fineRADstructure@noreply.github.com Cc: Benjamin N. Sacks bnsacks@ucdavis.edu; Author author@noreply.github.com Subject: Re: [millanek/fineRADstructure] cannot get tree building to work (#3)

I worked around this issue by using the original finestructure for tree-building step:

  1. I installed finestructure (v2) using this conda packagehttps://anaconda.org/bioconda/finestructure from Bioconda channelhttps://bioconda.github.io/.
  2. I then replaced ./finestructure (the fineRADstructure version) with fs fs (the finestructure version)
  3. It finished successfully and I could load the data into R to make plots.

I'm considering to re-run the second MCMC step in original fs just to see if it makes any difference.

I've also found finestructure v4 in other channelshttps://anaconda.org/search?q=finestructure, if somebody wants to test it out (there is no need to add the channels permanently).

Moreover there is a fork repo of fineRADstructurehttps://github.com/danjlawson/fineRADstructure made by the original author of finestructure, with some fixes in the program - it could solve the problems, but it requires GSL 2.5 that I just couldn't make working.

Hope this helps

Jan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/millanek/fineRADstructure/issues/3?email_source=notifications&email_token=ABQFTGNLNP2GGD6XHUVY5G3PYZLJ7A5CNFSM4F3VMMBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW4LH7Q#issuecomment-498643966, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABQFTGO4NGKVDCJVEV74TELPYZLJ7ANCNFSM4F3VMMBA.

millanek commented 5 years ago

Hello

I added Dan Lawson's putative fix for the tree building issue to my repo. Please try: git pull make and then re-run the tree building. Please, let me know if it helps.

Cheers Milan

janxkoci commented 5 years ago

I cloned the repo to one of our servers and tried ./configure but it fails because GSL >= 2.5 is required. I'll try to see if I can make it work this time...

janxkoci commented 5 years ago

So I finally figured out how to point to the right installation of GSL using:

./configure --with-gsl-prefix=/home/koci/bin/GSL --with-gsl-exec-prefix=/home/koci/bin/GSL

However I still get a build error:

...
checking for gsl-config... /home/koci/bin/GSL/bin/gsl-config
checking for GSL - version >= 0.2.5... no
*** Could not run GSL test program, checking why...
*** The test program compiled, but did not run. This usually means
*** that the run-time linker is not finding GSL or finding the wrong
*** version of GSL. If it is not finding GSL, you'll need to set your
*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point
*** to the installed location  Also, make sure you have run ldconfig if that
*** is required on your system
***
*** If you have an old version installed, it is best to remove it, although
*** you may also be able to get things to work by modifying LD_LIBRARY_PATH
configure: error: could not find required version of GSL

I noticed the version doesn't match exactly, as GSL reports 2.5 while the configure script checks for GSL >= 0.2.5.

$ bash /home/koci/bin/GSL/bin/gsl-config --version
2.5

Could this be the problem?