Question: FreeBayes Error - Variant calling
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gravatar for manasanani2011
3 months ago by
manasanani20110 wrote:

Hi, I gave output file from clean sam as an input for Free Bayes for variant calling and getting the following error - Fatal error: Exit code 93 () freebayes: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory Reference genome - hg19 Please let me know how to proceed. Thanks, Manasa

software error • 186 views
ADD COMMENTlink modified 3 months ago by thedavidwblack0 • written 3 months ago by manasanani20110
0
gravatar for thedavidwblack
3 months ago by
thedavidwblack0 wrote:

I'm having the same problem. I ran into the solution, but I'm having a problem with it. I'll list my problem and then not the solution. When I click on the "Version" button from the UseGalaxy.org site, nothing appears. I'll try on a cloud-based galaxy, perhaps therefore being able to install a specific version.

Solution: I ran into the following post:

https://biostar.usegalaxy.org/p/26453/#26454

When trying to run Galaxy on the platform I keep having the same error message when using FreeBayes and BamLeftAlign Fatal error: Exit code 1 () freebayes: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory Fatal error: Exit code 127 () bamleftalign: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory @kry_8

Hello, This is recently discovered problem with the Freebayes tools (this one included) and we are still working on the correction. Please see the issue tracking ticket for the workaround (use an earlier tool version). When the dependencies are fixed, the ticket will be updated/closed out. https://github.com/galaxyproject/usegalaxy-playbook/issues/79 Thanks for reporting the problem! Jen, Galaxy team @Jennifer_Hillman_Jackson

The workaround is as follows: Current workaround until fixed Use the 1.0.2.29-3 version of Freebayes or BamLeftAlign

  • Click on Freebayes or BamLeftAlign from the left Tool Panel
  • Use the Versions menu on the loaded tool form to select 1.0.2.29-3
  • The earlier version of the tool form will load
  • Before using, confirm the version switch is correct. The tool name/version will be noted at the very top of the tool form

It seems that the admins are looking at making sure the libraries are installed.

ADD COMMENTlink modified 3 months ago • written 3 months ago by thedavidwblack0

THIS WILL LIKELY BE USEFUL TO DEVELOPERS I was able to change to version on Firefox, but not on Chrome. This should probably be investigated. Thanks, Dave

ADD REPLYlink written 3 months ago by thedavidwblack0
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