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
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:
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 126.96.36.199-3 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 188.8.131.52-3
- 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.