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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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OSError: [Errno 18] Invalid cross-device link: #268

Open yujun2017 opened 1 year ago

yujun2017 commented 1 year ago

tb-profiler 4.4.1 has "OSError: [Errno 18] Invalid cross-device link" error. Same error has been fixed in ntm-profiler.

jodyphelan commented 1 year ago

Thanks @yujun2017, glad to ntm-profiler is running ok on your side. I thought this also fixed the tb-profiler issue but there might still be a bug hiding in the code. I'll check it out and let you know what I find.

jodyphelan commented 1 year ago

Could you attach the full log file?

jodyphelan commented 1 year ago

I found it! Another use of os.rename which I've changed to shutil.move. I'll get a new bioconda release going.

jodyphelan commented 1 year ago

This sould be fixed in v4.4.2 on bioconda

yujun2017 commented 1 year ago

Thank you so much!
By the way, do you have connect with snpEff author? There are lot of vulnerabilities (11 so far) in snpEff.jar file. We got the notice from NIH and ask to fix these vulnerabilities. Most vulnerabilities are library version. I want to know if we can build snpEff.jar file in tb-profiler because I have submitted an issue in snpEff github and no people response.