vcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory vcfuniq: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory

[shangguan77]

Hello,I encountered the following problems when using snippy. Has anyone encountered similar problems? snippy is installed with conda.(conda install -c conda-forge -c bioconda -c defaults snippy)

vcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory
vcfuniq: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/home/y17319172851/miniconda3/envs/snippy/bin/vcffirstheader", line 10, in
print(line.strip())
BrokenPipeError: [Errno 32] Broken pipe

[pvanheus]

The problem here is coming from the vcflib dependency. This is configured in the snippy recipe as vcflib >=1.0.0_rc3,<=1.0.2. If you install the latest version matching this, vcflib 1.0.2, and try and run e.g. vcfuniq, you get the same error as reported here. This also affects the bactopia-variants package.

The underlying problem is that the vcflib package depends on tabixpp (with no version pin) but tabixpp since version 1.1.2 builds a libtabixpp.so.1. Installing tabixpp=1.1.0 in your environment should solve your problem.

[rpetit3]

I think this is now fixed in #46458