Closed lounaDeO closed 9 months ago
Hi there! Can you check to see if tabix was successfully installed? For example, try typing which tabix
in your pixy conda environment.
Yes, it seems to be installed:
which tabix
/kingdoms/tools/anaconda3/envs/pixy/bin/tabix
Ah, I see the error now. You are encountering the issue described here: https://github.com/bioconda/bioconda-recipes/issues/12100#issuecomment-461466897. They have a solution posted there as well, have a look and see if that solves your problem!
Edit: different link, same problem!
Oh yes it works! thank you very much for your help!
Excellent, glad to hear it!
Hi!
I install pixy using following conda install commands:
conda create --name pixy
conda activate pixy
conda install --yes -c conda-forge pixy
conda install --yes -c bioconda htslib
But when I want to use pixy with this command:
pixy --stats pi --vcf allPOP.combineGVCF.filter.4fold.10%NA.PASS.vcf.gz --populations pop.txt --window_size 10000 --n_cores 4
I have the following error:
[pixy] pixy 1.2.7.beta1 [pixy] See documentation at https://pixy.readthedocs.io/en/latest/
[pixy] Validating VCF and input parameters... [pixy] Checking write access...OK [pixy] Checking CPU configuration...OK [pixy] Checking for invariant sites...OK tabix: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory [pixy] Checking chromosome data...subprocess.CalledProcessError: Command 'tabix -l allPOP.combineGVCF.filter.4fold.10%NA.PASS.vcf.gz' returned non-zero exit status 127.
It seems I have an issue with the tabix command but I don't know how to fix it. Any help would be really appreciated.
Thanks in advance! Louna