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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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subprocess.CalledProcessError: Command '[ ]' returned non-zero exit status 1 #3675

Open KTison opened 2 years ago

KTison commented 2 years ago

I am having an issue installing the pipeline more specifically conda. I have attached a screenshot of my terminal. I am new to programming/bioinformatics so I am not well versed in troubleshooting. Please let me know if you have seen this error before. I really appreciate the help!

subprocess CalledProcessError

naumenko-sa commented 2 years ago

Hi @KTison !

It looks like the older system python3.6 interferes with bcbio python3.7. Could you please try exporting PATH in the following way? https://bcbio-nextgen.readthedocs.io/en/latest/contents/intro.html#install-bcbio-python-package-and-tools

Also this instruction might be useful: https://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#importerrors

SN

KTison commented 2 years ago

Hello @naumenko-sa! Exporting the path as you advised definitely helped but now I have approached another issue. I am receiving a LinkError where the post-link script failed for package bioconda::deepvariant-1.4.0-py36hf3e76ba_0 (first screenshot). While handling this error there was another exception where a process error occurred (second screenshot). Any suggestions for these issues?

naumenko-sa commented 2 years ago

Hi @KTison ! Have you attached the screenshots? I don't see them. Sergey