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snakemake-workflows / dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow
MIT License
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Help with dna-seq-gatk-variant-calling #42

Open Sahu-Mousumi opened 10 months ago

Sahu-Mousumi commented 10 months ago

Hi!

I have installed the pipeline on HPC and trying to run the pipeline. I updated pip and I am getting below error. Any help will be appreciated!

Thank you Mousumi

Error1: -bash-4.2$ snakemake --cores all --use-conda ImportError in file /home/sahum2/DNA-seq/workflow/Snakefile, line 19: You are trying to use the http functionality of smart_open but you do not have the correct http dependencies installed. Try:

pip install smart_open[http]

File "/home/sahum2/DNA-seq/workflow/Snakefile", line 19, in File "/cm/shared/apps/python/3.7.2/lib/python3.7/site-packages/smart_open/smart_open_lib.py", line 81, in parse_uri File "/cm/shared/apps/python/3.7.2/lib/python3.7/site-packages/smart_open/transport.py", line 92, in get_transport

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-bash-4.2$ pip install smart_open[http] Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: smart_open[http] in /cm/shared/apps/python/3.7.2/lib/python3.7/site-packages (6.4.0) Requirement already satisfied: requests in /cm/shared/apps/python/3.7.2/lib/python3.7/site-packages (from smart_open[http]) (2.31.0) Requirement already satisfied: charset-normalizer<4,>=2 in /cm/shared/apps/python/3.7.2/lib/python3.7/site-packages (from requests->smart_open[http]) (3.3.0) Requirement already satisfied: idna<4,>=2.5 in /cm/shared/apps/python/3.7.2/lib/python3.7/site-packages (from requests->smart_open[http]) (2.8) Requirement already satisfied: urllib3<3,>=1.21.1 in /cm/shared/apps/python/3.7.2/lib/python3.7/site-packages (from requests->smart_open[http]) (2.0.6) Requirement already satisfied: certifi>=2017.4.17 in /cm/shared/apps/python/3.7.2/lib/python3.7/site-packages (from requests->smart_open[http]) (2019.3.9)