Help with dna-seq-gatk-variant-calling

[Sahu-Mousumi]

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

--------------------------|

-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)