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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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Error : dedup' is not a UMI-tools command #598

Closed mohamedbahru closed 1 year ago

mohamedbahru commented 1 year ago

Hi I used this command : umi_tools dedup -I SRSF3.bam --output-stats=deduplicated -S deduplicated.bam But it is saying, "'dedup' is not a UMI-tools command. See 'umi_tools -h'".

I found that the error occurred in the following step in the script umi_tools.py.

"module = importlib.import_module("umi_tools." + command, "umi_tools")".

*** ImportError: /data/groups/anko/mohamed/Install_packages/miniconda3/lib/python3.10/site-packages/matplotlib/../../../libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /data/groups/anko/mohamed/Install_packages/miniconda3/lib/python3.10/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-310-x86_64-linux-gnu.so)

Could you please let me know, how to fix this error?

Thanks

mohamedbahru commented 1 year ago

I fixed the issue. I used this command: 'conda install -c conda-forge gcc=12.1.0'.