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MannLabs / alphatims

An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry.
https://doi.org/10.1016/j.mcpro.2021.100149
Apache License 2.0
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File extension not understood #180

Closed PatrickvanZalm closed 2 years ago

PatrickvanZalm commented 2 years ago

Hi all,

Im trying to pack alphatims in a docker container and run use the CLI version of the tool. Here I use Alphatims 0.3.2 but I run into an error where it does not recognize the file extension. I run the line below and get the following output. The bruker-Directory without quotations does lead to the same error.

root@70689f3fe955:/var/opt/project# alphatims export hdf "/var/opt/project/K562_post_1_S1-A1_1_12197.d/"

  • AlphaTims 0.3.2 *

    2022-04-09 21:09:09> Platform information: 2022-04-09 21:09:09> system - Linux 2022-04-09 21:09:09> release - 5.13.0-30-generic 2022-04-09 21:09:09> version - #33~20.04.1-Ubuntu SMP Mon Feb 7 14:25:10 UTC 2022 2022-04-09 21:09:09> machine - x86_64 2022-04-09 21:09:09> processor - 2022-04-09 21:09:09> cpu count - 24 2022-04-09 21:09:09> cpu frequency - 1.66 Mhz 2022-04-09 21:09:09> ram - 6.3/11.7 Gb (available/total) 2022-04-09 21:09:09> 2022-04-09 21:09:09> Python information: 2022-04-09 21:09:09> alphatims - 0.3.2 2022-04-09 21:09:09> bokeh - 2022-04-09 21:09:09> click - 8.1.2 2022-04-09 21:09:09> datashader - 2022-04-09 21:09:09> h5py - 3.6.0 2022-04-09 21:09:09> hvplot - 2022-04-09 21:09:09> numba - 0.55.1 2022-04-09 21:09:09> pandas - 1.4.2 2022-04-09 21:09:09> psutil - 5.9.0 2022-04-09 21:09:09> python - 3.9.12 2022-04-09 21:09:09> python-lzf - 2022-04-09 21:09:09> pyzstd - 0.15.2 2022-04-09 21:09:09> selenium - 2022-04-09 21:09:09> tqdm - 4.64.0 2022-04-09 21:09:09> 2022-04-09 21:09:09> Current AlphaTims version is up-to-date with GitHub. 2022-04-09 21:09:09> 2022-04-09 21:09:09> Running CLI command alphatims export hdf with parameters: 2022-04-09 21:09:09> bruker_raw_data - /var/opt/project/K562_post_1_S1-A1_1_12197.d/ 2022-04-09 21:09:09> disable_log_stream - False 2022-04-09 21:09:09> disable_overwrite - False 2022-04-09 21:09:09> enable_compression - False 2022-04-09 21:09:09> log_file - /usr/local/lib/python3.9/site-packages/alphatims/logs/log_20220409210909.txt 2022-04-09 21:09:09> threads - 23 2022-04-09 21:09:09> 2022-04-09 21:09:10> Importing data from /var/opt/project/K562_post_1_S1-A1_1_12197.d/ 2022-04-09 21:09:10> Something went wrong, execution incomplete! Traceback (most recent call last): File "/usr/local/lib/python3.9/site-packages/alphatims/cli.py", line 114, in parse_cli_settings yield kwargs File "/usr/local/lib/python3.9/site-packages/alphatims/cli.py", line 272, in export_hdf data = alphatims.bruker.TimsTOF(parameters["bruker_raw_data"]) File "/usr/local/lib/python3.9/site-packages/alphatims/bruker.py", line 1022, in init raise NotImplementedError( NotImplementedError: WARNING: file extension not understood

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PatrickvanZalm commented 2 years ago

Forget what I said. resolved by using the same solution as in this post. https://github.com/MannLabs/alphatims/issues/154

The slash at the end is the issue.