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error running with mzML file #316
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Hi, |
Hi, Specifically in file interface.py, the following code section seems to raise an error when the file is not .raw or .d, I am not sure if this is intended? Is feature finding not supported for mzML files? The pipeline seems to run fine when i just input a single mzML files, though #Limit number of processes for Bruker FF |
Good catch. I made some fixes in the https://github.com/MannLabs/alphapept/tree/qc_fixes branch. Do you mind testing if this solves the problem? This will then be included in the next release. |
Thanks. I just tested the fixes and it works! On side note i was wondering if you can help me with a different issue. While I was testing the branch codes. I noticed, some of my mzML files takes a really long time for feature finding to run (i.e. > 1 day). But my other files finish in like < 20 min. They are all from similar samples. I was wondering if you can help me see why this set of files is special and takes so long to do feature finding. here is the file: https://seer.box.com/s/yofs6w3vy3twodsbiigf2d1yj8z1kime |
Hi, |
Hi, |
Hi�, |
Bug was related to having zero intensities in the mzML, should now be fixed. Feel free to check out the develop branch, otherwise it will be included in the next release. |
Great! Thanks. I just confirmed the fixes works. |
Describe the bug
I tried to run the pipeline on a two mzml files, but I got the error
An exception occured running AlphaPept version 0.3.28:
File extension .mzML not understood.
I read in the documentation that the pipeline is relying on pyteomics to read/parse mzml files.
So i tried to load the mzml file with pyteomics separately and it seems to be fine
....................................................
File extension .mzML not understood.
....................................................
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The pipeline finish all the steps
Screenshots
![image](https://user-images.githubusercontent.com/85585753/131960492-67b995b6-69d5-45da-a841-45a5c7fda54f.png)
Version (please complete the following information):
Additional context
Add any other context about the problem here. Attached log files or upload data files if possible.
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