Unknown error during alignment

[YojanaGadiya]

I followed the tutorial using my dataset, and I get this error on the alignment step, although the files for the previous steps are created (see screenshot). I have used the default parameters here.

Welcome to the untargeted metabolomics workflow.                                                                                                  low()"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Step 1: Preparing the workflow...
        Workflow is prepared.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Step 2: Processing individual files for feature detection...
        57 files to process out of 57 files.
        A total of 32 CPU cores are detected, 25 cores are used.
        Processing files from 0 to 57
^[[B    Individual file processing is completed.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Step 3: Aligning features...
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 57/57 [00:02<00:00, 26.51it/s]
/home/ubuntu/.pyenv/versions/3.9.17/lib/python3.9/site-packages/masscube/alignment.py:204: RuntimeWarning: invalid value encountered in scalar div█████████████████████████████████████████| 57/57 [00:02<00:00, 26.51it/s]
f.detection_rate = np.sum(f.feature_id_arr[v] != -1) / np.sum(v)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/ubuntu/.pyenv/versions/3.9.17/lib/python3.9/site-packages/masscube/workflows.py", line 199, in untargeted_metabolomics_workflow
    features = feature_alignment(params.single_file_dir, params)
  File "/home/ubuntu/.pyenv/versions/3.9.17/lib/python3.9/site-packages/masscube/alignment.py", line 209, in feature_alignment
    features = merge_features(features, params)
  File "/home/ubuntu/.pyenv/versions/3.9.17/lib/python3.9/site-packages/masscube/alignment.py", line 297, in merge_features
    tmp = [features[0]]
IndexError: list index out of range

The files inside single_files are all having features but then in project_files there is a file called features.msp which is empty.

[YojanaGadiya]

Maybe, it is a problem parsing the individual feature files in this module?

[huaxuyu]

Hi Yojana,

Would it be possible for you to share several raw files to me (maybe 3-5 files, email: hxuyu@ucdavis.edu)? I will check from my side and get it back to you soon.

Thanks for testing and feedbacks!

Huaxu

[Sehrawatsurender]

Hi haixyu
I have tried to run mass cube, al Although the run was complete, it skipped several steps in the analysis

.
Step 6: MS signal drift normalization is skipped.

Step 6: Sample normalization is skipped.
Step 7: Statistical analysis is skipped.

Plotting MS2 matching...
0it [00:00, ?it/s]
MS2 plotting is completed.
The workflow is completed.

No MS2 features were detected. I used the library dowling from your website in .PKl format. What could be the possible reasons?
MS2 folder is empty, no annotation were performed.

Thanks 'Surender

[huaxuyu]

Dear Surender,

Please let us know if you still need help with this issue.

Thanks,
Huaxu