Issue with time data error.

[hisl6802]

Hello,

I have just downloaded the MassCube 1.2.10, and I am continuing to get an error having to do with

ValueError: time data '2024-06-19T22:35:44' does not match format '%Y-%m-%dT%H:%M:%SZ'

I have tried to downgrade the package (1.2.9, and 1.2.8), I have used the generate-sample-table to create a sample_table, and downloaded the csv parameters file. I continue to get the time data error. I have also updated my data to be QC1, QC2, S1, S2, S3 and no luck.

Thanks,

Brady

[huaxuyu]

Hi Brady,

This error occurred because the timestamp in your file is not in a standardized format — it’s missing the trailing “Z” (e.g., it should be 2024-06-19T22:35:44Z).

Could you let me know how your mzML/mzXML files were generated?

Best,
Huaxu

[hisl6802]

Hi Huaxu,

I previously used an msconvert commandline tool on our linux supercomputer. I am currently trying to reconvert our raw files following the exact parameters from convert raw data files. I should be able to get to this at somepoint today and let you know if this worked.

Thanks,

Brady

[hisl6802]

Hi Huaxu,

I was able to get things up and running. But now the RAM memory used is really high somewhere in the 36GB range for only 23GB of files. I have a M1 pro with 16GB ram.

Best,

Brady

[huaxuyu]

Dear Brady,

Great! We recently received feedback about unusually high memory usage. We will address this issue in the next version (likely to be released this week). In the meantime, you can increase the intensity cutoff for MS1 data to speed up the output and reduce the memory cost (e.g. change ms1_abs_int_tol from 1000 to 5000).

Best,
Huaxu

[hisl6802]

Hi Huaxu,

Thanks for letting me know. I am using Orbitrap at 30000 (ms1_abs_int_tol), but I am bumping it up to 50000 to see if this works.

Best,

Brady

[huaxuyu]

Dear Brady,

I have updated MassCube 1.2.11 with the memory issue fixed. Please let me know if it works for you.

Thanks,
Huaxu

[hisl6802]

HI Huaxu,

Thank you! I have upgraded masscube to 1.2.11 and am running new now.

Best,

Brady

[leofossilis]

Hello @huaxuyu,
regarding this, time issue

masscube version 1.2.20

implementation:

from masscube.workflows import untargeted_metabolomics_workflow

untargeted_metabolomics_workflow(path="demo/", return_results=False, 
                                 only_process_single_files=False, return_params_only=False)

output:
ValueError: time data '2026-05-11T13:26:18.287Z' does not match format '%Y-%m-%dT%H:%M:%SZ'

timestamps on my .mzML files have milliseconds, i.e. Time format: '%Y-%m-%dT%H:%M:%S.%fZ'

for this bug i have to alter the timestamps in my .mzML files separately.

it would be better if you provided an option for passing the timestamp format.