ERROR: Workflow failed for ..... with error No objects to concatenate

MannLabs / alphadia

modular & open DIA search

https://alphadia.readthedocs.io

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ERROR: Workflow failed for ..... with error No objects to concatenate #176

Closed Andre-C-M closed 3 months ago

Andre-C-M commented 3 months ago

Describe the bug Fantastic App! Maybe just a setting issue: Running timsTOF DIA files with predicted DIANN library runs through, using the alphadia prediction causes 'no objects to concatenate' error though. Logfiles attached. thx!

To Reproduce sent you the files for reproduction

Logs Please provide the log (see the AlphaDIA terminal on where to find it).

Additional context Add any other context about the problem here. Attached log files or upload data files if possible. log.txt

JoergDoellinger commented 3 months ago

Hi,

I receive the same error with my timsTOF diaPASEF data.

best

DenysOliinyk commented 3 months ago

Hi, Encountering same error for diaPASEF data. log.txt

tobiasko commented 3 months ago

Me tooo! All my diaPASEF files fail with this error. Already filed an issue. Is alphadia not running any CI tests on the stable release?

GeorgWa commented 3 months ago

Hi, can you describe the library and send the log for which you have experienced this issue?

This hasnt appeared in our library based tests so far and is most likely due to a 1) malformed library or 2) fully predicted library which is not yet fully supported on the timstof.

tobiasko commented 3 months ago

see essue #208 for details

JoergDoellinger commented 3 months ago

Hi, can you describe the library and send the log for which you have experienced this issue?

This hasnt appeared in our library based tests so far and is most likely due to a 1) malformed library or 2) fully predicted library which is not yet fully supported on the timstof.

Hi, I tried to use a library predicted by alphaDIA. So if this is not supported, it is misleading that "timsTOF " can be selected as the instrument in the library prediction tab. Maybe you should remove this option? Of course, I would like to add direct-diaPASEF analysis as a feature request for further releases.

GeorgWa commented 3 months ago

Hi, Here you can find some basic HeLa test data including a diaPASEF library. Please let me know if you can process your data with this library.

This issue has two components:

AlphaDIA should be able to process .d data wit empirical libraries as well as predicted libraries. We will provide a fix for the bug which should enable processing.
The feature free processing algorithm is very sensitive and flexible (diaPASEF, synchroPASEF, midiaPASEF, slicePASEF) but also not the fastest for large libraries. I've updated the Readme to reflect this better. We have been working towards a prototype for the first pass but have decided to focus mostly on the Astral for now.

JoergDoellinger commented 3 months ago

Hi,

thanks for your quick reply. I am able to process my data with your library and also with a predicted .tsv library from DiaNN.

GeorgWa commented 3 months ago

Good to hear! The first point has been addressed in #213 and will be part of the next version.

michaelsteidel86 commented 3 months ago

Hi,

do you have an estimate when the diaPASEF bug will be fixed, resulting in this "No objects to concatenate" error?

Thanks in advance! Michael

GeorgWa commented 3 months ago

It's already available in the development install. We will most likely do a new release this week.