search

CCMS-UCSD / GNPS_Workflows

Public Workflows at GNPS
https://gnps.ucsd.edu/
Other
52 stars 43 forks source link

[Molnetenhancer] Needs update pushed #273

Closed jgauglitz closed 4 years ago

jgauglitz commented 4 years ago

This job failed: http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=89249a50d55e4c5094606c194f0f1667

A 'N/A' string sneaked into the SMILES file and caused the error.

Madeleine fixed this in version 0.1.1. of MolNetEnhancer: MolNetEnhancer version 0.1.1. needs to be updated on GNPS, then the issue should be fixed in the GNPS workflow also.

mwang87 commented 4 years ago

Can you confirm this also doesn't work on the development server?

amcaraballor commented 4 years ago

The MolNetEnhancer Release_14 does not work. I tested re-running previous jobs that were succesfully accomplished, but cloning them to the recent version [release 14] all failed. I can provide links to the ones that worked and failed. Cloned and failed: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=cb491f2d010643ddb363b7662239a5b7 Original [run with MolNetEnhancer v1.2.5]: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=420115527f604b3d8733cb248a52d132 I tested with other datasets with the same results, MolNetEnhancer release 14 does not provide CF output to any feature. Thoughts?

mwang87 commented 4 years ago

The dereplicator results are empty.

amcaraballor commented 4 years ago

Hey @mwang87, even the jobs only with NAP should (in theory) run fine with the MoNetEnhancer and get the CF output. The previous version worked. Check this out using only Dereplicator and VarQuest results with a small dataset also fails running MolNetEnhancer release 14: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6a69517976944abba449dea51faf8923

mwang87 commented 4 years ago

But the dereplicator results are not empty in this new example. The old job you provided, the dereplicator results are empty

amcaraballor commented 4 years ago

Hey @mwang87, the examples I provided above contained NAP and Dereplicator [I also tested with only NAP, only Dereplicator and/or VarQuest, even with MS2LDA and also failed with MolNetEnhancer release 14]. These contain Dereplicator, are not empty: Cloned and failed: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=cb491f2d010643ddb363b7662239a5b7 Original [run with MolNetEnhancer v1.2.5 and worked fine]: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=420115527f604b3d8733cb248a52d132 Check this out using only Dereplicator and VarQuest results with a small dataset also fails running MolNetEnhancer release 14: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6a69517976944abba449dea51faf8923

justinjjvanderhooft commented 4 years ago

Hi @amcaraballor, release 15 running at proteomics2 should finish okay. Looks like the servers are down on your end now so I can't test, but that's the most up-to-date version. That also displays the ClassyFire scores properly.

mwang87 commented 4 years ago

@amcaraballor

In the failure case you list, the dereplicator results are empty and so the software fails. Please don't include tasks where the result set is 0. We don't handle that case.

amcaraballor commented 4 years ago

Two examples of failed MolNetEnhancer release 14:

Original [MolNetEnhancer version 1.2.5 worked fine]: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=420115527f604b3d8733cb248a52d132

mwang87 commented 4 years ago

I think this job is too old for us to process. We need it to be at least release_8. I would recommend running again.

mwang87 commented 4 years ago

Rerunning on Proteomics2 with fix:

https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=3efc8b1dda3b46d098b190731d46c9ab https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=f38d1cd5eff84bc8b36f9262c3d5b30a https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=a58c0dedc3cd418a999dca466c83110f

mwang87 commented 4 years ago

Closing as should be addressed by release_15