Error in NAP workflow

[Jessica Gomez]

IF YOU ARE REPORTING AN ISSUE, PLEASE MAKE SURE:

1. Your questions was not addressed previously in the GNPS FORUM.

2. Is not already reported in our GitHub repository : https://github.com/CCMS-UCSD/GNPS_Workflows.

3. You have consulted the GNPS documentation : https://ccms-ucsd.github.io/GNPSDocumentation/

===> if the problem couldn't be solved:

Create a post on the GNPS forum or an issue on GitHub. Include the GNPS URL link to the job(s). Specify the mass spectrometer type and manufacturer, as well as the procedure for data conversion to mzML/mzXML. If this is relevant for the issue/discussion, indicate the experimental conditions (chromatography, ionisation mode, MS/MS acquisition parameters, ...).

Hi,

This was my first time trying the NAP function as I intend to use MolNetEnhancer. 

I encountered the following error message for ID=570829e8f83a4bfaa3b38b0aea5bea14

Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection Calls: load -> readChar In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'split_data/tabgnps.rda', probable reason 'No such file or directory' Execution halted Traceback (most recent call last): File "/data/beta-proteomics2/tools/nap_ccms2/merge_fragments.py", line 32, in <module> main() File "/data/beta-proteomics2/tools/nap_ccms2/merge_fragments.py", line 14, in main fls = os.listdir('fragmenter_res') FileNotFoundError: [Errno 2] No such file or directory: 'fragmenter_res' Tool execution terminates abnormally with exit code [1]

Could you please tell me where I went wrong?

Thanks,

Jessica

[Ricardo Silva]

Hi Jessica,

I just fixed a small bug for V2 workflow

https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=81afb7b8e3394bbdaef3e775f665335a

For more info, take a look at the documentation

https://ccms-ucsd.github.io/GNPSDocumentation/nap/

Cheers,

Ricardo

[Jessica Gomez]

Hi Ricardo,

This fixed my problem, thanks so much.

[Jessica Gomez]

Sorry, I'm actually mistaken.

I went to view the results via Cytoscape and saw this message on the job window:

Could not find result view specification for workflow [NAP_CCMS2] version [1.2.5]

Why has this happened?

[Upendra Sharma]

Dear All,

I dont know I should post my query or not. I am just new user to this source. So can somebody guide me how to use this.

My aim is match the data we have with already exciting data.

Regards

Upendra

[rsilva...@gmail.com]

Dear Upendar,

If you are referring to the " Could not find view .." error, take a look at your url, it should say "proteomics2" instead of "gnps", see the working example

https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=2d7b00ff710c42438146f2bc311f1785

Cheers,

Ricardo