NAP_CCMS2 Error

[PennyM40]

NAP_CCMS2 Error

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
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]

[lydia1201]

Hi I have the same issue. Could anyone help to solve this problem?
http://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=ae27cc7176e04dd5ab1c4a01a12a48ba

[ridasilva]

Hello,

Please, post questions with taskids here
https://groups.google.com/g/molecular_networking_bug_reports

@PennyM40 I need your taskid or job link.

@lydia1201 avoid using the old snets workflow, user snets-V2, I was able to change an import in the tool and run your job
https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=8641aef95c8644a59c8f305fe51c9cb0

Cheers,
Ricardo

[lydia1201]

Hello,

Please, post questions with taskids here https://groups.google.com/g/molecular_networking_bug_reports

@PennyM40 I need your taskid or job link.

@lydia1201 avoid using the old snets workflow, user snets-V2, I was able to change an import in the tool and run your job https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=8641aef95c8644a59c8f305fe51c9cb0

Cheers, Ricardo

Hi Ricardo,

Yes, I tried, It worked. Thank you very much for solving the problem.

Cheers

Lydia

[PennyM40]

Hello,I am actually sorted now I realised that it was my pre-processing that was not right in MZmine (MS1 and MS2) pairing. I managed to run the job once I pre-processed carefully. Thanks Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Ricardo da Silva ***@***.***> Sent: Tuesday, October 25, 2022 8:55:26 PM To: CCMS-UCSD/GNPS_Workflows ***@***.***> Cc: PennyM40 ***@***.***>; Mention ***@***.***> Subject: Re: [CCMS-UCSD/GNPS_Workflows] NAP_CCMS2 Error (Issue #851) Hello, Please, post questions with taskids here https://groups.google.com/g/molecular_networking_bug_reports @PennyM40<https://github.com/PennyM40> I need your taskid or job link. @lydia1201<https://github.com/lydia1201> avoid using the old snets workflow, user snets-V2, I was able to change an import in the tool and run your job https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=8641aef95c8644a59c8f305fe51c9cb0 Cheers, Ricardo — Reply to this email directly, view it on GitHub<#851 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A2ZV7DQ57XKRXD6WOGGCVRLWFAUJ5ANCNFSM576QVWBQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[MuyaoXi9271]

Hi all,

I also meet the same error. I preprocess the data by using XCMS and run FBMN (7b85647fe2a4446dbcc52549d8f28dce), then I continue to run NAP (31dea4f0d098449496c6844a7ab098e5) by typing the id of FBMN.

Could you please share the solution to solve this error, I appreciate it a lot.

Best,
Muyao

[BioGavin]

I encountered the same issue. After some research, I found two possible solutions online. It turns out I imported the FBMN data but mistakenly chose the wrong workflow type. Once I switched to MZmine, the problem was resolved.

• Error in NAP workflow

• Error message in performing NAP