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Public Workflows at GNPS
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NAP_CCMS2 Error #851

Open PennyM40 opened 1 year ago

PennyM40 commented 1 year ago

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 commented 1 year ago

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

![Uploading 3680453E-F66B-4CB9-8EE4-7E3A1C1354B2.png…]()

ridasilva commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

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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

@PennyM40https://github.com/PennyM40 I need your taskid or job link.

@lydia1201https://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 GitHubhttps://github.com/CCMS-UCSD/GNPS_Workflows/issues/851#issuecomment-1291003824, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2ZV7DQ57XKRXD6WOGGCVRLWFAUJ5ANCNFSM576QVWBQ. You are receiving this because you were mentioned.Message ID: @.***>

MuyaoXi9271 commented 1 year ago

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