NAP error message related to FBMN

[장혜미S]

I got the error message as below. What should I try to resolve the error below..?
Also, is it impossible to use NAP for FBMN data of GNPS using data exported to Metaboscape?
(error message)
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]

[장혜미S]

EDIT 

My data information is  as follows.

GNPS job ID:  9a8d40cfda1b49b086acee5d16e64575

Number of a cluster index: 84

Cosine value to subselect inside a cluster: 0.7

N first candidates for consensus score: 10

 Use fusion result for consensus : (left blank)
Accuracy for exact mass candidate search (ppm).: 15

Acquisition mode: Positive

Adduct ion type: [M+H]
Multiple adduct types: (left blank)

Structure databases: none

Compound class to be selected: (left blank)

User provided database: in- house database (using website, txt file)

Files:

Hyemi/Novel Capsaicinoids candidate_FORMATED.txt
CCMS_SpectralLibraries/GNPS_Beta_Libraries/BEN.mgf

 Skip parent mass selection : (left blank)
User provided MetFrag parameter file: sl_mock_parameter

Files:

Hyemi/sl_mock_parameter.txt

Maximum number of candidate structures in the graph: 10

Workflow type: MZmine
   

I also checked if there was an ID character, and of course I tried changing the Workflow type to standard.
But the same error occurred. I'm really wonder about the cause.
thank you.

2023년 7월 29일 토요일 오후 6시 22분 28초 UTC+9에 장혜미S님이 작성:

[Kyo Bin Kang]

1) 'Workflow type' should be set to 'Standard' because the molecular network was generated in the classical workflow.

2) 'Number of a cluster index' should be set to 0 if you want to annotate all the network nodes. When you put 84 here, the NAP workflow will annotate the singleton node of which cluster index is 84 (m/z 479.188).

3) The structural database and Metfrag parameters need to be formatted properly; I cannot get if you did well or not without the files.

Best,

KB

Kyo Bin Kang, PhD

Assistant Professor

College of Pharmacy, Sookmyung Women's University

Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Korea

Tel: +82-2-2077-7103. Mobile: +82-10-8836-8839

https://www.kyobinkanglab.org

2023년 8월 1일 (화) 오후 2:26, 장혜미S <jhm...@ust.ac.kr>님이 작성:

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