NAP always failed!

[裴继影]

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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.

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===> 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, ...).

When I conducted a NAP task with a FBMN result, the task always failed. I don't know which parameter is wrong. The following parameters were used:

GNPS job: 7732d3295b1a48b58deb96cd59e223f0

Number of a cluster index:620

Cosine value to subselect inside a cluster: 0.5

N first candidates for consensus score:10

 Use fusion result for consensus: selected

Accuracy for exact mass candidate search (ppm).:15

Acquisition mode:Positive

Adduct ion type:[M+H]

Multiple adduct types: none

Structure databases: GNPS, HMDB(a space between comma and HMDB)

Compound class to be selected: none

User provided database:none

 Skip parent mass selection: not selected

User provided MetFrag parameter file: template file (sl_mock_parameter.txt)

Maximum number of candidate structures in the graph: 10

Workflow type:mzmine

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]

Thanks for the answer!

[Ricardo Silva]

Hello,

can you provide the taskid for your NAP job?

thanks,

Ricardo

[裴继影]

https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=1e35a8ccd5fa40aea38c8dad3a850554

After removing the characters of ID in the parameter of GNPS job ID, the problem has been solved, but the EXPERIMENTAL - NAPviewer result can not be opened. Why? Thank you!

Jiying

在 2020年6月19日星期五 UTC+8上午4:01:11，裴继影写道：

[Ricardo Silva]

Dear Jiying,

the server is back running, sorry for the trouble.

abs,

Ricardo

[裴继影]

Thank you

在 2020年6月20日星期六 UTC+8上午1:31:43，Ricardo Silva写道：