openms in KNIME

When I execute AccurateMassSearch, Which comes from Openms tutorial .it occurred a wrong about it , I need help.
ERROR AccurateMassSearch 3:18 Failing process stdout: [Error: Unexpected internal error (the value ‘LM_ID SYSTEMATIC_NAME EXACT_MASS FORMULA’ was used but is not valid; Mapping file (C:\Users\leiyuanluo\Desktop\lyl\lipid database\LipidMapsFile.tsv’) must contain “database_name {NAME}” as first line.!)]
ERROR AccurateMassSearch 3:18 Failing process stderr:
ERROR AccurateMassSearch 3:18 Return code: 8
ERROR AccurateMassSearch 3:18 Execute failed: Failed to execute node AccurateMassSearch

Hi,

You have to structure your file like the following:

I try to solve it according to your suggestion, but another error occurres. I can not download the HMDBMappingFile and other Files.

This looks like a problem with your internet connection.
The files are definitely available. Can you try again?

I try it again through Google Chrome. However, it doesn’t work.
Thank you very much.

Can you access github.com at all?

Yes, I can do it. I can access the HDMBMappingFiles but I can’t download the tsv File.

Ok… I uploaded them somewhere else but you should really check your VPN/DNS settings. This error is not normal. And the file can get updated regularly.

I’m so appreciate it for you suggestions.Now I have downloaded the File from Github.
but the warn about it ,I wonder if I need change the format the MappingFile.
If need ,I should how to solve the problem.
ERROR AccurateMassSearch 4:18 Failing process stdout: [Error: Unexpected internal error (the value ‘HMDB:HMDB0000001 1-Methylhistidine CN1C=NC(CC@HC(O)=O)=C1 InChI=1S/C7H11N3O2/c1-10-3-5(9-4-10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12)/t6-/m0/s1’ was used but is not valid; Mapping file (D:\HMDB\HMDB2StructMapping.tsv’) must contain “database_name {NAME}” as first line.!)]
ERROR AccurateMassSearch 4:18 Failing process stderr:
ERROR AccurateMassSearch 4:18 Return code: 8
ERROR AccurateMassSearch 4:18 Execute failed: Failed to execute node AccurateMassSearch
屏幕截图 2021-06-26 200709

Hi,

this is the wrong order of input files. The mass to IDs “mapping” input file is HMDBMappingFile.tsv,
the IDs to “structure mapping” input file is HMDB2StructMappingFile.tsv.

Thanks, I have solved it.

Hi all,
I have some trouble about the AccurateMassSearch node.
a) When I execute the node It makes my computer stuck. My computer is 16G internal storage.
b) the error is following
ERROR AccurateMassSearch 3:18 Failing process stdout: [Read 11531 entries from mapping file!, Read 33 entries from adduct file ‘D:\HMDB\PositiveAdducts.tsv’., Read 15 entries from adduct file ‘D:\HMDB\NegativeAdducts.tsv’., , Found 269889 matched masses (with at least one hit each), from 413289 features, → 65% explained]
ERROR AccurateMassSearch 3:18 Failing process stderr:
ERROR AccurateMassSearch 3:18 Return code: -1073740791
ERROR AccurateMassSearch 3:18 Execute failed: Failed to execute node AccurateMassSearch

Hi!

Hmm yes, this is strange indeed. Do you mean internal storage (where 16GB in total would not be much) or RAM (where it definitely should be sufficient)?

If you are using open data, you could upload the featureXML or consensusXML that goes into the AccurateMassSearch node. (You can use a File Output node to write it to a non-temporary location).
Then I can check if I can reproduce the problem.

Ok,I will try it as you said.

Thank you very much
My computer is sufficient for run the workflow.
Now I try to solve it with your suggestions.
I use my data in KNIME.
Can you describe the plan in detail. I don’t know how to find the open data.

My plan is that you send me the file on which the tool is failing.
To do that you need to store the file somewhere you can access it. For this you need to connect a File Output node the port where you also connect to AccurateMassSearch.

metabonomics.knwf (47.0 KB)
Ok,I have shared the workflow.

Can you rightclick on the upper Output Folder, click on View: Open the output folder and upload the files online somewhere?

Yeah, I send the workflow with E-mail. Can you read it?

Dear,
No, I can’t upload the files as you suggested.
I wonder if the workflow uploaded is ok.
If it doesn’t work, I want to try your open data on my computer, but I don’t know how to load the data.
Thanks.