error in openms execution

KCH Workflows
1

WARN TileUpdateMessageInjector Could not modify intro page: connect timed out
Dears,

I am a first time user of OPENMS trying to analse some sciex TT5600 files.

No ssoner i start the workflow, following errors appear. I nned your suggestions for troubleshootong the errors.

Thanks in advance
Javaid

WARN PeakPickerIterative 0:11 Invalid MIMEtype at port number 0 : has extension: ‘fasta’; expected one of: [mzml]
WARN Input File 2:1 No File selected.
WARN Input File 2:2 No File selected.
WARN Input File 2:3 No File selected.
WARN Output Folder 2:7 Please select a target folder for the Output Folder node.
ERROR OMSSAAdapter 2:5 Failing process stdout:
ERROR OMSSAAdapter 2:5 Failing process stderr:
ERROR OMSSAAdapter 2:5 Return code: -1073741515

2

Hi,
would you mind sharing the whole workflow or a fraction that is representative of the error? From what I see in the output, you are trying to pass a fasta file to a tool that expects an mzML file. However, this is just a warning message and the error of the OMSSAAdapter does not say much.
Kind regards
Alexander

3

(upload://m29IijKK2Rrp4LhpPpMKiZBzGGc.jpeg)

4

Thanks Alexander,

Here is the workflow to take a look.

Best
Javaid

openms
openms960×720 35.6 KB

5

Hi,
what types of files do you pass into your Input File nodes?
Can you also attach the workflow as a .knwf file and the data instead of an image, so I can try it out myself? I also asked an OpenMS developer to have a look at this topic, maybe he wants to have a look, too.
Kind regards
Alexander

6

Here is the KNIME file…
KNIME_project 2.knwf (25.4 KB)

Best
Javaid

7

Hi,
thank you for your response. Is the data very large? Otherwise it would be very good to have that as well, so we can reproduce the error.
Kind regards
Alexander

8

Hi Alexander,

It is an mzml file, something like 10GB generated from sCIEX .WIFF by MSCONVERT,
and a fasta file which is few mbs.

I am not sure how to send those files to you.

Best
Javaid

9

Hi,
that is indeed a bit too large. I will make sure the OpenMS developer will have a look at this topic and maybe he can help. From the workflow alone I cannot see any problem, unfortunately.
Kind regards
Alexander

10

Thanks Alexander, i would highly appreciate your kind help.

Best

Javaid