Problem with getting Cytoscape Preview/Download file

[Kourosh Hooshmand]

Hi, 

I performed a Feature Based Molecular Networking Analysis (Super quick Start option) by using my MS2 spectra mgf file and quantification table file for each of the feature which was exported from MS-DIAL. The link below was emailed to me after my data was processed:

https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=e7247f6dad2f45ff946e39a0132686ce

However, my problem is that I could not get the Direct Cytoscape Preview/Download file (from Advanced Views - Experimental Views) to visualize the network on Cytoscape. The following error message was popping up after I clicked on the Direct Cytoscape Preview/Download option:

Error in creating cytoscape file, please utilize graphml import manually (photo attached below).

May I ask what I should do to fix this issue? I am using google chrome and I am a Windows 10 user.

Thank you in advance for your assistance

Best Regards

Kourosh

[Kelly Weldon]

Hello Kourosh,

While I am unsure of what exactly would be the problem with the direct download, please try using the graphml import to see if that will work!

On GNPS download from the "Download Cytoscape Data" option under "Export/Download Network Files"

Then in Cytoscape, under the "file" tab, select "import" then "Network from file" - select your downloaded graphml file from GNPS.

Please let me know if this works so we can continue troubleshooting!

Best,

Kelly

[Kourosh Hooshmand]

Hi Kelly,

Thank you for your quick reply. I did as you said and imported the graphml file into the Cytoscape. However, the first message I got was:   

Do you want to create a view for your large networks now? This could take a long time.  

I clicked on yes and then after 20 minutes of processing I got the following error message: java.lang.out of memory errror:Java heap space

So, unfortunately it did not work. I thought that if I could get the Direct Cytoscape Preview/Download file then I might be able to get the file compatible with the Cytoscape.

I was listening to a Dr. Mingxun Wang video HERE where at minutes 4:50 he mentioned that by clicking on the Direct Cytoscape Preview/Download we get the cytoscape file that we don't need to do any import of graphicml or individual pairs files anymore and it will do everything for us.

But my problem is that when I click on the Direct Cytoscape it does not work and I get the error message (photo correctly attached this time).

Kind regards,

Kourosh

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[Mingxun Wang]

Kourosh,

Since your network includes 55K nodes, which is extremely large, the Cytoscape exporter cannot handle that large of a network to give you a cys file. Additionally, your computer does not have enough memory to open such a large network. 

If you are super interested in this network you've generated, I'd recommend viewing the network in the browser:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=e7247f6dad2f45ff946e39a0132686ce&view=network_components

for example, here is one molecular family:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?view=network_displayer&componentindex=2&task=e7247f6dad2f45ff946e39a0132686ce#%7B%7D

However, I think the number of features you are exporting is likely way more than are truly there and would suggest revisiting feature finding. 

Swing by GNPS Office hours if you want to ask questions in person:

https://ccms-ucsd.github.io/GNPSDocumentation/contact/

Ming

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[Kourosh Hooshmand]

Hi Ming,

Thank you for your suggestion that I could look at my individual cluster directly on the GNPS website. However, I was also interested in visualizing the whole network in Cytoscape.

After I read your message, I realized that in The Super quick Start page for FBMN I could not change the Advanced Network Options parameters and the only thing that I could change is Networking Parameters Preset (High/low resolution). So, that is the main reason that I could not set the cosine score threshold to reduce the number of nodes.

However, in The standard GNPS interface page, I see that I can manipulate the similarity cut-off values (Min Pairs Cos) or change the Minimum Peak Intensity but the problem is that my quantification table file exceeds 20 MB and GNPS does not allow me to drag and drop the file over 20 MB. I will try to learn how to install an FTP client then I might be able to upload the files and submit my work.

Best

Kourosh