Could not initialise preview

[Marcel Mrose]

I have a very large CSV file (35GB) in a {source, target \n} format that I try to load into cytoscape via File -> Import -> Network -> File. I have TBs of memory as I am working on a HPC platform.

However, it results in an error message stating "Error: Could not initialise preview. The selected file may be empty or contain invalid entries". The file is consistent though, I have checked it multiple times.

So unfortunately cytoscape fails to build a preview of the file so that I can choose source and target node. It can build a correct preview if I reduce the file size, but I need the full network -- is there any workaround to load my whole network?

[Scooter Morris]

Hi Marcel,
   Can you send us the first 1000 lines in the file?  That will help us diagnose the problem.

-- scooter

[b.lav...@gmail.com]

Hi,

Just wondering if you ever got to the bottom of this issue? I am having the same problem, but only with some files - and not necessarily related to file size.

Thanks
Bonnie

[Barry Demchak]

Bonnie --

Is there a small file that shows this? We need a reproduce case, even if it's a link to a Dropbox or other file system.

Thanks!

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[b.lav...@gmail.com]

I've sent you a link to Dropbox, with a test file in it. Other files up to 10 MB have worked fine - this one is 676 KB.

Thanks a lot

Bonnie

On Monday, May 15, 2017 at 7:54:06 PM UTC+12, Marcel Mrose wrote:

[b.lav...@gmail.com]

OK, I think I've got it - something to do with the line names. I changed them all so they had no units, and therefore no punctuation, and that seems to have solved it - this has not previously been a problem (with exactly the same samples), but at least it's working now!

Thanks

Bonnie

On Monday, May 15, 2017 at 7:54:06 PM UTC+12, Marcel Mrose wrote:

[Barry Demchak]

Thanks, Bonnie ... excellent clues.

Barry Demchak -- from my mobile phone

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[Ana]

hi I have th same problem here. My file was working yesterday and today when I try to import it in cytoscape it doesnt work. Can anybody help me please?

[Barry Demchak]

Hi, Ana --

Any chance you could make this file available to us for testing? ... or explain how it was built so we can create one ourselves?

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[Ana Deaconu]

As often happens, we found our own error!!  In case some future souls are lost on the matter, we had simply found a line in our excel that made a reference to a sheet from a different excel file, which is apparently illegal for cytoscape. Thanks for having our back in the learning process ;-)

Ana Deaconu

Doctoral Student in Nutrition

University of Montreal

Earth Systems BS/MS 2010/2012
Stanford University

On 21 November 2017 at 12:10, Barry Demchak <idekerlab...@gmail.com> wrote:

Hi, Ana --

Any chance you could make this file available to us for testing? ... or explain how it was built so we can create one ourselves?

On Tue, Nov 21, 2017 at 8:24 AM, Ana <adea...@gmail.com> wrote:

hi I have th same problem here. My file was working yesterday and today when I try to import it in cytoscape it doesnt work. Can anybody help me please?

On Monday, May 15, 2017 at 3:54:06 AM UTC-4, Marcel Mrose wrote:

I have a very large CSV file (35GB) in a {source, target \n} format that I try to load into cytoscape via File -> Import -> Network -> File. I have TBs of memory as I am working on a HPC platform.

However, it results in an error message stating "Error: Could not initialise preview. The selected file may be empty or contain invalid entries". The file is consistent though, I have checked it multiple times.

So unfortunately cytoscape fails to build a preview of the file so that I can choose source and target node. It can build a correct preview if I reduce the file size, but I need the full network -- is there any workaround to load my whole network?

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: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
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[abraianm...@fau.edu]

On Monday, May 15, 2017 at 3:54:06 AM UTC-4, Marcel Mrose wrote:

I'm still having the same issue. Would anybody like to take a look at my file and tell me any potential there might be for cytoscape to not be able to recognize the source and target columns?

[John Galloway]

Would love some help please. I am having the same problem. Have checked the file and edited out any strange characters. When loading via "Import network from file" it just repeatedly says "Error: Could not initialise preview. The selected file may be empty or contain invalid entries". File is attached. Thank you in anticipation.

[Marc Legeay]

Hi John,

The issue is that your file is not UTF-8, and contains some blank characters that Cytoscape does not know how to handle.

You can check your file encoding with the UNIX command 'file', and convert it with 'iconv'.

I encoded your file in UTF-8 (attached) and it's working.

Best,

Marc.

[John Galloway]

Many thanks Marc, its working, appreciated.

John

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