Long wait to start job

[Nanette Bishopric]

Hi, I have been waiting most of the day to run GSEA. I have "Please wait" and the spinning blue ball for hours at a time.  Is it just very busy this Saturday? I was at least getting some jobs attempted earlier in the morning.  Thanks!

[Ted (aka John) Liefeld]

Hi,

sorry that you are having problems.  From the back end it looks like your job finished with an error at 7:12 am this morning (PST, UTC+8).  Have you reloaded the page and/or what happens if you reload the page now?

Ted

On Sat, Jul 12, 2025 at 2:14 PM Nanette Bishopric <nbish...@gmail.com> wrote:

Hi, I have been waiting most of the day to run GSEA. I have "Please wait" and the spinning blue ball for hours at a time.  Is it just very busy this Saturday? I was at least getting some jobs attempted earlier in the morning.  Thanks!

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[Nanette Bishopric]

I ran Hierarchical Clustering and got the same ""ERROR: missing argument" - so no wait this time, but I haven't solved the error. What am I missing? 

[Nanette Bishopric]

Hi Ted,
Thanks! I did get that job report - with message "ERROR: missing argument". 

I was trying the run again (although I am not sure what was missed out).  But that job never got initiated, just "Please wait". 

I then tried to rn th GSEA module and that hanged at the same spinning blue ball. 

I will try again now and see if I can get a better result.

Nanette

On Saturday, July 12, 2025 at 5:27:18 PM UTC-4 Ted (aka John) Liefeld wrote:

[John Liefeld]

Hi,  the last 2 messages you sent didn't make it to the help forum for some reason, I just found them in the pending messages.  Can you give me some job numbers to look at if you haven't solved this yet?

Apologies for the delay

Ted

[Ted Liefeld]

Nanette,

what is the job number for your run?

Ted

To view this discussion visit https://groups.google.com/d/msgid/genepattern-help/b706b42c-2761-4cbc-908d-49bff1858fd1n%40googlegroups.com.

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Ted Liefeld                                      UC San Diego

Mesirov Lab                                    lie...@ucsd.edu                                
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[John Liefeld]

Found it.  The issue is the output filename you entered, "<HC.RAGEDOX>".  GenePattern treats any input values between the greater and and less than signs as a tag it is supposed to substitute from another parameter or from a server configuration item.  Since there is no module or server substitution for <HC.RAGEDOX> it is ending up with nothing for the output filename.

I think what you want for output filename is either "HC.RAGEDOX" without the <> or else "<input.filename_basename>" which will take the name of your input filename, strip off the 3-letter extension and substitute that in at runtime.  These will both have the same result with this input file, but the second option will also change to match different input files.

Hope this helps

Ted

[Nanette Bishopric]

Thank you! That makes sense. 

Apologies for not responding sooner- just got off a long plane flight.

Best,

Nanette 

On Jul 17, 2025, at 1:30 PM, John Liefeld <jlie...@cloud.ucsd.edu> wrote:

Found it.  The issue is the output filename you entered, "<HC.RAGEDOX>".  GenePattern treats any input values between the greater and and less than signs as a tag it is supposed to substitute from another parameter or from a server configuration item.  Since there is no module or server substitution for <HC.RAGEDOX> it is ending up with nothing for the output filename.

To view this discussion visit https://groups.google.com/d/msgid/genepattern-help/605e985f-3128-4c5c-a281-55984dcb8e5cn%40googlegroups.com.