Problem related to gfClient

[sneha murmu]

Dear Administrator,

I am using the standalone blat suite. After setting up gfServer, I ran gfClient but encountered a problem. I attach herewith a snapshot of the error. It will be great if you can help me out.

Error:

murmu@LAPTOP-BTKOJTJF:~/software/blat/blatSrc/gfClient$ gfClient LAPTOP-BTKOJTJF portX ~/software/blat/blatSrc/blat/hg38.2bit ~/softw
are/blat/blatSrc/blat/query1.fa out.psl
Error in TCP non-blocking connect() 111 - Connection refused
Operation now in progress
Sorry, the BLAT/iPCR server seems to be down.  Please try again later.

With regards,

Sneha Murmu 

Scientist (on Probation)
Division of Bioinformatics (IASRI)
Library Avenue Road, IARI
New Delhi-110012, INDIA.

[Gerardo Perez]

Hello Sneha,

Thank you for your interest in the UCSC Genome Browser and your question about running the gfClient utility.

One thing to confirm is that there are no old gfServer processes running on the port needed. You can stop the gfServer by running:

$ ./gfServer stop host port

Then use the ps command to check if any gfServer processes are still running. If there are, use the kill command to stop the gfServer pid (process id). Once you have confirmed that no gfServer processes running, then start the gfServer again.

The gfServer utility offers the -canStop parameter that makes it easier to start and stop the gfServer daemon without having to kill processes. You can run gfServer with the -canStop parameter such as:

$ ./gfServer -canStop start host port file(s)

Once there is ONLY ONE fresh gfServer process running, test the gfServer status by running:

$ ./gfServer status host port

It should report a status without error messages if it is working. Then try running the gfClient utility.

If you still get the error, could you provide more details on how you set up the gfServer?

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Gerardo Perez]

---------- Forwarded message ---------
From: sneha murmu <murmu....@gmail.com>
Date: Sun, Apr 25, 2021 at 6:10 AM
Subject: Re: [genome] Problem related to gfClient
To: Gerardo Perez <gpe...@ucsc.edu>

Thank you so much Gerardo. It worked.

With regards,

Sneha Murmu 

Scientist (on Probation)
Division of Bioinformatics (IASRI)
Library Avenue Road, IARI
New Delhi-110012, INDIA.