How to prepare index/server for blat?

Question

[kirannbishwa01]

I am trying to prepare a index for blat using gfServer for my reference genome (which is not for human).

While building the index I am getting the following error:

2016/02/23 22:26:15: info: gfServer version 36x1 on host localhost, port 50000  (2016-02-23 22:26)
2016/02/23 22:26:15: info: setting up untranslated index
2016/02/23 22:26:19: info: indexing complete
2016/02/23 22:26:19: warn: Couldn't bind socket to 50000: Address already in use
2016/02/23 22:26:19: error: Fatal Error: Unable to open listening socket on port 50000.
2016/02/23 22:26:19: error: gfServer aborted

I tried building the index in other port number:

gfServer start localhost 9000 /home/everestial007/ScanIndel-forTEST/chromFa/lyrata_genome.2bit

Message:

starting untranslated server...
Counting tiles in /home/everestial007/ScanIndel-forTEST/chromFa/lyrata_genome.2bit
Done adding
Server ready for queries!

Then I tried to run blat and its not being helpful, the blat is still tyring to listen at port 50000. What could be causing the issue.

Also, I am looking for a detailed workout on blat but not finding anything useful on google.

Thanks,

[GenoMax]

If you started the server on port 9000 then did you issue a correponding gfclient command?

gfClient host port seqDir in.fa out.psl

So in your case

gfClient localhost 9000 seqDir in.fa out.psl