Failed to start SequenceServer.

sequenceserver
#1

I am getting following error and unable to initiate sequenceserver:

== Failed to start SequenceServer.
== Is SequenceServer already running at: http://0.0.0.0:4567

Can anybody give suggestion to resolve this issue and probable reasons? Looking forward.Thanks.

#2

Looks like SequenceServer (or some other process) has a hold on port
4567. Do you see SS's BLAST interface if you direct your browser to
http://localhost:4567? If not, a previous process might have zombied
out. Can you run `ps aux | grep ruby` in the command line and tell me
the output? Try `ps auxwww | grep ruby` if you are on a Mac.

-- Priyam

#3

Thanks for reply.
SS BLAST interface not running on http://localhost:4567
‘ps aux| grep ruby’ output in commandline:
shrikant 41987 0.0 0.0 103236 864 pts/9 S+ 21:56 0:00 grep ruby

Let me know if u need any other specific info.SS still not running.Looking forward for help.

#4

Thanks for reply.
SS BLAST interface not running on http://localhost:4567
'ps aux| grep ruby' output in commandline:
shrikant 41987 0.0 0.0 103236 864 pts/9 S+ 21:56 0:00 grep ruby

Let me know if u need any other specific info.SS still not running.Looking
forward for help.

Maybe something else is on 4567. Try running SS on a different port,
say 7654. See ~/.sequenceserver.conf.

-- Priyam

#5

Port changing resolved the issue.SS is up and running.Thanks a lot.

#6

The problem keeps re-occurring and gets resolved on port changing.
Can you please recommend any alternative to resolve the problem permanently?

#7

I am having the same problem. This is causing SS to work for a while, then when I try to use the web interface the next day, it gives me a bunch of errors when I BLAST. I’ve tried changing ports, and this is only a temporary fix. I usually have to restart the computer and restart SS to get it to work because the program also won’t let me quit SS.

I don’t know which version of ruby Shrikant is running, but I am running 2.0.0-p0. Could this be the issue? Is SS incompatable with ruby 2.0+? If so, how do I downgrade to let the program work?

Another question related to ports: Is there a reason it won’t let me set the port to 80?

Thanks!

Matt

#8

Hi Matthew

sorry you’re having difficulties getting things running.

I don’t know which version of ruby Shrikant is running, but I am running 2.0.0-p0. Could this be the issue? Is SS incompatable with ruby 2.0+? If so, how do I downgrade to let the program work?

Mostly we’ve been using it on 1.9.x - so one of the 1.9 versions would probably be your best bet.

Another question related to ports: Is there a reason it won’t let me set the port to 80?

That’s not our fault but your computer’s! On my mac only superuser (root) can launch on port 80 or 8080. So try “sudo sequenceserver” to see if that works. (Make sure that Apache isn’t already running on that port!)

Cheers,

yannick

#9

Hi Shrikant,

I’m a little confused as to what you are doing exactly. Are you having to change from port to port to port (e.g. 4567 to 4568 to 4569), or are you simply saying that you are never able to use port 4567 and always have to use some other port?

Thanks,
ben

#10

Hi Ben,
Yeah first i used port 4567. Since problem occurred (as mentioned in earlier post) I was suggested to change port.Changing port to 7654 resolved the issue for timebeing. Now I am using port 4566.
I hope you this clarification will help you understand the issue in better way.
Looking forward to your help.

#11

And when you go to

http://localhost:7654

Doesn’t lead anywhere useful?

You could try

$ killall ruby

But note that this will kill all running ruby processes, not just sequenceserver

#12

Thanks again Ben.

And when you go to

http://localhost:7654

Doesn’t lead anywhere useful?

Yeah SS was running but after sometime it stopped running and I changed port to 4566 and then SS resumed.

You could try

$ killall ruby

But note that this will kill all running ruby processes, not just sequenceserver

I shall try and let you know.

is there any way to log SS usage.?

#13

You could try

#14

I don't know which version of ruby Shrikant is running, but I am running
2.0.0-p0. Could this be the issue? Is SS incompatable with ruby 2.0+? If so,
how do I downgrade to let the program work?

I have run SS a couple of times on Ruby 2.0.0-p0 and mostly it works.
Except, sometimes the default server (WEBrick) doesn't properly
shutdown. It is probable that this is the cause of the problem
Matthew and Shrikant are facing.

Matthew, please could you try running SS on Ruby 1.9 and let us know
if that works for you? We have been running SS just fine on 1.8.7 and
1.9.{2,3}.

Shrikant, which version of Ruby are you running? Also, are you
running SS on a Windows machine by any chance?

Another question related to ports: Is there a reason it won't let me set the
port to 80?

For historical reasons only the superuser (root) can start a service
on ports 1-1024. This thread [1] on unix.stackexchange has a
semi-satisfactory explanation.

If you start SS as root (using sudo) you can use port 80. However,
it's advised to run application servers like WEBrick and Think (which
SS uses) behind a daddy server like Apache or Nginx.

[1]: http://unix.stackexchange.com/questions/16564/why-are-the-first-1024-ports-restricted-to-the-root-user-only

-- Priyam

#15

SS is running on linux CentOS Server.On this server ruby 1.8.7 (2011-06-30 patchlevel 352) [x86_64-linux] is running.
Do you have any other recommendation to improve SS performance.
Sometimes users are also facing issues with non-working on BLASTN push button on SS page through Internet explorer and BLAST failure when selecting multiple databases ( more than 3).

I don’t know which version of ruby Shrikant is running, but I am running
2.0.0-p0. Could this be the issue? Is SS incompatable with ruby 2.0+? If so,
how do I downgrade to let the program work?

I have run SS a couple of times on Ruby 2.0.0-p0 and mostly it works.
Except, sometimes the default server (WEBrick) doesn’t properly
shutdown. It is probable that this is the cause of the problem
Matthew and Shrikant are facing.

Matthew, please could you try running SS on Ruby 1.9 and let us know
if that works for you? We have been running SS just fine on 1.8.7 and
1.9.{2,3}.

Shrikant, which version of Ruby are you running? Also, are you
running SS on a Windows machine by any chance?

ruby 1.8.7 (2011-06-30 patchlevel 352) [x86_64-linux]