Hi Anurag,
I’ll keep an eye on my system and “play” around with filenames in the meantime to see I can help shine some light on this.
Thanks, totally understandable regarding development cycles. Now that I know the “trick” for naming alias files, it will be nothing but a little combination of grep/sed/awk to take care of populating them for my production purposes.
Cheers,
Halocaridina
Good Day,
as well thanks for developing and maintaining SequenceServer. I believe I have a similar problem. I am trying to work with the MD5nr database, which as well uses an alias file:
`
$ cat md5nr.pal
Hi Bert,
I wonder what stage seqserv is being slow on. What happens if you run a query (and so get the spinning wheel), and then look at the command line where seqserv is running from? Also, if you use the command “top”, what process is taking the most CPU?
ben
Hi Ben,
thanks for the quick reply.
Serverside output:
`
D, [2013-08-29T09:13:12.854989 #10647] DEBUG – : method: blastp
D, [2013-08-29T09:13:12.855219 #10647] DEBUG – : sequence: MTGTTGATAWR
D, [2013-08-29T09:13:12.855494 #10647] DEBUG – : database: [“69d7ff233621b78e5ef844130befbae9”]
D, [2013-08-29T09:13:12.855640 #10647] DEBUG – : advanced:
`
top:
`
top - 09:15:03 up 1 day, 16:50, 3 users, load average: 0,77, 0,31, 0,15
Tasks: 144 total, 2 running, 142 sleeping, 0 stopped, 0 zombie
%Cpu(s): 20,9 us, 7,7 sy, 0,0 ni, 26,0 id, 45,1 wa, 0,0 hi, 0,3 si, 0,0 st
KiB Mem: 1017684 total, 950224 used, 67460 free, 31272 buffers
KiB Swap: 2074620 total, 370312 used, 1704308 free, 602548 cached
D, [2013-08-29T09:14:38.228354 #10707] DEBUG – : sequence: MTGTTGATAWR
10742 jfk 20 0 2301m 308m 306m R 50,4 31,1 0:12.15 blastp
23 root 20 0 0 0 0 S 9,3 0,0 0:54.39 kswapd0
9096 root 20 0 0 0 0 S 0,3 0,0 0:01.67 kworker/0:2
10737 jfk 20 0 23300 1644 1136 R 0,3 0,2 0:00.12 top
`
The runtime is so high, since it does not seem to be stopped since my last trials yesterday, despite me killing the process.
WOW…it suddenly worked with a short query. The output also indicates that the full database is read. Thank you and sorry for bothering…I simply need more powerful hardware and some old machine i had lying around…