issues with the precalculated lookup in Interproscan-5.17-56.0

Question

[Chao.wang2]

Hello guys,

Is there anyone who are familiar with Interproscan-5.17-56.0? I am trying to annotate 60000 proteins on my laptop, several hours after however, it pop up that the web service failed, and suggested me to modified the interproscan.properties file. So I changed the precalculated match lookup as followed:

precalculated.match.lookup.service.url=
#proxy set up
precalculated.match.lookup.service.proxy.host=
precalculated.match.lookup.service.proxy.port=

It now calculate locally, However I have no local look up service. I am not sure what happened and should I keep running it or is there any way to fix it.

Thanks a lot amazing people

Answer 1

[Amitm]

Hi, These are the settings that I ran with (5.7.48 rel.) -

precalculated.match.lookup.service.url=http://www.ebi.ac.uk/interpro/match-lookup

#proxy set up
precalculated.match.lookup.service.proxy.host=
precalculated.match.lookup.service.proxy.port=3128

The log reads as -

15/11/2014 21:32:55:265 Welcome to InterProScan-5.7-48.0
15/11/2014 21:33:06:520 Running InterProScan v5 in STANDALONE mode...
Loading file /path/to/Input_Fasta.txt
15/11/2014 21:33:16:984 Running the following analyses:
[jobTIGRFAM-13.0,jobPfamA-27.0,jobSMART-6.2,jobSuperFamily-1.75]
Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally.
15/11/2014 21:54:46:493 Uploaded/Stored 98639 sequences for analysis
16/11/2014 03:41:53:705 25% completed
16/11/2014 13:05:47:869 50% completed
16/11/2014 16:22:26:169 75% completed
16/11/2014 19:28:12:064 90% completed
17/11/2014 03:07:32:486 100% done:  InterProScan analyses completed

So, you can see how much time it took to scan ~98k sequences. Max. no. of embedded workers was 3

[Chao.wang2]

Thanks for your response. I got the same settings as you did. Probably, I should be patient and run it again, considering it takes a huge amount of time for larger number of sequences.

[Chao.wang2]

Hi Amitm,

I ran it again, but I encountered the following problem again: Do you have any idea of what is going on there, or can I continue to analyse it locally? Thanks

03/03/2016 01:01:03:759 Uploaded/Stored 65534 sequences for analysis 2016-03-03 01:01:03,760 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:257] WARN -

The following problem was encountered by the pre-calculated match lookup service: www.ebi.ac.uk

Pre-calculated match lookup service failed - analysis proceeding to run locally

The pre-calculated match lookup service has been configured in the interproscan.properties file.
precalculated match lookup service url : http://www.ebi.ac.uk/interpro/match-lookup precalculated match lookup service proxy host : proxy port : 3128

Unfortunately the web service has failed. Check the configuration of this service in the interproscan.properties file and, if necessary, set the following property to look like this:

precalculated.match.lookup.service.url=

If the problem persists, check if this is a firewall or proxy issue. If it is a proxy issue, then setting the following property in the interproscan.properties file should work:

precalculated.match.lookup.service.proxy.host= precalculated.match.lookup.service.proxy.port=

If this still does not work please inform the InterPro team of this error by sending an email to:

[e-mail]

In the meantime, the analysis will continue to run locally.

[Amitm]

hi, As per here (scroll to the bottom), Iprscan is configured to fetch annotations from the match-lookup URL. In case it is not able to do so (like in you case, maybe because of firewall restrictions??), it will then attempt to run locally. For the 2nd option to happen you need to install/ download the huge file here. I hadn't as in my case Iprscan was able to access the match-lookup URL. Check if firewall is the culprit. If yes, then probably you need to install the local service.

[Chao.wang2]

Thanks for your reply.