Version incompatibility of interproscan and lookup service

Question

[waqasnayab]

Hi,

I am using interproscan-5.15-54.0. For uaing lookup service, I did all as mentioned in https://code.google.com/p/interproscan/wiki/LocalLookupService.

My command is: ./interproscan.sh -t n -i ../../interproscan-5.15-54.0/seq_38.fa

I got the following error:

2015-11-26 14:37:28,661 [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:283] WARN -

The version of InterProScan you are using is 5.15-54.0
The version of the lookup service you are using is 5.14-53.0
As the data in these versions is not the same, you cannot use this match lookup service.
InterProScan will now run locally
If you would like to use the match lookup service, you have the following options:
i) Download the newest version of InterProScan5 from our FTP site:
   ftp://ftp.ebi.ac.uk/pub/databases/interpro/
ii) Download the match lookup service for your version of InterProScan from our FTP site and install it locally.
    You will then need to edit the following property in your configuration file to point to your local installation:
    precalculated.match.lookup.service.url=

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

Than to find the solution for that, I installed interproscan-5.14-53.0 which seems to me the compatible with the lookup version 5.14-53.0. I executed the command and now the error is:

2015-11-26 15:35:55,463 [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:283] WARN -

The version of InterProScan you are using is 5.14-53.0
The version of the lookup service you are using is 5.15-54.0
As the data in these versions is not the same, you cannot use this match lookup service.
InterProScan will now run locally
If you would like to use the match lookup service, you have the following options:
i) Download the newest version of InterProScan5 from our FTP site:
   ftp://ftp.ebi.ac.uk/pub/databases/interpro/
ii) Download the match lookup service for your version of InterProScan from our FTP site and install it locally.
    You will then need to edit the following property in your configuration file to point to your local installation:
    precalculated.match.lookup.service.url=

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

Here, it says that the lookup service is 5.15-54.0 so can not run.

Kindly help me in this regard.

Thanks,
Waqas

Answer 1

[thiesgehrmann]

Hello,

It seems you have downloaded the wrong version of the lookup service. It should match your interproscan database.

However, I have had similar problems and it may also be that you didn't configure it properly, so it defaults to an online version which doesn't match with your installed version.

If you want to run the lookup service, you also need to change your local configuration file. Make sure that the service is running with

nmap localhost

You should see (depending on your configuration), a port which corresponds to your lookup server. Then, in your interproscan properties file (at (interpro_diretory)/interproscan.properties), change the variable precalculated.match.lookup.service.url to match that server, e.g. http://localhost:200

Good luck!

[waqasnayab]

thanks for that,

the output of nmap localhost is:

kamran@kamran-OptiPlex-755:~/Desktop/new_interproscan/interproscan-5.14-53.0$ nmap localhost

Starting Nmap 6.40 ( http://nmap.org ) at 2015-11-28 13:51 PKT
Nmap scan report for localhost (127.0.0.1)
Host is up (0.00043s latency).
Not shown: 996 closed ports
PORT    STATE SERVICE
22/tcp  open  ssh
139/tcp open  netbios-ssn
445/tcp open  microsoft-ds
631/tcp open  ipp

Nmap done: 1 IP address (1 host up) scanned in 0.19 seconds

so I changed my interproscan.properties file as:

# set on the command line.
precalculated.match.lookup.service.url=http://localhost:127.0.0.1

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

Is it right? The error is changed now:

26/11/2015 22:17:19:665 Uploaded/Stored 19730 sequences for analysis
2015-11-26 22:17:19,669 [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:257] WARN -

The following problem was encountered by the pre-calculated match lookup service:
Connect to localhost:127 [localhost/127.0.0.1] failed: Connection refused
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://localhost:127.0.0.1
  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.

I am just around, need the help.

Thanks,

Waqas.