Blast on 5.1.0

[Aitor Bleda]

Hi Hector!

I have migrated our installation to 5.1.0 and now I find that the blast from the web interface doesn't work.  I tried with a fresh install/test with mvn/jetty and it also fails to return a result or even run a blast using blastn.. this used to work with v4.

Has something changed?  am I doing it wrong?

BLAST 2.2.31+

Regards

Aitor

[Alan Williams]

On 08-Dec-16 14:25, Aitor Bleda wrote:
> Hi Hector!

Hello

Probably no help, but we (synbiochem) upgraded to 5.1.0 and the blast
works OK for search. I found that it does not work well with other
search options, in particular bio safety level, so we have to leave that
on "Choose one".

> Regards
>
> Aitor

Alan

[Hector Plahar]

Hello,

Are there any error messages in the logs? Try rebuilding the blast index on the admin page -> Rebuild blast. Also click on "Rebuild Indexes" while you are at it. This may take a few minutes depending on the number of entries you have. 

Alan, this might also fix your issue. If not let mw know and I will look at it in more detail

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[Aitor Bleda]

Hi Hector!

I have run a lot of tests to check that it doesnt work.

In short: blastn does not work for me with version 5.1, it worked on 4.

There are no log files if blastn is selected,  and if I delete the blastn binary still no error, so I can only guess it is not being called.  With tblastx (it is not what I need, but..) I get a wrong parameter call.

Same happens when I call with the api:

curl -X POST --insecure -H "Content-Type: application/json" -H "X-ICE-Authentication-SessionId: 7157ab6c-4f3b-41ce-8681-9ebfe918bd4c" -d '{ blastQuery: { blastProgram: "BLAST_N", sequence: "atgaaactgagcaccaagc" }, parameters: { retrieveCount: 5 } }' "https://localhost:8443/rest/search"

(0 results, no log)

As the App Server restarts, and upon request, both on the web and by API, the blastDB gets rebuilt.

It does not work with the following systems:

System one.  Configuration one

Linux Mint Sarah kernel 4.4.0-47, based on ubuntu 16.04 LTS

Tomcat 8 

Open JDK 1.8.0_111 64 bit

Postgres as DDBB  

Installed from WAR, DDBB migrated from ICE 4

It is my dev machine

Blast: tried 2.2.31++ and tried compiling and using 2.5.0++ .  Works from command line, no change to ICE (I did change the parameter and restarted tomcat)

System one.  Configuration one

do a git clone and get a clean install

run an app server with mvn and let ice build a DDBB

edit conf and put blast path (both versions)

reboot

Add en entry, and give it a short DNA sequence.

Try blast both using web and API: same as before.

System two.

Linux Ubuntu 16.04 kernel 4.4.0-47

Tomcat 8 

Open JDK 1.8.0_111 64 bit

Postgres as DDBB

Installed from WAR, DDBB migrated from ICE 4

Same results as system one.  

Worked with ice 4

So I tried a different linux distro, tried with CentOS 7

kernel 3.10.0-327

Some jdk, running jetty and Blast 2.5.0++ compiled on system
ICE install with git clone and running on jetty.

Still does not work

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[alaninmcr]

On 13/12/2016 14:06, Aitor Bleda wrote:
> Hi Hector!
>

[snip]

> System one. Configuration one
> do a git clone and get a clean install
> run an app server with mvn and let ice build a DDBB
> edit conf and put blast path (both versions)
> reboot
> Add en entry, and give it a short DNA sequence.
> Try blast both using web and API: same as before.

Do you try blast immediately after adding an entry? In my experience,
you have to rebuild blast to get it to match the sequence.

Alan

[Aitor Bleda]

------------------

Hi Alan.

I put the data, rebuild blast and test.. doesnt work, restart server, nope, does not work.  On 4.8.1, I do the same, and works. 

[Hector Plahar]

Hi, Aitor,

I will take a closer look at it today or tomorrow with a new 5.1.0 install and see what is going on. 

Thanks,

Hector

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[Hector Plahar]

So I have tested a clean build and the only issue I encountered was what Alan mentioned: having to re-build the blast search index after each new sequence is added in order to get results. This should not happen and is a bug. I hope to have a fix next week. 

Aitor, check to make sure you have set the data directory correctly (and that there is a blast folder in there with files that look like "ice.nhr", "ice.nsq" etc). Also make sure your blast install directory is set to the location of the blast executable (e.g. /usr/share/ncbi-blast-2.5.0+/bin). These are all on the admin configuration page. I will also include more logging for blast searches when I release the bug fix in version 5.2.1

Thanks