Help to use Blast2go

islandemiaj · 07-20-2012, 12:28 PM

Hello,

Could anyone show me what I'm doing wrong: I import the blast results in xml. After that I go to Tools -> database configuration, and use a local database. The problem occurs when I start mapping, this process start well but after some time the program lock. This is relationated with the program's memory?

Thanks in advance,

gprakhar · 07-21-2012, 01:57 AM

Hello,

Might be RAM issue, Blast2go uses a lot of memory.
For our node with 96 Gb RAM, we still have to split the blast xml results and then run Blast2Go.

Try spliting the xml input and then run.

--
pg

JackieBadger · 07-21-2012, 09:39 AM

Open the java file in a text edit program. At the bottom it should say something like
"<j2se version="1.5+" initial-heap-size="64m" max-heap-size="2048M"/>"

Delete " max-heap-size="2048M" " and save the file.

This removes any cap on memory allocation and hopefully will work

islandemiaj · 07-23-2012, 10:09 AM

Thanks for the replies,

I was using less RAM and also was using an earlier java version.

So, I updated the java and increase the maximum JVM Heap Size (-Xmx).

monikadii · 07-02-2015, 01:13 PM

hi everyone

How can I separate annotated sequences from no annotated, and then use to run blast against nr database

sgoetz · 09-23-2015, 08:38 AM

Hi Monika.
Just use the "Select by Colour" function in Blast2GO to select sequences by their analysis status.
If you want to select all non-blue sequences just choose all the non-blue colours and than remove the existing blast results of the selected sequences to redo the blast against the NR database.

Tip: Please note that In any way, Blast2GO, by default, only blasts sequences which are not yet blasted (white, red or lila) so no need to select them specifically. Of course, if you want to redo the blast for some sequences you will have to select them and remove the blast results first.

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07-20-2012, 12:28 PM	#1
islandemiaj Junior Member Location: São Paulo Join Date: Jul 2012 Posts: 5	Help to use Blast2go Hello, Could anyone show me what I'm doing wrong: I import the blast results in xml. After that I go to Tools -> database configuration, and use a local database. The problem occurs when I start mapping, this process start well but after some time the program lock. This is relationated with the program's memory? Thanks in advance,

07-21-2012, 01:57 AM	#2
gprakhar Member Location: India Join Date: Aug 2010 Posts: 78	Hello, Might be RAM issue, Blast2go uses a lot of memory. For our node with 96 Gb RAM, we still have to split the blast xml results and then run Blast2Go. Try spliting the xml input and then run. -- pg

07-21-2012, 09:39 AM	#3
JackieBadger Senior Member Location: Halifax, Nova Scotia Join Date: Mar 2009 Posts: 381	Open the java file in a text edit program. At the bottom it should say something like "<j2se version="1.5+" initial-heap-size="64m" max-heap-size="2048M"/>" Delete " max-heap-size="2048M" " and save the file. This removes any cap on memory allocation and hopefully will work

07-23-2012, 10:09 AM	#4
islandemiaj Junior Member Location: São Paulo Join Date: Jul 2012 Posts: 5	Thanks for the replies, I was using less RAM and also was using an earlier java version. So, I updated the java and increase the maximum JVM Heap Size (-Xmx).

07-02-2015, 01:13 PM	#5
monikadii Junior Member Location: Chile Join Date: Jul 2015 Posts: 1	hi everyone How can I separate annotated sequences from no annotated, and then use to run blast against nr database

09-23-2015, 08:38 AM	#6
sgoetz Member Location: Spain Join Date: May 2010 Posts: 11	Hi Monika. Just use the "Select by Colour" function in Blast2GO to select sequences by their analysis status. If you want to select all non-blue sequences just choose all the non-blue colours and than remove the existing blast results of the selected sequences to redo the blast against the NR database. Tip: Please note that In any way, Blast2GO, by default, only blasts sequences which are not yet blasted (white, red or lila) so no need to select them specifically. Of course, if you want to redo the blast for some sequences you will have to select them and remove the blast results first.