BLAST2GO using questions

SDPA_Pet · 08-09-2014, 05:38 PM

Hi, I just started to use blast2go. I have some questions.

1> When I start the java program, I suppose I should keep my computer connecting to internet until the analysis finishes. Right?

2>Unfortunately, I have a large data set and it will run for several days, but my school internet is not stable these days. If it disconnects in the middle of analysis, will some sequences fail to mapping or annotations, etc.

3> Can I keep saving blast2go data files, if the internet is not stable Will this help?

4> I am using windows7. My computer has 16GB RAM, but I can only start 1G java program? Does anyone know how to fix it?

Thank you.

GenoMax · 08-10-2014, 04:52 PM

Quote:

Originally Posted by SDPA_Pet

Hi, I just started to use blast2go. I have some questions.

4> I am using windows7. My computer has 16GB RAM, but I can only start 1G java program? Does anyone know how to fix it?

Thank you.

If you are using the webstart option then the click-able link on this page allows you to set amount of memory to use: http://www.blast2go.com/start-blast2go

If you are using the command line you can probably adjust the amount by changing the highlighted number

Code:

$ javaws http://blast2go.com/webstart/blast2go1000.jnlp

SDPA_Pet · 08-10-2014, 05:03 PM

I used the webstart option. The point is the the program didn't launch, even I choose the large RAM (e.g., 10G). The maximum ram I can start the program is 1.2G.

GenoMax · 08-10-2014, 05:12 PM

Do you have 64-bit java installed (in addition to the 32-bit)? If not, you would want to install that first.

Then open a terminal window (PC/Mac/Unix) and then type the command I indicated below. javaws should be in your $PATH. If it is not then you can provide the full path to it.

Try this to allocate ~4GB RAM

Code:

$ javaws http://blast2go.com/webstart/blast2go4000.jnlp

SDPA_Pet · 08-10-2014, 05:46 PM

I have 64 bit java. I tried the command line, but it didn't work.

GenoMax · 08-10-2014, 05:56 PM

Were you specifically running javaws in the 64-bit java/bin directory? Just checking because many systems may run the 32-bit version by default if you just used the command line I included before.

SDPA_Pet · 08-10-2014, 06:01 PM

Yes. I ran it in the 64bit folder.

SDPA_Pet · 08-10-2014, 06:04 PM

I just tried 10GB memory and the program started. I don't why. I don't know it is a bug or not? It shouldn't be like this. Randomly starts.

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08-09-2014, 05:38 PM	#1
SDPA_Pet Senior Member Location: US Join Date: Apr 2013 Posts: 222	BLAST2GO using questions Hi, I just started to use blast2go. I have some questions. 1> When I start the java program, I suppose I should keep my computer connecting to internet until the analysis finishes. Right? 2>Unfortunately, I have a large data set and it will run for several days, but my school internet is not stable these days. If it disconnects in the middle of analysis, will some sequences fail to mapping or annotations, etc. 3> Can I keep saving blast2go data files, if the internet is not stable Will this help? 4> I am using windows7. My computer has 16GB RAM, but I can only start 1G java program? Does anyone know how to fix it? Thank you.

08-10-2014, 05:12 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	Do you have 64-bit java installed (in addition to the 32-bit)? If not, you would want to install that first. Then open a terminal window (PC/Mac/Unix) and then type the command I indicated below. javaws should be in your $PATH. If it is not then you can provide the full path to it. Try this to allocate ~4GB RAM Code: $ javaws http://blast2go.com/webstart/blast2go4000.jnlp

08-10-2014, 05:03 PM	#3
SDPA_Pet Senior Member Location: US Join Date: Apr 2013 Posts: 222	I used the webstart option. The point is the the program didn't launch, even I choose the large RAM (e.g., 10G). The maximum ram I can start the program is 1.2G.

08-10-2014, 05:46 PM	#5
SDPA_Pet Senior Member Location: US Join Date: Apr 2013 Posts: 222	I have 64 bit java. I tried the command line, but it didn't work.

08-10-2014, 05:56 PM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	Were you specifically running javaws in the 64-bit java/bin directory? Just checking because many systems may run the 32-bit version by default if you just used the command line I included before.

08-10-2014, 06:01 PM	#7
SDPA_Pet Senior Member Location: US Join Date: Apr 2013 Posts: 222	Yes. I ran it in the 64bit folder.

08-10-2014, 06:04 PM	#8
SDPA_Pet Senior Member Location: US Join Date: Apr 2013 Posts: 222	I just tried 10GB memory and the program started. I don't why. I don't know it is a bug or not? It shouldn't be like this. Randomly starts.