seqminer running in windows 7

[Paddy]

Hi Tao,

I am trying to run seqmincer in windows 7, which is 64 bit with 16 GB
ram. But I could not get the seqminer started by double clicking the
bat file. I could start the programme by clicking the java file, but
when I checked the statistics in seqminer, the max memory shows only
247 Mb memory. Do you how I can solve the problem? The java intalled
is 32 bit version. Is that the problem?

Thanks.

[Tao]

Hi Paddy,
Yes, you are right. Why not download and install the 64bit JRE? You
can find it here:
http://www.java.com/fr/download/manual.jsp

Make sure to uninstall the 32bit JRE before installing the new one.

BTW, it's seqMINER but not mincer ^_^
Tao

[Paddy]

Thanks a lot. Now it works :)

[Paddy]

By the way, one more question:) When I upload the BAM files, it always
shows that the read size is 25, although the real read size of the
samples is either 40 or 50. Do you think it is a problem?

Thanks.

[Tao]

Where did you see that the read size is 25?

[Paddy]

Hi Tao,

It is indicated in the C:\\windows\system32\cmd.exe window.

But when I visualize the data with IGV, the fragment size is 50.


Cheers,

[Tao]

Hi Paddy,
I couldn't remember why I had put that in the debug information but
it's sure that the 25 doesn't make sense. By default, seqMINER will
extend every reads to 200bp along the read strand.
In the newest version which you can get from sourceforge page below,
this message is already deleted.
https://sourceforge.net/projects/seqminer/

best,

[liuxi...@126.com]

Dear Tao,

I am using seqMINER and it always present an error with "A JNI error has occured, please check your installation and try again". But I have install JDK correct and javac can also be tested normaly in cmd. I realy want to know how to solve this problem. Thank you very much.

Liu

在 2011年10月28日星期五 UTC+8上午12:02:53，Tao写道：