bimbam_lin_0.99
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Daphna
Dec 8, 2008, 2:44:45 PM12/8/08
to BIMBAM HELP
Hi,
Previously I had issues with bimbam v.0.95 when attempting to run
imputations and permutations together (I get an ‘illegal prob’
message).
I just realized that a beta version 0.99 is available for download. I
tried to execute the linux version but I believe the file might be
carpeted somehow, since although I saved it not as a ‘txt’ file I get
a message that it is not executable since it is a binary file.
Could you pleas check that the file was saved ok or is ok?
Alternatively, if the v.0.99 source code is available, I can use that
instead.
Lastly, were you able to fix the ‘illegal prob’ issue in the 0.99
version? (my main concern)
Thank you in advance and for all your help thus far,
Best regards,
Daphna
Previously I had issues with bimbam v.0.95 when attempting to run
imputations and permutations together (I get an ‘illegal prob’
message).
I just realized that a beta version 0.99 is available for download. I
tried to execute the linux version but I believe the file might be
carpeted somehow, since although I saved it not as a ‘txt’ file I get
a message that it is not executable since it is a binary file.
Could you pleas check that the file was saved ok or is ok?
Alternatively, if the v.0.99 source code is available, I can use that
instead.
Lastly, were you able to fix the ‘illegal prob’ issue in the 0.99
version? (my main concern)
Thank you in advance and for all your help thus far,
Best regards,
Daphna
Yongtao Guan
Dec 8, 2008, 2:57:30 PM12/8/08
to DaphnaA...@gmail.com, BIMBAM HELP
Daphna,
On Mon, Dec 8, 2008 at 1:44 PM, Daphna <DaphnaA...@gmail.com> wrote:
>
> Hi,
> Previously I had issues with bimbam v.0.95 when attempting to run
> imputations and permutations together (I get an 'illegal prob'
> message).
The bug (when imputation and permutation ran together) has been fixed.
But please be advised that doing permutation for large number of snps
can be very slow.
> I just realized that a beta version 0.99 is available for download. I
> tried to execute the linux version but I believe the file might be
> carpeted somehow, since although I saved it not as a 'txt' file I get
> a message that it is not executable since it is a binary file.
I don't understand the problem. The executable should be a binary file.
Maybe you want to try to chmod ?
> Could you pleas check that the file was saved ok or is ok?
> Alternatively, if the v.0.99 source code is available, I can use that
> instead.
The source code is not very stable at the moment. I will distributed it later.
> Lastly, were you able to fix the 'illegal prob' issue in the 0.99
> version? (my main concern)
Is this related to the bug you mentioned? or an independent scenario?
The illegal prob. usually suggests that your input files are problematic.
So in order to fix the issue I have to have your sample input files so
that I can recreate the problem.
Grant
>
> Thank you in advance and for all your help thus far,
> Best regards,
> Daphna
>
> >
>
--
Yongtao Guan, PhD
Postdoctoral Fellow
Dept of Human Genetics
University of Chicago
http://home.uchicago.edu/~ytguan/
On Mon, Dec 8, 2008 at 1:44 PM, Daphna <DaphnaA...@gmail.com> wrote:
>
> Hi,
> Previously I had issues with bimbam v.0.95 when attempting to run
> imputations and permutations together (I get an 'illegal prob'
> message).
But please be advised that doing permutation for large number of snps
can be very slow.
> I just realized that a beta version 0.99 is available for download. I
> tried to execute the linux version but I believe the file might be
> carpeted somehow, since although I saved it not as a 'txt' file I get
> a message that it is not executable since it is a binary file.
Maybe you want to try to chmod ?
> Could you pleas check that the file was saved ok or is ok?
> Alternatively, if the v.0.99 source code is available, I can use that
> instead.
> Lastly, were you able to fix the 'illegal prob' issue in the 0.99
> version? (my main concern)
The illegal prob. usually suggests that your input files are problematic.
So in order to fix the issue I have to have your sample input files so
that I can recreate the problem.
Grant
>
> Thank you in advance and for all your help thus far,
> Best regards,
> Daphna
>
> >
>
Yongtao Guan, PhD
Postdoctoral Fellow
Dept of Human Genetics
University of Chicago
http://home.uchicago.edu/~ytguan/
Daphna
Dec 8, 2008, 8:46:58 PM12/8/08
to BIMBAM HELP
Hi Grant,
Thank you for your reply
>The bug (when imputation and permutation ran together) has been fixed.
> But please be advised that doing permutation for large number of snps
> can be very slow.
I’m glad to hear the bug was fixed, in which bimbam versions is it
fixed?
(I downloaded the 0.95 linux 32bit again just now, but I get the same
error)
> I don't understand the problem. The executable should be a binary file.
> Maybe you want to try to chmod ?
As you can see, I’m really not a computer savvy. I don’t have a
problem executing the 0.95 linux 32bit but I do have problems with the
64bit file of the 0.95 and 0.99 versions.
I noticed that it recognizes the file as a txt file, so I think that
although I save it as an all ‘FILE’ it gets corrupted in the process.
I did try chmod (it is ’x’ for all users and groups) but from looking
at the gibberish I think the file went bad.
> The source code is not very stable at the moment. I will distributed it later.
OK thanks!
> Is this related to the bug you mentioned? or an independent scenario?
> The illegal prob. usually suggests that your input files are problematic.
> So in order to fix the issue I have to have your sample input files so
> that I can recreate the problem.
Yes, it is the same bug I mentioned also in our previous discussion
(Aug subject: ’illegal prob’ when trying to run the commands –i and -
pval).
With the older version (0.9.1), using the exact same files, this issue
didn’t occur. however it would be great if you could take a look at my
files.
I enclosed these files in my email sent from my UCLA email account.
Please let me know if you haven't received it and/or need additional
information
Thank you so much again,
Best regards
Daphna
Thank you for your reply
>The bug (when imputation and permutation ran together) has been fixed.
> But please be advised that doing permutation for large number of snps
> can be very slow.
fixed?
(I downloaded the 0.95 linux 32bit again just now, but I get the same
error)
> I don't understand the problem. The executable should be a binary file.
> Maybe you want to try to chmod ?
problem executing the 0.95 linux 32bit but I do have problems with the
64bit file of the 0.95 and 0.99 versions.
I noticed that it recognizes the file as a txt file, so I think that
although I save it as an all ‘FILE’ it gets corrupted in the process.
I did try chmod (it is ’x’ for all users and groups) but from looking
at the gibberish I think the file went bad.
> The source code is not very stable at the moment. I will distributed it later.
> Is this related to the bug you mentioned? or an independent scenario?
> The illegal prob. usually suggests that your input files are problematic.
> So in order to fix the issue I have to have your sample input files so
> that I can recreate the problem.
(Aug subject: ’illegal prob’ when trying to run the commands –i and -
pval).
With the older version (0.9.1), using the exact same files, this issue
didn’t occur. however it would be great if you could take a look at my
files.
I enclosed these files in my email sent from my UCLA email account.
Please let me know if you haven't received it and/or need additional
information
Thank you so much again,
Best regards
Daphna
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