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williamslab / ibis

Algorithm for rapid, phase-free detection of long identical by descent segments
GNU General Public License v3.0
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ibis beginner error #1

Closed karens99 closed 6 months ago

karens99 commented 4 years ago

Hi, I am trying to run IBIS on a set of plink binary files, with no additional options, but am getting no output, and a comment that says "Illegal instruction". The plink binary files work fine in plink and king, so I wonder if I am doing something else wrong. Please see my code and log below; any help is appreciated!

Here is my command:

ibis -b freeze1.chr10.allfam.filtered

Here is the log:

IBIS Segment Caller! v1.19.2 (Released March 9, 2020) Viewing arguments... -b - Running with input files: freeze1.chr10.allfam.filtered.bed, freeze1.chr10.allfam.filtered.bim, freeze1.chr10.allfam.filtered.fam No prefix given. Defaulting filenames to prefix "ibis" Parsing SNP file... WARNING: Setting genetic position from physical done. Parsing individual file... done. Parsing genotype file... initiated, to complete later. Chromosome map shorter than 6 units of genetic distance. Morgan input detected - Converting to centimorgans. (Prevent this by running with -noConvert argument) Defining Windows... done. Organizing genotype data for analysis... done. Beginning segment detection with 1 thread(s)...Illegal instruction (core dumped)

DanielSeidman commented 4 years ago

Hello!

It looks like you are using v1.19.2. As of the most recent release, we changed the behaviors of ibis in the event that you do not include a genetic map in the bim file, so that it replaces the 0s for the genetic map with a mapping of 1Mb to 1cM. You may be experiencing problems due to IBIS not properly handling the lack of map in the input. Did you not insert a map into the bim file you were using? If you did not, it may be worth trying v1.19.3 in the release we sent out yesterday, or try inserting a map into the bim file yourself.

On Wed, Apr 29, 2020 at 4:07 PM karens99 notifications@github.com wrote:

Hi, I am trying to run IBIS on a set of plink binary files, with no additional options, but am getting no output, and a comment that says "Illegal instruction". The plink binary files work fine in plink and king, so I wonder if I am doing something else wrong. Please see my code and log below; any help is appreciated!

Here is my command:

ibis -b freeze1.chr10.allfam.filtered

Here is the log:

IBIS Segment Caller! v1.19.2 (Released March 9, 2020) Viewing arguments... -b - Running with input files: freeze1.chr10.allfam.filtered.bed, freeze1.chr10.allfam.filtered.bim, freeze1.chr10.allfam.filtered.fam No prefix given. Defaulting filenames to prefix "ibis" Parsing SNP file... WARNING: Setting genetic position from physical done. Parsing individual file... done. Parsing genotype file... initiated, to complete later. Chromosome map shorter than 6 units of genetic distance. Morgan input detected - Converting to centimorgans. (Prevent this by running with -noConvert argument) Defining Windows... done. Organizing genotype data for analysis... done. Beginning segment detection with 1 thread(s)...Illegal instruction (core dumped)

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DanielSeidman commented 4 years ago

After discussing this, we realize that it is also possible that your computer may not have the popcount functionality. We didn't have access to a processor without the popcount function to confirm whether or not this could be an issue for certain machines. Is it possible for you to compile IBIS yourself? That should theoretically resolve the issue if you do (though you may also still want v1.19.3 for a separate reason). If not, let us know, and we could look into making an executable that will work for you.

On Wed, Apr 29, 2020 at 4:25 PM Daniel S architeuthis.boy@gmail.com wrote:

Hello!

It looks like you are using v1.19.2. As of the most recent release, we changed the behaviors of ibis in the event that you do not include a genetic map in the bim file, so that it replaces the 0s for the genetic map with a mapping of 1Mb to 1cM. You may be experiencing problems due to IBIS not properly handling the lack of map in the input. Did you not insert a map into the bim file you were using? If you did not, it may be worth trying v1.19.3 in the release we sent out yesterday, or try inserting a map into the bim file yourself.

On Wed, Apr 29, 2020 at 4:07 PM karens99 notifications@github.com wrote:

Hi, I am trying to run IBIS on a set of plink binary files, with no additional options, but am getting no output, and a comment that says "Illegal instruction". The plink binary files work fine in plink and king, so I wonder if I am doing something else wrong. Please see my code and log below; any help is appreciated!

Here is my command:

ibis -b freeze1.chr10.allfam.filtered

Here is the log:

IBIS Segment Caller! v1.19.2 (Released March 9, 2020) Viewing arguments... -b - Running with input files: freeze1.chr10.allfam.filtered.bed, freeze1.chr10.allfam.filtered.bim, freeze1.chr10.allfam.filtered.fam No prefix given. Defaulting filenames to prefix "ibis" Parsing SNP file... WARNING: Setting genetic position from physical done. Parsing individual file... done. Parsing genotype file... initiated, to complete later. Chromosome map shorter than 6 units of genetic distance. Morgan input detected - Converting to centimorgans. (Prevent this by running with -noConvert argument) Defining Windows... done. Organizing genotype data for analysis... done. Beginning segment detection with 1 thread(s)...Illegal instruction (core dumped)

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karens99 commented 4 years ago

Thanks for your responses. We did update to v1.19.3 based on your recommendation, but we are still having the same issue. I am not inserting a map into the bim file yet, as I am just getting started with IBIS, and wanted to see how it would work without it. I will try adding the map, and see how it goes. In addition, I will discuss your 2nd comment with our IT manager, and let you know his response.

williamslab commented 6 months ago

I'm going to close this, but please let us know if we can help further.