RaisD and the sfs_code2ms converter

[demetris taliadoros]

Hi Niko, Pavlo, and community,

I am trying to assess the false positive rate for my dataset using SFS_CODE to simulate data with background selection, under the best demographic model that I have previously inferred.

I have used the tool "convertSFS_CODE" to convert the SFS_CODE output to ms format.

The problem is that when I am trying to run RaisD on the converted ms-format file I get the following error message:

RAiSD: sources/RAiSD.c:256: main: Assertion `(uint64_t)RSDDataset->setSNPs==RSDDataset->preLoadedsetSNPs' failed.
Aborted (core dumped)

I suspect that there is something wrong with the file. however, I couldn't identify the difference by comparing  it with files produced by ms. Maybe you have an idea about what might be causing this problem.

Best regards

Demetris

[Nikolaos Alachiotis]

Hello Demetris,
Can you please send me the input file that is causing this error?
Which version are you using?
Best regards,
Nikos A.

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Nikolaos Alachiotis

[demetris taliadoros]

Hi Nikos,

Thank you for helping.

I am using RaisD v. 2.8.

I was not subscribed to the group and it would not let me upload my file. Please find a test simulated dataset in this dropbox link: https://www.dropbox.com/sh/csddbawnbx87k3g/AAA1J3trt2TcEs7yAdYuzWKZa?dl=0

However, I think that after this message this issue will be resolved and I will be able to upload the file here as well.

Best regards

Demetris

[demetris taliadoros]

Hi again! Now I am able to upload the test file here as well so maybe it is just more convenient to have it here.

Best regards

Demetris

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[Nikolaos Alachiotis]

Hello Demetris,
It seems that there are monomorphic columns in your file, and this is
what is causing the assertion to fail.
RAiSD discards such sites in VCF and FASTA files but not in ms (I can
also implement this in the next version, but it is not going to be
very soon). Is it possible to generate your file without including
monomorphic files?
Best regards,
Nikos A.

On Fri, Mar 19, 2021 at 5:52 PM demetris taliadoros

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Nikolaos Alachiotis

[demetris taliadoros]

Hello Nikos,

Thanks again. A quick solution I found now is to convert the SFS_CODE output to fasta format instead of ms. This can be easily done with the same "convertSFS_CODE" tool, provided with the sfs_code software!

Have a great week.

Best regards

Demetris

[Mariia Selifanova]

Hello! 

I am getting the same error ( "RAiSD: sources/RAiSD.c:256: main: Assertion `(uint64_t)RSDDataset->setSNPs==RSDDataset->preLoadedsetSNPs' failed.") while trying to asses FPR with my data. My simulations were generated using Slim3 and I don't have monomorphic columns in my file (https://drive.google.com/file/d/1-fkTPCYBcnnou8-ws7Nx27Oseydq5el1/view?usp=sharing).  What could be the problem? Thank you! 

Best regards, 

Masha

понедельник, 22 марта 2021 г. в 19:54:38 UTC+4, demetris....@gmail.com:

[Nikolaos Alachiotis]

Hello Masha,
I checked your file and there are monomorphic columns. RAiSD assumes
that ms files do not contain monomorphic columns. You can remove this
check by removing lines 255 and 256 in RAiSD.c file and then
recompile.
Best regards,
Nikos A.

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Nikolaos Alachiotis