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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Segmentation fault when reading BGEN file #38

Open jielab opened 7 years ago

jielab commented 7 years ago

Dear Xiaowei:

When I use the latest version of rvtest and the BGEN input file, why the log says "Loaded [ 0 ] samples from VCF files"? There is NO VCF file at all. Also, the BGEN file has two part, one is .bgen and the other part is .sample. So, how do I specify the .sample file?

In the phenotype file, does my header line must have the following five as the header names: "fid iid motid fatid sex"? It seems that the command options in RVTEST is very similar to PLINK, such as --covar-name --pheno-name. But in PLINK, the phenotype file only needs the first two columns "FID IID" and then the rest could be anything.

Thank you very much & best regards, jie

Below is the LOG file:

Thank you for using rvtests (version: 20170818, git: 72ab2236f3be72afc5329dcea9a770747aa13330) .... .... Effective Options --inBgen ukb_imp_chr20_v2.bgen --out chr20.rvtest --pheno bmi.EUR.ped --pheno-name bmi --single score

[INFO] Program version: 20170818 [INFO] Analysis started at: Wed Sep 13 21:46:39 2017 [INFO] Loaded [ 0 ] samples from VCF files [INFO] Loaded [ 334348 ] sample pheontypes Segmentation fault

dajiangliu commented 7 years ago

Did you try --meta score option? --single score is less actively maintained for now.

jielab commented 7 years ago

still got the same error. I think the segmentation fault error came from reading the input file, RVTESTS has not gone to --meta or --single part yet. I still don't understand why the log file says "from VCF files" even when i specify it to read a .bgen file. And i don't know where to specify the .sample file.

BTW, I used PLINK2a to read this .bgen file, and there is no problem.

best regards, Jie

zhanxw commented 7 years ago

Hi Jie,

I will look into this issue.

Our initial goal is to use bgen files as genotype inputs and ped files as phenotype inputs. I will see how to incorporate .sample file.

Xiaowei

On Sep 13, 2017, at 10:01 PM, jiehuang001 notifications@github.com wrote:

still got the same error. I think the segmentation fault error came from reading the input file, RVTESTS has not gone to --meta or --single part yet. I still don't understand why the log file says "from VCF files" even when i specify it to read a .bgen file. And i don't know where to specify the .sample file.

BTW, I used PLINK2a to read this .bgen file, and there is no problem.

best regards, Jie

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zhanxw commented 6 years ago

The current version of RVTESTS requires that .bgen file includes sample names. In that case a separate .sample file is not be needed. I just learned that many other .bgen files do not include sample names. In that case, I need to make RVTESTS support loading .sample file. I will work that, and update this issue.

jielab commented 6 years ago

I see. i will not use RVTESTS for .bgen files based association analyses, for now then. Hopefully you will release a new version soon that address the issues that I raised.

Best regards, Jie

zhanxw commented 6 years ago

@jiehuang001 This version (https://github.com/zhanxw/rvtests/releases/tag/v2.0.6) should support BGEN format. Please let me know if you have additional questions. Thanks.