FastBAT not recognizing .bim file CHROMOSOME X

Dear Jian, I am using fastBAT to run a gene-based analysis in chromosome X.



However, somehow when I read my data using

gcta --bfile good_imp --fastBAT BMItoBAT.txt --fastBAT-gene-list /home/r549001/ukb/glist-hg19.txt --out test



It states that it has only one SNP

*******************************************************************

* Genome-wide Complex Trait Analysis (GCTA)

* version v1.94.1 Linux

* Built at Aug 3 2022 14:39:54, by GCC 8.3

* (C) 2010-present, Yang Lab, Westlake University

* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>

*******************************************************************



Reading PLINK FAM file from [good_imp.fam].

40000 individuals to be included from [good_imp.fam].

Reading PLINK BIM file from [good_imp.bim].

1 SNPs to be included from [good_imp.bim].

Reading PLINK BED file from [good_imp.bed] in SNP-major format ...

Genotype data for 40000 individuals and 1 SNPs to be included from [good_imp.bed].



However, if I use other GCTA commands as



gcta --bfile good_imp --make-grm-xchr --out test_xchr

*******************************************************************

* Genome-wide Complex Trait Analysis (GCTA)

* version v1.94.1 Linux

* Built at Aug 3 2022 14:39:54, by GCC 8.3

* (C) 2010-present, Yang Lab, Westlake University

* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>

*******************************************************************

Analysis started at 16:07:28 CET on Wed Jan 18 2023.

Hostname: cofa001.research.erasmusmc.nl



Options:



--bfile good_imp

--make-grm-xchr

--out test_xchr



Note: this function takes X chromosome as non-PAR region.

Reading PLINK FAM file from [good_imp.fam]...

40000 individuals to be included from FAM file.

40000 individuals to be included. 18739 males, 21261 females, 0 unknown.

Reading PLINK BIM file from [good_imp.bim]...

167075 SNPs to be included from BIM file(s).

Computing the genetic relationship matrix (GRM) v2 ...

Subset 1/1, no. subject 1-40000

40000 samples, 167075 markers, 800020000 GRM elements

IDs for the GRM file have been saved in the file [test_xchr.grm.id]

Computing GRM...