解决Decon-eQTL分析报错Exception in thread “main“ java.lang.IndexOutOfBoundsException: Index: 1, Size: 1

在进行分析Decon2中Decon-eQTL时发生Exception in thread “main” java.lang.IndexOutOfBoundsException: Index: 1, Size: 1报错，具体如下：

cat Decon_eQTL.err
nohup: ignoring input
Writing output and logfile to result/
Starting deconvolution
2024/02/29 10:49:21
Running deconvolution version: Decon-eQTL_v1.4
======= DECONVOLUTION paramater settings =======
Expression file (-e): fpkm_ENSG.txt
Genotype file (-g): genotype_transpose.txt
Cellcount file (-c): predicted.cellcounts.scaled.txt
SNPs to test file (-sn): gene_snp.txt
Outfolder (-o): result/
Outfile (-of): deconvolutionResults.csv
Round dosage (-r): false
test run doing only 100 QTL (-t): false
Add whole blood eQTL (pearson correlation genotypes and expression) (-w): false
Do not ouput logging info to console (-no): false
Write predicted expression to output file (-oe): false
Genotype configuration to use (-gc): one
Add genotype term (-a): false
Use OLS(-uo): false
=================================================
Cell types to use:
Granulocytes
B cells (CD19+)
CD4+ T cells
CD8+ T cells
DN (CD4- CD8-)
NK dim (CD56+ CD16+)
Monocytes (CD14+)
Lymphocytes
CD45RO- CD45RA+ T cells
CD4+ Naive CD45RA+ CD27+
CD4+ Naive CD45RO- CD27+
Intermediate monocytes (CD14+CD16+)
CD8+ Naive CD45RA+ CD27+
CD8+ EM CD45RA- CD27-
CD8+ Naive CD45RO- CD27+
IgD+ IgM+
IgD+ IgM-
IgD- IgM-
NaiveB cells (IgD+ IgM+ CD27-)
Memory B cells (IgD+ IgM+ CD27+)
CD24+ CD38+
T cells (CD3+ CD56-)
Transitional B cells (CD24++ CD38++)
Naive mature B cells (CD24+ CD38+ CD27- IgM+)
CD24+ CD38+ CD27+ IgM+
IgM-
Natural effector (CD24+ CD38+ IgD+ IgM+)
NK cells (CD3- CD56+)
IgD- CD5+
IgD+ CD5+
Prol CD4+ Tconv
Prol CD4+ Treg
Treg HLA-DR+
Number of cell types: 33
Number of samples: 225
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
	at java.util.ArrayList.rangeCheck(ArrayList.java:657)
	at java.util.ArrayList.get(ArrayList.java:433)
	at main.java.decon_eQTL.Utils.parseSnpPerGeneFile(Utils.java:188)
	at main.java.decon_eQTL.Deconvolution.readInputData(Deconvolution.java:40)
	at main.java.decon_eQTL.Main.main(Main.java:24)

发现是由于gene_snp.txt文件有问题。gene_snp.txt文件为基因与snp两列，且需要以制表符tab分隔，由于是以空格分隔，故报错。具体解决措施为：

# vim 打开该文件
vim gene_snp.txt
:%s/ /\t/g # 制表符替换空格

#注意：输入的每一个数据都应是制表符间隔，利用vim里的%s/ /\t/g替换。
#注意：基因型数据为0，1，2编码，若有NA可替换为-1，%s/NA/-1/g

Decon2分析教程及代码地址：https://kkgithub.com/molgenis/systemsgenetics/tree/master/Decon2