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Description
$ /public/home/lihao/anaconda3/envs/xpclr/bin/xpclr --format vcf \
--input /vol2/niesijia2/huada_project/XHS_GWAS/2_rm_GWAS/2_rm_sample/chr10.filtered.rm.renamed.vcf.gz \ --out /vol2/niesijia2/huada_project/XHS_GWAS/2_rm_GWAS/XP-CLR/chr10/chr10_xpclr_si100k_st15k_v2_acbf \ --samplesA /vol2/niesijia2/huada_project/XHS_GWAS/2_rm_GWAS/pheno_text/high_yield.id \ --samplesB /vol2/niesijia2/huada_project/XHS_GWAS/2_rm_GWAS/pheno_text/low_yield.id \ --map /vol2/niesijia2/huada_project/XHS_GWAS/2_rm_GWAS/XP-CLR/chr10/chr10_HIGH_LOW.map.distance \ --chr 10 \ --gdistkey None \ --phased \ --size 100000 --step 15000 --maxsnps 200 --ld 0.95
2025-05-22 19:53:55 : INFO : running xpclr v1.1.0
2025-05-22 19:53:55 : INFO : Loading VCF
2025-05-22 19:54:17 : INFO : VCF loading complete
2025-05-22 19:54:19 : INFO : 686,026 SNPs in total are in the provided input files
2025-05-22 19:54:19 : INFO : 0 SNPs excluded as multiallelic
2025-05-22 19:54:19 : INFO : 0 SNPs excluded as missing in all samples in a population
2025-05-22 19:54:19 : INFO : 23,017 SNPs excluded as invariant or singleton in population 2
2025-05-22 19:54:19 : INFO : 663,009/686,026 SNPs included in the analysis (96.64%)
2025-05-22 19:54:19 : INFO : Done dropping above SNPs from analysis. XP-CLR algorithm starting.
2025-05-22 19:54:19 : INFO : No genetic distance provided; using rrate of 1e-08/bp
2025-05-22 19:54:21 : INFO : Omega estimated as : 0.026371
Traceback (most recent call last):
File "/public/home/lihao/anaconda3/envs/xpclr/bin/xpclr", line 195, in
main()
File "/public/home/lihao/anaconda3/envs/xpclr/bin/xpclr", line 185, in main
rrate=args.rrate)
File "/public/home/lihao/anaconda3/envs/xpclr/lib/python3.5/site-packages/xpclr/methods.py", line 308, in xpclr_scan
ix, n_avail = determine_window(bpositions, start, end, maxsnps)
File "/public/home/lihao/anaconda3/envs/xpclr/lib/python3.5/site-packages/xpclr/methods.py", line 248, in determine_window
if (stop_ix - start_ix) > maximum_size:
TypeError: unorderable types: int() > str()
什么问题,怎么解决