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hardingnj / xpclr

Code to compute the XP-CLR statistic to infer natural selection
MIT License
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number of threads #84

Open XiaXiaTianTian opened 1 year ago

XiaXiaTianTian commented 1 year ago

Hi, everyone. If it is possible to set the number of threads for xpclr? Because xpclr always call all avaliable threads of the queue. May influence other running jobs.

XiaXiaTianTian commented 1 year ago

Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)2022-08-30 09:30:36 : INFO : running xpclr v1.1.2 2022-08-30 09:30:36 : INFO : Loading VCF 2022-08-30 09:30:37 : INFO : VCF loading complete 2022-08-30 09:30:37 : INFO : 144,800 SNPs in total are in the provided input files 2022-08-30 09:30:37 : INFO : 0 SNPs excluded as multiallelic 2022-08-30 09:30:37 : INFO : 1,544 SNPs excluded as missing in all samples in a population 2022-08-30 09:30:37 : INFO : 60,967 SNPs excluded as invariant or singleton in population 2 2022-08-30 09:30:37 : INFO : 82,289/144,800 SNPs included in the analysis (56.83%) 2022-08-30 09:30:37 : INFO : Done dropping above SNPs from analysis. XP-CLR algorithm starting. 2022-08-30 09:30:37 : INFO : No genetic distance provided; using rrate of 1e-08/bp 2022-08-30 09:30:37 : INFO : Omega estimated as : 0.683824 2022-08-30 12:22:11 : INFO : Analysis complete. Output file ./e_m/e.m.LG01.out

XiaXiaTianTian commented 1 year ago

And this is the command /ds3200_1/users_root/miniconda3/envs/xpclr/bin/xpclr --format vcf --input /ds3200_1/users_root/final/1.ld.vcf.gz --samplesA e --samplesB m --chr LG01 --minsnps 10 --maxsnps 300 --size 20000 --step 10000 --out ./e_m/e.m.LG01.out