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ksiewert / BetaScan

Genome-wide scan for balancing selection using beta statistic
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ZeroDivisionError: float division by zero #16

Closed owfh closed 2 years ago

owfh commented 2 years ago

when I use --freq of vcftools, then "awk -F "\t|:" '(NR>1) && ($8!='0') && ($8!='1') && ($3=='2') {OFS="\t"; print$2,$8*$4,$4}' chr5.southAmerica.frq > chr5.southAmerica.frq.txt" and "python betascan.py -i chr5.USAMS.frq.txt > chr5.USAMS.betascore" count one chromosome of ten individuals the fllowing promblem occour: Traceback (most recent call last): File "betascan.py", line 613, in main() File "betascan.py", line 529, in main freq = freqCount/sampleN ZeroDivisionError: float division by zero

ksiewert commented 2 years ago

Hello! It sounds like for some reason the sample size at one of your SNPs is 0. I would look at your chr5.southAmerica.frq.txt file and see if this is the case. If it is, I would remove any SNP with a sample size of 0.

owfh commented 2 years ago

Thank you very much for your reply. I used to make batascan with selected sites of two populations  sweep selection without any problem, but now I make batascan with one population, and the SNPs is 0. The attachment is my chr5.southAmerica.frq.txt file，Trouble you！

------------------ 原始邮件 ------------------ 发件人: "ksiewert/BetaScan" @.>; 发送时间: 2022年7月8日(星期五) 上午7:53 @.>; @.**@*.**@*.***>; 主题: Re: [ksiewert/BetaScan] ZeroDivisionError: float division by zero (Issue #16)

Hello! It sounds like for some reason the sample size at one of your SNPs is 0. I would look at your chr5.southAmerica.frq.txt file and see if this is the case. If it is, I would remove any SNP with a sample size of 0.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

owfh commented 1 year ago

Thank you very much for your reply. I used to make batascan with selected sites of two populations  sweep selection without any problem, but now I make batascan with one population, and the SNPs is 0. The attachment is my chr5.southAmerica.frq.txt file，Trouble you！

------------------ 原始邮件 ------------------ 发件人: "ksiewert/BetaScan" @.>; 发送时间: 2022年7月8日(星期五) 上午7:53 @.>; @.**@*.**@*.***>; 主题: Re: [ksiewert/BetaScan] ZeroDivisionError: float division by zero (Issue #16)

Hello! It sounds like for some reason the sample size at one of your SNPs is 0. I would look at your chr5.southAmerica.frq.txt file and see if this is the case. If it is, I would remove any SNP with a sample size of 0.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>