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thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data
http://chibba.pgml.uga.edu/snphylo/
GNU General Public License v2.0
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There are too small number of SNP data in the file #13

Open hechuweiran opened 8 years ago

hechuweiran commented 8 years ago

Dear, I want to change the removing rate. How to alter the [-p Maximum_PNSS (5)]. my Error message is There are too small number of SNP data in the file (snphylo.output.filtered.hapmap)! Please restart this script with different parameter values (-p). Does anyone give me help? All the best . You

dpchris commented 7 years ago

same issue, i merged my vcf files into one with vcf-merge. I then ran snphylo.sh with my merged file and get the same error :

Error: There are too small number of SNP data in the file (snphylo.output.filtered.vcf)! Please restart this script with different parameter values (-p and/or -c)

Anyone ?

DongnaMa commented 7 years ago

I met the same problem as you, did you solve it?

dpchris commented 7 years ago

No, I did not. sorry

De : DongnaMa [notifications@github.com] Envoyé : lundi 8 mai 2017 16:35 À : thlee/SNPhylo Cc : CHRISTIANY David; Comment Objet : Re: [thlee/SNPhylo] There are too small number of SNP data in the file (#13)

I met the same problem as you, did you solve it?

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AgatheJouet commented 7 years ago

Hi,

I am not sure whether that is something that you would consider doing, but you have the option to set the -r flag so that the software won't perform this step of removing low quality reads. If you are worry about those, I imagine you can remove them using vcftools for example.

SGarciaCobos commented 6 years ago

Hi,

I got the same problem and I used the -r flag and still got it... Any help?

Thanks!

jorisbertrand commented 5 years ago

If it can help, I had something similar and actually something was wrong in the syntax of the command line I typed so SNPylo was running but ignoring the last part of the command line (which included the arguments -l and -M)...

MboiTui commented 4 years ago

I get a similar problem.

I have a hapmap file with 38 individuals and ~3000 SNPs.

I ran it with the command: username$ ./snphylo.sh -H input_file_name.tsv -r -b -B 100 -o outgroupName

And i got the error: input file input_file_name.tsv is too small to run this script!

Yichel518 commented 4 years ago

I met the same error, but I have not get a solvation. please help us for this! thank you!

Yichel518 commented 4 years ago

我遇到类似的问题。

我有一个包含38个人和3000个SNP的hapmap文件。

我使用以下命令运行它： username $ ./snphylo.sh -H input_file_name.tsv -r -b -B 100 -o outgroupName

我得到一个错误： 输入文件input_file_name.tsv太小，无法运行此脚本！

Have you solved this problem? I'm worried about it.