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millanek / fineRADstructure

A package for population structure inference from RAD-seq data
https://www.milan-malinsky.org/fineradstructure
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finestructure Tree Building Issue (step 3) #6

Closed crcardenas closed 5 years ago

crcardenas commented 5 years ago

I have a preliminary data set, which was run through the ipyrad pipeline without a reference genome. I used the alleles.loci outputfile with fineRADstructure-tools, following their recommendations. I have attached the file here fineradtools_converted.txt, since I am not sure if this is the issue. I will be using a reference genome in the future, but I am attempting some comparative analyses with this small data set first.

Any ways, I run step 1 and 2 fine, at least I think so. Step 2 does not give me any arguments other than that it has finished...

like so:

################################################### 100%
################################################### 100%

So I assume this has run correctly?

Yet, when I run step 3 I keep getting outputs like this:

################################################### 100%
Lgamma error: z=-8.37464e+08
terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >'
Aborted (core dumped)

and 

################################################### 100%
Lgamma error: z=-2.47596e+08
terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >'
Aborted (core dumped)

The only thing different I can tell is that the Lgamma error changes... Perhaps it is related to the missingness output from step 1. I have a few samples that are well above 0.50 that I thought were supposed to be filtered out. I thought fineRADstructure-tools was supposed to clean up missing data... It certainly reduced my data set...

I may just run Stacks in the future, since I will be getting some paired end reads as opposed to this preliminary data set I have. But for the time being, I wonder if there is anything I can do to resolve this? I see that there was another person who had a similar issue but their question did not get resolved.

I appreciate your time!

janxkoci commented 5 years ago

Hi @crcardenas I worked around this issue by using original finestructure for the tree-building step - see https://github.com/millanek/fineRADstructure/issues/3#issuecomment-498643966 for more info.

millanek commented 5 years ago

Hello

I added Dan Lawson's putative fix for the tree building issue to my repo. Please try: git pull make and then re-run the tree building. Please, let me know if it helps.

Cheers Milan