Problems launching Lositan
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2.5 years ago
lleipnitz • 0

Hello all!

I am currently working on an NGS dataset (~34K snps, 34 individuals, 10 populations, RADseq data) and I need to evaluate how many loci are possibly under selection. To do so I intend to use Lositan and BayeScan. While BayeScan runs with no major problems, Lositan does not even open.

I already have java installed and updated and I have downloaded and installed all dependencies (batik, biopython, etc), but I cannot run the program. I have also searched Biostars, ResearchGate, Google groups, etc, for a solution, but came up short (none of the solutions I have found so far solved the problem).

The error that occurs, specifically, is that once I run the "selwb4.jnpl" application, a java screen pops up but then the error "Cannot launch the application" appears; when I look at the error's details, it says that it is not possible to load the lositan webpage. ( http://popgen.net/soft/lositan/code2/selwb4.jnpl ).

Could anyone help me? Thank you so much in advance!

Very best, Leonardo.

snp next-gen outliers lositan • 981 views
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There is a possible solution at LOSITAN - illegal URL redirect .

Problems with Lositan crop up regularly, I think the best solution is to use an alternative software. Just a sample of the most recent posts:

Problem launching LOSITAN

Lositan error: Unable to launch this application

LOSITAN: Unable to launch the application

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Entering edit mode

Hello h.mon, and thank you for your reply! Sadly, I had read the topics you have posted before, and none of them really helped me solve the problem. At least I learned that, apparently, Lositan is not compatible with recent versions of Java because of its security protocols (version 1.6 is recommended by the authors of the software precisely because of that problem). I'll keep track of the posts, thanks a lot!

Edit: I have downloaded the standalone version of the program, as someone posted in the first post you referred to in your reply. There is a problem with one of the bash scripts, but I believe I can solve it. Many thanks!

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