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bwringe / hybriddetective

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getTopLoc error #4

Closed slambert-git closed 6 years ago

slambert-git commented 6 years ago

I get the following output and error running getTopLoc. I'm attaching the output "for_FST.txt" file.

for_FST.txt

getTopLoc(GPD ="/mydirs/Mytidy.txt" , panel.size = 100, where.PLINK = your_plink_path, where.PGDspider = your_pgdspider_path) Reading Data Creating training and working datasets Calculating Fst INFO 20:19:52 - load PGDSpider configuration from: /home/shea/software/PGDSpider_2.1.1.0/spider.conf.xml Warning: Could not get charToByteConverterClass! initialize convert process... read input file... read input file done. write output file... WARN 20:19:54 - FSTAT accepts a maximum of 100 loci!!! WARN 20:19:55 - The name of a population is missing (no name attribute). It is now recoded as "pop_1" WARN 20:19:55 - The name of a population is missing (no name attribute). It is now recoded as "pop_2" write output file done. Read 4 items Read 2997 items Read 56962 items Error in data.frame(colnames(for.fst)[-1], FSTs) : arguments imply differing number of rows: 2997, 2221

slambert-git commented 6 years ago

This may be due to an input file that had a large amount of missing data. In this case the "missing" data was erroneously coded as missing during filetype conversion with another R package, so there could be something else malformed about the input file. I'm having no issues with a new file.

rspfau commented 3 years ago

What does "WARN 20:19:54 - FSTAT accepts a maximum of 100 loci!!!" mean? Sounds serious if we have more than 100 loci in our dataset.

bwringe commented 3 years ago

This is not truly an error. It is a warning from PGDSpider during the conversion from genepop format to FSTAT format, that gets displayed in the terminal as the function runs. This warning is specific to the program FSTAT, which hybriddetective does not use. Hybriddetective uses the R package hierfstat, which does not have a limit on the number of loci.