Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) : is.character(gds.fn) is not TRUE

rspfau commented 2 years ago

First time using radiator...see below for details of error. Thanks, Russell

data <- radiator::filter_rad( data = "Final.recode.vcf", strata = "strata-frog.txt", output = c("genind", "stockr") )

################################################################################ ############################# radiator::filter_rad ############################# ################################################################################ Execution date@time: 20211212@1743 Folder created: filter_rad_20211212@1743 Function call and arguments stored in: radiator_filter_rad_args_20211212@1743.tsv File written: random.seed (255217) Filters parameters file generated: filters_parameters_20211212@1743.tsv

Reading VCF... Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) : is.character(gds.fn) is not TRUE

Computation time, overall: 11 sec ############################# completed filter_rad #############################

devtools::session_info()

Session info -----------------------------------------------------------------------------------------------------------------

Packages --------------------------------------------------------------------------------------------------------------------- package version date lib source
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adegenet * 2.1.4 2021-07-17 [1] CRAN (R 4.1.0)
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[1] C:/Users/pfau/OneDrive/Documents/R/win-library/4.1 [2] C:/Program Files/R/R-4.1.0/librar Final.recode.vcf.zip strata-frog.txt y

thierrygosselin commented 2 years ago

Thanks Russell and sorry about the issue, I'll have a look at it less than a day. Thierry

thierrygosselin commented 2 years ago

It's a problem reading the freeBayes VCF file, I'll see what I can do on my end.

thierrygosselin commented 2 years ago

@rspfau You have missing information on the last line of the VCF Verify if it was generated in freeBayes (or by the name of the vcf, I'm assuming VCFTools) Update radiator and re-open the issue if the problem persist

thierrygosselin commented 2 years ago

@rspfau You also have missing information for some samples (check the AD field of the VCF), I see this with VCF that are multi-allelic, with most of the VCF bi-allelic.

rspfau commented 2 years ago

This VCF file is the unedited output of the dDocent pipeline, which uses FreeBayes and VCFtools to call/filter SNPs. I'm not able to parse the complex VCF file to know what exactly is wrong with it, but are you saying that FreeBayes and/or VCFtools is outputting a faulty VCF file? https://www.ddocent.com/UserGuide/#snp-filtering

rspfau commented 2 years ago

Also, I'm on my work computer now and am unable to download radiator in RStudio, I think, because our university has really high security. Do you have suggestions? https://support.rstudio.com/hc/en-us/articles/206827897-Secure-Package-Downloads-for-R

devtools::install_github("thierrygosselin/radiator") Downloading GitHub repo thierrygosselin/radiator@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : internet routines cannot be loaded

thierrygosselin / radiator

Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) : is.character(gds.fn) is not TRUE #144