search

thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
59 stars 23 forks source link

genomic converter is having problem with GT column #27

Closed Carol-Symbiomics closed 6 years ago

Carol-Symbiomics commented 6 years ago

Hi Thierry,

Could you please check the code of the genomic converter? For some reason, it is failing to generate output files.

Please, find the code I used and the console output. Thanks

radiator::genomic_converter(data = "tidy.data.snp.ld.rad", output = c("finestructure")) ####################################################################### ##################### radiator::genomic_converter ##################### ####################################################################### Function arguments and values: Working directory: /Users/buitracn/Documents/RADseq/RADseq-Big-project/VCF-files-poptest/stacks.v2/6pop_448samples/after.dDocent.filters.6pop_345samples/filter_rad_20180914@0156/07_filter_snp_number_20180914@0156 Input file: tidy.data.snp.ld.rad Strata: no Population levels: no Population labels: no Output format(s): tidy, finestructure Filename prefix: no Filters: Blacklist of individuals: no Blacklist of genotypes: no Whitelist of markers: no monomorphic.out: TRUE snp.ld: no common.markers: TRUE max.marker: no pop.select: no maf.thresholds: no

Imputations options: imputation.method: no

parallel.core: 7

#######################################################################

Importing data

Using markers common in all populations: Number of markers before/blacklisted/after:24757/0/24757 Scanning for monomorphic markers... Number of markers before/blacklisted/after: 24757/0/24757

Tidy genomic data: Number of common markers: 24757 Number of chromosome/contig/scaffold: 905 Number of individuals: 309 Number of populations: 6

Preparing data for output

Error in $<-.data.frame(*tmp*, "GT", value = character(0)) : replacement has 0 rows, data has 7649913 In addition: Warning message: Unknown or uninitialised column: 'GT'.

thierrygosselin commented 6 years ago

I think this one is easy, try using fineradstructure instead of finestructure I don't have spell checking code, yet. But I'll have matching arguments rule soon.