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thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
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genomic_converter & read_vcf - Error: Can't recycle `ID_SEQ` #119

Closed rlfrench closed 3 years ago

rlfrench commented 3 years ago

Hello Thierry,

Describe the bug I'm having difficulty reading a vcf file into R using read_vcf and converting my file to bayescan format using genomic_converter. In both cases, I get the same error message related to a size incompatibility (see full description of the error message below). I generated the vcf file in Stacks 2.3e then filtered it in vcftools, and I'm working with Mac OS 10.14.5. I noticed that the same error message is mentioned here: https://github.com/thierrygosselin/radiator/issues/109, but I think the error I'm getting will require a different solution because bayescan is implemented as an output option for genomic_converter.

To Reproduce

I tried to read my vcf (2200 SNPs, 49 individuals) into R using:

cic_2200_rad <- read_vcf("pops.recode.vcf")

And I got the following error:

################################################################################
############################## radiator::read_vcf ##############################
################################################################################
Execution date@time: 20210206@0934
Folder created: read_vcf_20210206@0934
Function call and arguments stored in: radiator_read_vcf_args_20210206@0934.tsv
File written: random.seed (91616)

Reading VCF... 

Data summary: 
    number of samples: 49
    number of markers: 2200

Read time: 0 sec

GDS file written: radiator_20210206@0934.gds

Analyzing the vcf...
VCF source: Stacks v2.3e
Data is bi-allelic
Reads assembly: de novo
Filters parameters file generated: filters_parameters_20210206@0934.tsv

Filter monomorphic markers
Number of individuals / strata / chrom / locus / SNP:
    Blacklisted: 0 / 0 / 0 / 0 / 0
Filter common markers: only 1 strata, returning data

Preparing output files...
File written: whitelist.markers.tsv
File written: strata.filtered.tsv

Generating individual stats...
Error: Can't recycle `ID_SEQ` (size 107800) to match `length` (size 2200).
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning message:
Outer names are only allowed for unnamed scalar atomic inputs 

Computation time, overall: 2 sec
############################## completed read_vcf ##############################

I checked rlang::last_error() and saw the following:

<error/vctrs_error_incompatible_size>
Can't recycle `ID_SEQ` (size 107800) to match `length` (size 2200).
Backtrace:
  1. radiator::read_vcf("pops.recode.vcf")
 19. vctrs::stop_incompatible_size(...)
 20. vctrs:::stop_incompatible(...)
 21. vctrs:::stop_vctrs(...)
Run `rlang::last_trace()` to see the full context.

I then tried importing my data using the vcf.R function from vcfR:

cic_2200 <-read.vcfR("pops.recode.vcf")

And that was successful.

After my unsuccessful attempts to read in my file using read_vcf, I tried to use genomic_converter to convert my data from vcf format to bayescan format:

cic_49 <- genomic_converter(
  data = "pops.recode.vcf",
  strata = "STRATA_Bayescan_n49_popsRpca_2021.02.06.txt",
  output = "bayescan",
  filename = "cic_49_strataRpca_bayescan")

Again, I got an error message related to size incompatibility:

################################################################################
######################### radiator::genomic_converter ##########################
################################################################################
Execution date@time: 20210206@1011
Folder created: 03_radiator_genomic_converter_20210206@1011
Function call and arguments stored in: radiator_genomic_converter_args_20210206@1011.tsv
Filters parameters file generated: filters_parameters_20210206@1011.tsv

Importing data: vcf.file

Reading VCF... 

Data summary: 
    number of samples: 49
    number of markers: 2200

Filter monomorphic markers
Number of individuals / strata / chrom / locus / SNP:
    Blacklisted: 0 / 0 / 0 / 0 / 0

Filter common markers:
Number of individuals / strata / chrom / locus / SNP:
    Blacklisted: 0 / 0 / 0 / 0 / 0

Generating individual stats...
Error: Can't recycle `ID_SEQ` (size 107800) to match `length` (size 2200).
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning message:
Outer names are only allowed for unnamed scalar atomic inputs 

Computation time, overall: 4 sec

Computation time, overall: 4 sec
######################### completed genomic_converter ##########################

My devtools::session_info() is as follows:

─ Session info ─────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.2 (2019-12-12)
 os       macOS Mojave 10.14.5        
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_CA.UTF-8                 
 ctype    en_CA.UTF-8                 
 tz       America/Edmonton            
 date     2021-02-06                  

─ Packages ─────────────────────────────────────────────────────────────
 package          * version  date       lib
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 R6                 2.4.1    2019-11-12 [1]
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 raster           * 3.0-12   2020-01-30 [1]
 RColorBrewer     * 1.1-2    2014-12-07 [1]
 Rcpp               1.0.3    2019-11-08 [1]
 RCurl              1.98-1.2 2020-04-18 [1]
 readr              1.4.0    2020-10-05 [1]
 remotes            2.1.0    2019-06-24 [1]
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 rethinking         2.00     2020-04-12 [1]
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 stringr            1.4.0    2019-02-10 [1]
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[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

I have attached the first 40 lines of my vcf file here: vcf_subset.txt

Carol-Symbiomics commented 3 years ago

Same here! I'm also getting the same error while trying to read a vcf file using tidy_genomic_data function image

dylanHco commented 3 years ago

I will add to this, I am also getting the same error as the people above. My vcf file comes from ipyrad's output files. Is there a problem with vcf from ipyrad?

-Dylan

thierrygosselin commented 3 years ago

try with latest release please if still relevant