Error in purrr::map()

[dollykc]

Hi Dr. Gosselin,
I downloaded sticklebacks_Danish.vcf from https://datadryad.org/stash/dataset/doi:10.5061%2Fdryad.kp11q and the strata.stickleback.tsv from https://www.dropbox.com/s/ely3wp4j4tulkrc/strata.stickleback.tsv?dl=0. I executed the following code

library("grur")
ibm <- grur::missing_visualization(
data = "sticklebacks_Danish.vcf",
strata = "strata.stickleback.tsv", parallel.core = 1L)

And I get the following error
Analysing percentage missing ...
Error in purrr::map():
i In index: 1.
Caused by error in env_get():
! object 'term' not found
Run rlang::last_error() to see where the error occurred.
Warning message:
package ‘fstcore’ was built under R version 4.1.3

rlang::last_error()
Backtrace:

1. grur::missing_visualization(...)
2. tidyr:::pivot_wider.data.frame(...)
3. tidyr::build_wider_spec(...)
4. tidyselect::eval_select(enquo(names_from), data)
5. tidyselect:::eval_select_impl(...)
6. tidyselect:::vars_select_eval(...)
7. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
8. tidyselect:::eval_sym(expr, data_mask, context_mask)
9. rlang::env_get(env, name, default = missing_arg(), inherit = TRUE)

I tried again with a dataset of mine from Stacks population output and a popmap turned into a strata file and I got the same result.

The entire output I got is below

################################################################################
######################## grur::missing_visualization ###########################
################################################################################
Execution date/time: 20230106@1055

::grurmissing_visualization function call arguments:
data = sticklebacks_Danish.vcf
strata = strata.stickleback.tsv
strata.select = POP_ID
distance.method = euclidean
ind.missing.geno.threshold = 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90
filename = NULL
parallel.core = 1
write.plot = TRUE

Default "..." arguments assigned in ::grurmissing_visualization:
path.folder = NULL

Folder created: missing_visualization_20230106@1055
File written: grur_missing_visualization_data_args_20230106@1055.tsv

Importing data
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’

Reading VCF...

Data summary:
number of samples: 177
number of markers: 31802

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

Number of chromosome/contig/scaffold: 196
Number of locus: 17095
Number of markers: 31802
Number of strata: 8
Number of individuals: 177

Number of ind/strata:
HAD = 21
HAL = 19
KIB = 17
KRO = 20
MOS = 20
MAR = 20
NOR = 20
ODD = 40

Number of duplicate id: 0
radiator Genomic Data Structure (GDS) file: radiator_20230106@1055.gds
File written: individuals qc info and stats summary
File written: individuals qc plot

Informations:
Number of populations: 8
Number of individuals: 177
Number of ind/pop:
HAD = 21
HAL = 19
KIB = 17
KRO = 20
MOS = 20
MAR = 20
NOR = 20
ODD = 40

Number of duplicate id: 0
Number of chrom/scaffolds: 196
Number of locus: 17095
Number of SNPs: 31802

Proportion of missing genotypes (overall): 0.022169

Identity-by-missingness (IBM) analysis using
Principal Coordinate Analysis (PCoA)...
fstcore package v0.9.12
(OpenMP detected, using 12 threads)
Generating Identity by missingness plot
Redundancy analysis...
Redundancy Analysis using strata: POP_ID
RDA model formula: data.pcoa$vectors ~ POP_ID
Permutation test for Redundancy Analysis using strata: POP_ID

Hypothesis based on the strata provided
Null Hypothesis (H0): No pattern of missingness in the data between strata
Alternative Hypothesis (H1): Presence of pattern(s) of missingness in the data between strata

A tibble: 1 x 3

STRATA VARIANCE P_VALUE

1 POP_ID 0.00597 0.000999
note: low p-value -> reject the null hypothesis

Analysing percentage missing ...
Error in purrr::map():
i In index: 1.
Caused by error in env_get():
! object 'term' not found
Run rlang::last_error() to see where the error occurred.
Warning message:
package ‘fstcore’ was built under R version 4.1.3

Computation time, overall: 46 sec
############################ missing_visualization #############################

[clorenzo1]

Hi, I am getting the exact same error when trying to do the same thing with a vcf produced from STACKS2 and a popmap also turned into a strata file. Any updates on this?

Cheers

[thierrygosselin]

I'll have a look at it over the weekend thanks for reporting