Error: Problem with `mutate()` input `MISSING_PROP`.

[fraser-combe]

I keep getting the following error when trying to import a vcf file directly from stacks output, hopefully, you can help:

Generating individual stats... Error: Problem with mutate() input MISSING_PROP. x One of the nodes produced an error: Can not open file 'C:\Users\frasc\Dropbox\My PC (DESKTOP-4P6AFFC)\Documents\filter_rad_20201007@1646\01_radiator\radiator_20201007@1646.gds'. The process cannot access the file because it is being used by another process.

i Input MISSING_PROP is round(...). Run rlang::last_error() to see where the error occurred.

My input is: data <- radiator::filter_rad(data = "populations.snps.vcf", strata = "strata.filtered.tsv")

output: ################################################################################ ############################# radiator::filter_rad ############################# ################################################################################ Execution date@time: 20201007@1646 Folder created: filter_rad_20201007@1646 Function call and arguments stored in: radiator_filter_rad_args_20201007@1646.tsv File written: random.seed (214838) Filters parameters file generated: filters_parameters_20201007@1646.tsv

Reading VCF Data summary: number of samples: 94 number of markers: 18041 done! timing: 9 sec

Generating individual stats... Error: Problem with mutate() input MISSING_PROP. x One of the nodes produced an error: Can not open file 'C:\Users\frasc\Dropbox\My PC (DESKTOP-4P6AFFC)\Documents\filter_rad_20201007@1646\01_radiator\radiator_20201007@1646.gds'. The process cannot access the file because it is being used by another process.

i Input MISSING_PROP is round(...). Run rlang::last_error() to see where the error occurred.

Computation time, overall: 18 sec

Computation time, overall: 18 sec ############################# completed filter_rad #############################

I have also tried read_vcf simply : data <- radiator::read_vcf(data = "populations.snps.vcf") Execution date@time: 20201007@1650 Folder created: read_vcf_20201007@1650 Function call and arguments stored in: radiator_read_vcf_args_20201007@1650.tsv File written: random.seed (609688)

Reading VCF Data summary: number of samples: 94 number of markers: 18041 done! timing: 7 sec

GDS file written: radiator_20201007@1650.gds

Analyzing the vcf... VCF source: Stacks v2.53 Data is bi-allelic Cleaning VCF's sample names File written: cleaned.vcf.id.info_20201007@1650.tsv Error in if (locus.missing) ref.genome <- FALSE : argument is of length zero

Computation time, overall: 8 sec

VCF file header

fileformat=VCFv4.2

fileDate=20200915

source="Stacks v2.53"

INFO=

INFO=

INFO=

INFO=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

INFO=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MDNF021_R1 MDNF023_R1 MDNF029_R1 MDNF031_R1 NW_018326927.1 76729 8:27:- A G . PASS NS=94;AF=0.011

[thierrygosselin]

radiator should have no problem reading stacks VCF, sorry about that.

Try this:

test1 <- radiator::read_vcf(data = "populations.snps.vcf", strata = "strata.filtered.tsv")

If the command above generate the same error you get when running radiator::filter_rad, try the next one:

test2 <- radiator::read_vcf(data = "populations.snps.vcf", strata = "strata.filtered.tsv", parallel.core = 1L)

[thierrygosselin]

I think it's similar to this issue #44 PC and parallel computing problem, setting parallel.core = 1L should fix it.

I have no idea why some PC works and others don't.

[fraser-combe]

Excellent thank you so much for a quick reply and an excellent package, this has solved the problem running

test2 <- radiator::read_vcf(data = "populations.snps.vcf", strata = "strata.filtered.tsv", parallel.core = 1L)

I had been searching through the issues pages but had missed the parallel sentence.

[thierrygosselin]

perfect, feel free to re-open the issue if you're still experiencing problem reading the file or filtering.