filter_rad issue error/dplyr:::mutate_error ! & DynamicClusterCall()

[leoneago]

Hi Thierry, Unfortunately I got an error after trying to filter my vcf file (from dDocent) using radiator.

After trying:

shark <- radiator::filter_rad( data = "neutralloci.recode.vcf", strata = "strata.blues.tsv", output = "genind", filename = "shark")

I got this errors. Hope you can help me to understand where the problem is located:

Reading VCF...

IMPORTANT: VCF from freeBayes Dirty version: only GT and DP fields will be kept...

Data summary: number of samples: 203 number of markers: 14713

Generating individual stats... Error in dplyr::mutate(): ! Problem while computing MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\HP\Desktop\blues_R\filter_rad_20221007@2011\01_radiator\radiator_20221007@2011.gds'. Impossibile accedere al file. Il file è utilizzato da un altro processo. Run rlang::last_error() to see where the error occurred. Warning messages: 1: In SeqArray::seqVCF2GDS(vcf.fn = data, out.fn = filename, parallel = FALSE, : Unknown FORMAT ID 'AD' is ignored (it should be defined in the meta-information lines). 2: In SeqArray::seqVCF2GDS(vcf.fn = data, out.fn = filename, parallel = FALSE, : Unknown FORMAT ID 'RO' is ignored (it should be defined in the meta-information lines). 3: In SeqArray::seqVCF2GDS(vcf.fn = data, out.fn = filename, parallel = FALSE, : Unknown FORMAT ID 'QR' is ignored (it should be defined in the meta-information lines). 4: In SeqArray::seqVCF2GDS(vcf.fn = data, out.fn = filename, parallel = FALSE, : Unknown FORMAT ID 'AO' is ignored (it should be defined in the meta-information lines). 5: In SeqArray::seqVCF2GDS(vcf.fn = data, out.fn = filename, parallel = FALSE, : Unknown FORMAT ID 'QA' is ignored (it should be defined in the meta-information lines). 6: In SeqArray::seqVCF2GDS(vcf.fn = data, out.fn = filename, parallel = FALSE, : Unknown FORMAT ID 'GL' is ignored (it should be defined in the meta-information lines).

Computation time, overall: 26 sec completed filter_rad

rlang::last_error() <error/dplyr:::mutate_error> Error in dplyr::mutate(): ! Problem while computing MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\HP\Desktop\blues_R\filter_rad_20221007@2011\01_radiator\radiator_20221007@2011.gds'. Impossibile accedere al file. Il file è utilizzato da un altro processo.

Backtrace:

1. radiator::filter_rad(...)
   12. SeqArray::seqMissing(gdsfile = gds, per.variant = FALSE, parallel = parallel.core)
   13. SeqArray::seqParallel(...)
   14. SeqArray::seqParallel(...)
   15. SeqArray:::.DynamicClusterCall(...)
   16. base::stop("One of the nodes produced an error: ", as.character(dv)) Run rlang::last_trace() to see the full context.

       rlang::last_trace() <error/dplyr:::mutate_error> Error in dplyr::mutate(): ! Problem while computing MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\HP\Desktop\blues_R\filter_rad_20221007@2011\01_radiator\radiator_20221007@2011.gds'. Impossibile accedere al file. Il file è utilizzato da un altro processo.

Backtrace: ▆

1. ├─radiator::filter_rad(...)
2. │ └─radiator::read_vcf(...)
3. │ ├─... %$% info
4. │ └─radiator::generate_id_stats(...)
5. │ └─id.info %<>% ...
6. ├─base::with(., info)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(., MISSING_PROP = round(SeqArray::seqMissing(gdsfile = gds, per.variant = FALSE, parallel = parallel.core), digits))
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
   10. │ ├─base::withCallingHandlers(...)
   11. │ └─mask$eval_all_mutate(quo)
   12. ├─SeqArray::seqMissing(gdsfile = gds, per.variant = FALSE, parallel = parallel.core)
   13. │ └─SeqArray::seqParallel(...)
   14. │ └─SeqArray::seqParallel(...)
   15. │ └─SeqArray:::.DynamicClusterCall(...)
   16. │ └─base::stop("One of the nodes produced an error: ", as.character(dv))
   17. └─base::.handleSimpleError(...)
   18. └─dplyr (local) h(simpleError(msg, call))
   19. └─rlang::abort(...)