download_refseq: bfcadd() failed; see warnings()

[esraagithub]

I appreciate your effort. I've recently started using metascope when I run download_refseq function i get the following error message. I see the progress proceed but stop and gives bfcadd() failed; see warnings() how can i solve the problem

sapply(all_species, download_refseq,

• reference = TRUE, representative = TRUE, compress = TRUE,
• out_dir = target_ref_temp, caching = TRUE)

No ENTREZ API key provided Get one via taxize::use_entrez() See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ No ENTREZ API key provided Get one via taxize::use_entrez() See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ C:\Users\DELL\AppData\Local/R/cache/R/MetaScope does not exist, create directory? (yes/no): C:\Users\DELL\AppData\Local/R/cache/R/MetaScope does not exist, create directory? (yes/no): yes |====================================================================================| 100%

|================================================== | 60%bfcadd() failed; see warnings()
|====== | 7%bfcadd() failed; see warnings() |= | 1%bfcadd() failed; see warnings() | | 0%bfcadd() failed; see warnings() | | 0%bfcadd() failed; see warnings() | | 0%bfcadd() failed; see warnings() |= | 2%bfcadd() failed; see warnings() |= | 2%bfcadd() failed; see warnings() | | 1%bfcadd() failed; see warnings() |== | 2%bfcadd() failed; see warnings() |======= | 8%bfcadd() failed; see warnings() |=== | 4%bfcadd() failed; see warnings() |= | 1%bfcadd() failed; see warnings() |======= | 8%bfcadd() failed; see warnings() |= | 1%bfcadd() failed; see warnings() |== | 2%bfcadd() failed; see warnings() | | 0%bfcadd() failed; see warnings() |====================================================== | 64%bfcadd() failed; see warnings() |======== | 9%

[aubreyodom]

Hi, can you give an example of what species are in the vector all_species?

[esraagithub]

all_species= c("Eukaryote", "bacteria", "Viruses")

[aubreyodom]

"Eukaryota" should be used in place of "Eukaryote"; can you see if that resolves your issue?

Edit to add that bfcadd() is only invoked when caching = TRUE so you can try removing it completely.

[esraagithub]

when i used "Eukaryote" i get this error: Error in value[3L] : NCBI request not granted Error in value[3L] : NCBI request not granted Error in value[3L] : NCBI request not granted Error in FUN(X[[i]], ...) : Process halted. Your input is not a valid taxon

i see the downloading message when i write Eukaryota

[aubreyodom]

Good, stick with "Eukaryota". Now can you try running with caching = FALSE?