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multiple check_xml_errors when using entrez_link of protien IDs of Metagenomic assembled genomes from NCBI #186

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DeaconOfBiology opened this issue Mar 25, 2023 · 2 comments

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@DeaconOfBiology
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When I run the following I get the results I am looking for:
entrez_link(db="taxonomy",
dbfrom="protein",
id=c("QNO56202.1","RCV65969.1","OYV13592.1",
"WP_138323301.1","WP_007546357.1","KPJ68349.1",
"RLB10506.1"), by_id=TRUE)

However, if I run any protein id of a MAG thats on NCBI it errors out, for example:
image

However, if I take that same accession number and put it in NCBI, I get the result I am looking for:
image

Am I doing something wrong?

@allenbaron
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The last comment on this biostars question suggests that error occurs when the ID does not exist in the entrez system. The error is not due to rentrez. I suggest you reach out to NCBI about this.

If you get a response that might help others, please share it.

@DeaconOfBiology
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Sorry for the delay reply. Just now seeing this. Ok, I'll reach out to NCBI and see what they say. If I get a response from them I will post it here

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