Question

cannot download atena annotation for human

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Davide • 0

@acfa65d3

Last seen 3 months ago

Italy

Hey there, atena won't download annotation for human

atena • 874 views

ADD COMMENT • link 6 months ago • updated 3 months ago Davide • 0

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That's the error that comes up:

> rmskann <- atena::annotaTEs(genome = "hg38", parsefun = "rmskbasicparser")
Connecting to the AnnotationHub
2 UCSC RepeatMasker tracks found for genome hg38, using the latest one
Downloading annotations
Errore in .local(x, i, j = j, ...) : 'i' must be length 1

ADD REPLY • link 6 months ago Davide • 0

score 0 · Answer 1 · 2025-04-11

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Robert Castelo ★ 3.4k

@rcastelo

Last seen 6 days ago

Barcelona/Universitat Pompeu Fabra

Hi, sorry for the delay in getting back to you, probably by now you found the solution yourself, but just in case you didn't or anybody else stumbles upon the same problem, you should call the function as follows:

rmskann <- atena::annotaTEs(genome = "hg38", parsefun = rmskbasicparser)

That is, the name of the parse function without quotes. If you still have an error, please read carefully the Bioconductor posting guide to learn how to put the code within the text box of your question, and not as a comment, and how to include your session information.

cheers,

robert.

ADD COMMENT • link 4 months ago Robert Castelo ★ 3.4k

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Hi Robert,

I was able to solve the problem. Indeed, it stems from the co-occurrence of two different AnnotationHub available for hg38.

  AH99003  | UCSC RepeatMasker annotations (Sep2021) for Human (hg38)
  AH111333 | UCSC RepeatMasker annotations (Oct2022) for Human (hg38)

Just by adding the correct AnnotationHb unique identifier I was able to download correctly the last annotations available for this human genome version (AH111333). I also wrote an issue on your GitHub with a code suggestion for the function, in order to avoid multiple occurrencies that would block the function.

Thank you,

Best wishes,

DB

ADD REPLY • link 3 months ago Davide • 0