Error in coverage: seqnames required

[amitjavilaventura]

Hello,

Thank you for your nice package.

I have been using megadepth for some time and I have never had a problem. Nevertheless, today I tried to compute the coverage of a bigwig file in a bed region and it gave me the following error.

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': seqnames required

Since this error was given by a custom function internally using megadepth::get_coverage(), I decided to try the example given in the megadepth vignette.

Here is my code:

library(megadepth)
example_bw <- system.file("tests", "test.bam.all.bw",
                          package = "megadepth", mustWork = TRUE
)
annotation_file <- system.file("tests", "testbw2.bed",
                               package = "megadepth", mustWork = TRUE
)
get_coverage(
  example_bw,
  op = "mean",
  annotation = annotation_file
)

And here is the error:

unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 1
Processing /home/amitjavila/R/x86_64-pc-linux-gnu-library/4.2/megadepth/tests/test.bam.all.bw
Error in asMethod(object) : seqnames required

I don't know what can be happening.

If you can help me solve this, it would be great.

Thank you very much.

[lcolladotor]

Hi!

Thanks for your interest in our software.

Thanks for the PR / issue. A close family of mine was diagnosed with cancer, so my availability is limited right now.

It might take me a few weeks to reply properly.

Best,
Leo

[amitjavilaventura]

Hi, Thanks for your answer. Don't worry about the time. I hope everything is going to get better for you. Best regards, *Adrià Mitjavila Ventura* Bioinformatician https://amitjavilaventura.github.io El lun, 17 oct 2022 a las 20:31, Leonardo Collado-Torres (< ***@***.***>) escribió:

…

Hi! Thanks for your interest in our software. Thanks for the PR / issue. A close family of mine was diagnosed with cancer, so my availability is limited right now. It might take me a few weeks to reply properly. Best, Leo — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMXXQXCDBLM4F2JSCZPP2F3WDWLPHANCNFSM6AAAAAARCJXKOY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[lcolladotor]

Can you look at this @dzhang32? Thanks!