error for macrodiversity

metaGmetapop / metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations

MIT License

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error for macrodiversity #3

Open Thexiyang opened 3 years ago

Thexiyang commented 3 years ago

Thanks for the very nice tool! I had run this tool on viral contigs. No error for the microdiversity part but show below error message for macrodiversity part. Could you provide some guidance on how to solve this? Thanks!

Error in uniroot(d1fun, c(1, 50), extendInt = "upX", S = S, N = N, ...) :
  f.lower = f(lower) is NA
Calls: metapop_macrodiv -> fisher.alpha -> apply -> FUN -> uniroot
Execution halted

ZongzhiWu commented 3 years ago

Hi~ I also came across this problem. Have you ever solved?

Thexiyang commented 3 years ago

Not yet. I am waiting for the developer to response.

ZongzhiWu commented 3 years ago

My raw_abundances_table.tsv was completed, while normalized_abundances_table.tsv was unfinished (There is only contigs, but no normalized abundance). Maybe this led to the Error in uniroot? What's your situation? @Thexiyang

Thexiyang commented 3 years ago

Same here. @ZongzhiWu

Thexiyang commented 3 years ago

Did you solve the issue? @ZongzhiWu

ZongzhiWu commented 3 years ago

@Thexiyang not yet~

y-hwang commented 3 years ago

I don't get this error when I remove ".bam" from the filenames in the ct file!

Thexiyang commented 3 years ago

I don't get this error when I remove ".bam" from the filenames in the ct file!

Thanks for the information. This works for me!

metaGmetapop commented 3 years ago

Sorry for the delay in response. We are working on updating the code with python in the front end. We are working on releasing the new version. These errors should be fixed in the newest version. More to come soon.

Thexiyang commented 3 years ago

@metaGmetapop Any update on new version?