rarefraction - seq default error

[sravani9408]

rarefraction - seq.default error

Hello,

When I try to run rarefraction on my data it returns the following error. Can you please help?

imm_raref = repDiversity(mydata$data, "raref", .extrapolation = 200000, .verbose = F) Error in seq.default(tail(seq(.step, sum(.data[[i]]), .step), 1) + .step, : wrong sign in 'by' argument

I am not sure if the error is because of huge datasets. mydata is a list of 3 dataframes.

dim(mydata[["data"]][["R_1"]]) [1] 143866 11 dim(mydata[["data"]][["R_2"]]) [1] 823220 11 dim(mydata[["data"]][["R_3"]]) [1] 980159 11

Thanks!

[vadimnazarov]

Hi @sravani9408

thank you for letting us know about the bug. Sorry for the late response!

Can you please tell me what version of immunarch do you use?

Does repDiversity fail on all three of data frames? Can you please run repDiversity separately on each one and see if it works on some?

Is it possible for you to send me a part of your data to test? Via support@immunomind.io

[jchenpku]

I came cross similar error and there will be no error without adding ".extrapolation = 200000".

[vadimnazarov]

Ping about the rarefaction issues @sravani9408

[vadimnazarov]

In the latest release we improved the diversity vignette to make sure people don't use the .extrapolation argument without a real need in it.

[sravani9408]

Hello @vadimnazarov,

Thank you so much for all the help. I did try running on individual data frames, but it still returns the same error. It works without extrapolation. Also, I was wondering if there is a way to use extrapolation. And Sorry, I cannot share the data as it is not published.

Thanks again.

[vadimnazarov]

Hello @sravani9408

We will update the package soon, I will ping you and let's continue the conversation after that. We'll look into this issue!

[sravani9408]

Sounds good, thanks!

[vadimnazarov]

Hi @sravani9408 !

We published immunarch on CRAN and moved it to GitHub, feel free to install the latest versions and check if everything is OK. I will leave this issue open until you confirm that everything is OK.

[sravani9408]

Hello @vadimnazarov,

That works! thank you so much!! Just a quick question, I am running rarefaction on a huge dataset and the job is running for 8 days now. Can we speed up rarefaction using multi-thread? Thanks!

[vadimnazarov]

@sravani9408

Wonderful, thank you!

Yes, I see the issue here. Would you be willing to have a 20 minute discussion about the issue and your pipelines over Zoom so we quickly discuss it in the details? Email us on support@immunomind.io and I will get back to you over the email so we can close this issue. Large-scale data support for the most common cases is what we aim to, and there are different approaches and workarounds already available.

[sravani9408]

@vadimnazarov Sure, that would be really helpful! I will send an e-mail shortly. Thanks!

[Manikgarg]

I am getting the same error with immunarch version ‘0.6.5’ with or without using the .extrapolation argument.