parsing phyloseq obj subscript out of bound error

Xio Lee

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Mar 21, 2018, 8:02:46 PM3/21/18

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Hi,

I am parsing phyloseq obj into metacoder obj using parse_phyloseq(); however, I encountered this error:

"Error in .subset2(x, i, exact = exact) : subscript out of bounds
In addition: Warning message:
The following 43507 of 44527 input indexes have `NA` in their classifications:
1, 2, 3, 4, 5, 6, 7 ... 44522, 44523, 44524, 44525, 44526, 44527"

Any suggestions would be appreciated.

xp

(phyloseq object is with the attached file)

parse_phyloseq_error.rds

Zachary Foster

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Mar 22, 2018, 4:50:27 PM3/22/18

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Hello Xio,

You found a bug! It was caused by rows in the taxonomy table that were all NA. I have never encountered that before. I think I fixed it. Try installing the dev versions of taxa and metacoder and see if the error goes away:

devtools::install_github("ropensci/taxa")
devtools::install_github("grunwaldlab/metacoder")

Best,

Zach

semorale...@gmail.com

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May 13, 2019, 5:23:23 PM5/13/19

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HI Zach,

I had the same error and when I tried your fix I still ended up with the same error. Any suggestions?

Zachary Foster

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May 15, 2019, 1:46:52 AM5/15/19

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Hello,

Sorry for the error. Can you send my your data or a subset that produces that same error so I can see what is happening? Thanks!