Error in dplyr::bind_rows(): ! Can't combine ..1$X35 <double> and ..9$X35 <character>.

[HajkD]

Message from Pablo FRESIA, PhD:

Hi Hajk,
I am trying to download a set of genomes from NCBI based on txid.

library(biomartr)
organisms <- c("9606", "10090", "10116")
class(organisms)
[1] "character"

getGenomeSet(db="refseq", organisms, reference=F, release=NULL, clean_retrieval=T, gunzip=T, update=F, path="genomes-by-txid", assembly_type="toplevel")

Starting genome retrieval of the following genomes: 9606, 10090, 10116 ...
Starting genome retrieval of '9606' from refseq ...

It seems that this is the first time you run this command for refseq.
Thus, 'assembly_summary.txt' files for all kingdoms will be retrieved from refseq. 
Don't worry this has to be done only once if you don't restart your R session.

Error in `dplyr::bind_rows()`:                                                                                     
! Can't combine `..1$X35` <double> and `..9$X35` <character>.
Run `rlang::last_trace()` to see where the error occurred.

I couldn't solve this error, didn't find anything that helps me on the web. Appreciate any help from your side!

Thanks in advance!
Best,
pablo

[HajkD]

Hi Pablo,

Thank you so much for letting me know!

The issue was that the assembly file for viruses (column X35) has the total_gene count stored as character while all other assembly files correctly as integers. So the error was on the NCBI side.

However, I now worked around this and can push a refined function so that your download process will work now.

You can reproduce the issue as follows:

test_viral <- biomartr::getSummaryFile(db = ‘refseq', kingdom = ‘viral') 

str(test_viral$X35)

test_plant <- biomartr::getSummaryFile(db = ‘refseq', kingdom = ‘plant') 

str(test_plant$X35)

This is why dplyr::bind_rows() cannot join the columns with different data types:

`dplyr::bind_rows()`:                                                                                     
! Can't combine `..1$X35` <double> and `..9$X35` <character>