Error in tabulate(taxon) : 'bin' must be numeric or a factor

[Anto007]

Hi,

I have got the below error when attempting to use gbtools to generate a GC-coverage plot. Any help here would be appreciated

library(gbtools)
d <-gbt(covstats="INT_metagenome.coverage",mark="INT_metagenome_taxonomy.tab",marksource="blobology")
plot(d)
Error in tabulate(taxon) : 'bin' must be numeric or a factor

In case you would like to inspect, the input files that I used here will be available at this link for the next 7 days

[Anto007]

Tried rerunning the R code after performing the below:

perl accessory_scripts/input_validator.pl --covsats INT_metagenome.coverage --mark INT_metagenome_taxonomy.tab --outdir checked_output

but the same error popped up

d <-gbt(covstats="INT_metagenome.coverage.mod",mark="INT_metagenome_taxonomy.tab.mod",marksource="blobology")
plot(d)
Error in tabulate(taxon) : 'bin' must be numeric or a factor

[Anto007]

The above errors were encountered in gbtools version 2.6.0 but when I tested the same input files on the older 2.5.8 version, the plot seems to come out OK

[kbseah]

Thanks for reporting the error. I'm sorry to say that this project is no longer actively maintained, so I'm not able to troubleshoot this for now. You could consider other programs with similar functionality, such as blobtools (https://github.com/DRL/blobtools) or anvi'o