Comments (3)
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
from genome-bin-tools.
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
from genome-bin-tools.
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 I'm sorry to say that this project is no longer actively maintained, so I'm not able to troubleshoot this for now.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
from genome-bin-tools.
Related Issues (20)
- have `winnowMark()` include SSU markers
- Implement connection distance `fastgFish()` HOT 1
- `plot.gbt()` error when `markCutoff=1` HOT 1
- improve input file checker HOT 1
- summary() should report average coverage for a bin HOT 2
- color contig points by parameter
- Import CheckM results
- Add support for Fastg output from other assemblers
- Header names sometimes don't match in SPAdes scaffolds.paths vs. scaffolds.fastg
- Add SSU marker overlay to `multiBinPlot`
- Documentation fix HOT 1
- alternative to Amphora2
- Alternative to Log::Message::Simple HOT 1
- Move accessory scripts to `inst` folder HOT 1
- Installation from Github with `devtools` HOT 1
- whitespace in contig names
- Empty scaffold list files HOT 4
- Coverage-GC plot in R error: 'legend' is of length 0 HOT 5
- Empty scaffolds list & Error: unexpected symbol in "perl fastg_paths_fishing.pl"
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from genome-bin-tools.