Exiting early because number of clusters is too high

[raw937]

#error 1
Use of uninitialized value in require at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Encode.pm line 69.
#error 2
Number of clusters (75436) exceeds limit (50000). Multifastas not created. Please check the spreadsheet for contamination from different species or increase the --group_limit parameter.
2018/08/09 15:34:36 Exiting early because number of clusters is too high

Prokka gff's
roary -e --mafft -p 8 *.gff -f my_folder

[andrewjpage]

The first is a warning and it's from a dependency of a dependency so out of our control.
The second is a warning to let you know there might be a problem with your input data and the message tells you what to do.

[raw937]

How do I fix the dependency of the dependency?

How do I change the --group_limit parameter? What is your suggesting here?
I can use kraken to check correct?

[tseemann]

-g INT maximum number of clusters [50000] ? (from roary -h)

[geraldmoreno993]

Greeting Dr. Tseeman, i has the same #error 2 only (of above), i did the reccomendation-g INT maximum number of clusters [50000] but i had the same respons:

Thanks in advance Dr.

Total time: 2.05 seconds Unique: 34/34 Bad splits: 0/31
Number of clusters (45604) exceeds limit (10000). Multifastas not created. Please check the spreadsheet for contamination from different species or increase the --group_limit parameter.
2024/07/08 22:34:52 Exiting early because number of clusters is too high

[andrewjpage]

In many cases this indicates your data has more than one species or is contaminated. I would start with QC of the data before running roary.