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Exiting early because number of clusters is too high #415
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The first is a warning and it's from a dependency of a dependency so out of our control. |
How do I fix the dependency of the dependency? How do I change the --group_limit parameter? What is your suggesting here? |
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Greeting Dr. Tseeman, i has the same #error 2 only (of above), i did the reccomendation Thanks in advance Dr.
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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. |
thank u, effectively, my data was contaminated.
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#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
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