Error: unexpected input in "_" Execution halted Use of uninitialized value in require at (eval 1407) line 1.

Question

[Neel]

Hi, I encountered this error and i don't know how to solve it because it showing " _ " in input file if i remove this "_" this file doesn't work on terminal. What should i do?

roary -e --mafft -p 8 ~/Desktop/AMR/roary_result/gff/*.gff -p 8 -o -f -e -t -qc -i 95 -y -r Value "-qc" invalid for option t (number expected)

Please cite Roary if you use any of the results it produces: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693 doi: http://doi.org/10.1093/bioinformatics/btv421 Pubmed: 26198102

Saving 7 x 7 in image Saving 7 x 7 in image Error: unexpected input in "_" Execution halted Use of uninitialized value in require at (eval 1407) line 1.

and my input file look like this - UNC_PaerCF05.gff UNC_PaerCF14.gff

Thank you!

Answer 1

[Mensur Dlakic]

It says right at the start:

invalid for option t (number expected)

You need to specify the translation table, or just leave the -t switch out.

Answer 2

[Neel]

I will do that, thank you so much.