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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Encode error #465

Open jflucier opened 5 years ago

jflucier commented 5 years ago

While exccuting the roary pipeline, I had this error:

` (roary) |09:51:44|jflucier@ip29:[roary]> roary -p 12 prokka_ann/13401/*.gff -cd 80 -f roary_ann/13401 Use of uninitialized value in require at /nfs3_ib/jacques-mp2.nfs/tank/nfs/jacques/nobackup/share/programs/miniconda3/envs/roary/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61.

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

Use of uninitialized value in require at /nfs3_ib/jacques-mp2.nfs/tank/nfs/jacques/nobackup/share/programs/miniconda3/envs/roary/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61. ` This did not seem to affect results produced. I solved the problem by excuting this command :

enc2xs -C

Maybe you should include this line on your install script. My installion was with conda.

JF

tseemann commented 5 years ago

No one seems to be able to get rid of that bug. It does not affect the outputs.