Strange Ouput

[ShuyiF]

Hi!

I'm trying to build a pangenome using Roary. However, I got some strange outputs and some warning.

The code I ran:
*(Roary) login-2:roary$ roary -p 128 .gff -i 90 -cd 95 -f roary_out
Use of uninitialized value in require at /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/5.22.0/x86_64-linux-thread-multi/Encode.pm line 59.

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

Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence this citation notice: run 'parallel --citation'.

Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence this citation notice: run 'parallel --citation'.

Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence this citation notice: run 'parallel --citation'.

Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence this citation notice: run 'parallel --citation'.

Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence this citation notice: run 'parallel --citation'.

Use of uninitialized value in require at /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/site_perl/5.22.0/Bio/Roary/CommandLine/RoaryPostAnalysis.pm line 10.
Can't locate File/Find/Rule.pm in @inc (you may need to install the File::Find::Rule module) (@inc contains: /scratch/zt1/project/akp-prj/user/sfeng124/roary/roary_out/lib /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/site_perl/5.22.0 /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/5.22.0/x86_64-linux-thread-multi /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/5.22.0 .) at /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/site_perl/5.22.0/Bio/Roary/CommandLine/RoaryPostAnalysis.pm line 10.
BEGIN failed--compilation aborted at /scratch/zt1/project/akp-prj/user/sfeng124/miniconda3/envs/Roary/lib/perl5/site_perl/5.22.0/Bio/Roary/CommandLine/RoaryPostAnalysis.pm line 10.
Compilation failed in require at /home/sfeng124/scratch/miniconda3/envs/Roary/bin/pan_genome_post_analysis line 12.
BEGIN failed--compilation aborted at /home/sfeng124/scratch/miniconda3/envs/Roary/bin/pan_genome_post_analysis line 12.
(Roary) login-2:roary$

The results I got:

I installed Roary (v3.12.0) through code: conda install -c bioconda roary

I used the same inputs (50 .gff documents from Prokka) to build the pangenome before on other server and get the expected results. So I guess my inputs should be OK.

Could you please give me any idea what's wrong and how could I fix that?

Much appreciate it!!

[samuelmontgomery]

I had this error until I created a new conda/mamba environment and installed it fresh
Was likely due to an incompatibility with perl

[ShuyiF]

I had this error until I created a new conda/mamba environment and installed it fresh Was likely due to an incompatibility with perl

Thank you! I used Panaroo instead :(