This points to the file of GFF's that I have prepared (ST398_GFF) with multiple .gff files in it.
Here is the initial output:
2023/02/17 12:12:51 Output directory name exists already so adding a timestamp to the end
2023/02/17 12:12:51 Output directory created: ./roary_output_1676657571
2023/02/17 12:12:51 Fixing input GFF files
2023/02/17 12:12:58 Extracting proteins from GFF files
Extracting proteins from /Users/jhill7/ST398_GFF/AF1744-IA-M06434-191216_S28_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF1746-IA-M06434-191216_S29_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2068-IA-M05216-200824_S32_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2069-IA-M05216-200829_S16_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2070-IA-M06434-201022_S11_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2137-IA-M05216-200227_S6_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2391-IA-M05216-200922_S46_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2572-IA-M05216-200219_S28_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2573-IA-M05216-200822_S29_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2574-IA-M06434-201022_S19_L001.gff
Extracting proteins from /Users/jhill7/ST398_GFF/AF2575-IA-M05216-201201_S1_L001.gff
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
This all looks fine and good. But then I receive the following error code
023/02/17 12:15:31 Running command: pan_genome_post_analysis -o clustered_proteins -p pan_genome.fa -s gene_presence_absence.csv -c _clustered.clstr --output_multifasta_files -i /Users/jhill7/roary_output_1676657571/O0mcS38zKh//_gff_files -f /Users/jhill7/roary_output_1676657571/O0mcS38zKh//_fasta_files -t 11 --dont_create_rplots -v --mafft -j Local --processors 11 --group_limit 50000 -cd 99
Use of uninitialized value in require at /Users/jhill7/miniconda3/envs/roary_pangenome/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: /Users/jhill7/roary_output_1676657571/lib /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0//x86_64-linux-thread-multi /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0/ /Users/jhill7/miniconda3/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /Users/jhill7/miniconda3/lib/perl5/site_perl/5.22.0 /Users/jhill7/miniconda3/lib/perl5/5.22.0/x86_64-linux-thread-multi /Users/jhill7/miniconda3/lib/perl5/5.22.0 .) at /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0/Bio/Roary/CommandLine/RoaryPostAnalysis.pm line 10.
BEGIN failed--compilation aborted at /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0/Bio/Roary/CommandLine/RoaryPostAnalysis.pm line 10.
Compilation failed in require at /Users/jhill7/miniconda3/envs/roary/bin/pan_genome_post_analysis line 17.
BEGIN failed--compilation aborted at /Users/jhill7/miniconda3/envs/roary/bin/pan_genome_post_analysis line 17.
I'm fairly new to command line work. I've tried loading all the dependencies for the program and I've also checked the other issues posted on here and tried some of their solutions with no luck.
Can somebody help me understand how to fix these errors and get the program to run correctly?
After activating roary I've been running the following command.
(roary) [jhill7@argon-itf-login-3 ~]$ roary -f ./roary_output -e -n -v -p 11 ST398_GFF/*.gff
This points to the file of GFF's that I have prepared (ST398_GFF) with multiple .gff files in it.
Here is the initial output: 2023/02/17 12:12:51 Output directory name exists already so adding a timestamp to the end 2023/02/17 12:12:51 Output directory created: ./roary_output_1676657571 2023/02/17 12:12:51 Fixing input GFF files 2023/02/17 12:12:58 Extracting proteins from GFF files Extracting proteins from /Users/jhill7/ST398_GFF/AF1744-IA-M06434-191216_S28_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF1746-IA-M06434-191216_S29_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2068-IA-M05216-200824_S32_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2069-IA-M05216-200829_S16_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2070-IA-M06434-201022_S11_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2137-IA-M05216-200227_S6_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2391-IA-M05216-200922_S46_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2572-IA-M05216-200219_S28_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2573-IA-M05216-200822_S29_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2574-IA-M06434-201022_S19_L001.gff Extracting proteins from /Users/jhill7/ST398_GFF/AF2575-IA-M05216-201201_S1_L001.gff Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite:
Tange, O. (2022, September 22). GNU Parallel 20220922 ('Elizabeth'). Zenodo. https://doi.org/10.5281/zenodo.7105792
This all looks fine and good. But then I receive the following error code
023/02/17 12:15:31 Running command: pan_genome_post_analysis -o clustered_proteins -p pan_genome.fa -s gene_presence_absence.csv -c _clustered.clstr --output_multifasta_files -i /Users/jhill7/roary_output_1676657571/O0mcS38zKh//_gff_files -f /Users/jhill7/roary_output_1676657571/O0mcS38zKh//_fasta_files -t 11 --dont_create_rplots -v --mafft -j Local --processors 11 --group_limit 50000 -cd 99 Use of uninitialized value in require at /Users/jhill7/miniconda3/envs/roary_pangenome/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: /Users/jhill7/roary_output_1676657571/lib /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0//x86_64-linux-thread-multi /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0/ /Users/jhill7/miniconda3/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /Users/jhill7/miniconda3/lib/perl5/site_perl/5.22.0 /Users/jhill7/miniconda3/lib/perl5/5.22.0/x86_64-linux-thread-multi /Users/jhill7/miniconda3/lib/perl5/5.22.0 .) at /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0/Bio/Roary/CommandLine/RoaryPostAnalysis.pm line 10. BEGIN failed--compilation aborted at /Users/jhill7/miniconda3/envs/roary_pangenome/lib/perl5/site_perl/5.22.0/Bio/Roary/CommandLine/RoaryPostAnalysis.pm line 10. Compilation failed in require at /Users/jhill7/miniconda3/envs/roary/bin/pan_genome_post_analysis line 17. BEGIN failed--compilation aborted at /Users/jhill7/miniconda3/envs/roary/bin/pan_genome_post_analysis line 17.
I'm fairly new to command line work. I've tried loading all the dependencies for the program and I've also checked the other issues posted on here and tried some of their solutions with no luck.
Can somebody help me understand how to fix these errors and get the program to run correctly?
Thanks!