Roary

Roary copied to clipboard

Use of uninitialized value in require at /Users/.....darwin-thread-multi-2level/Encode.pm line 61

1

Hi, I'm new to Roary and running it on 350ish .gff3 files. It seems to run for some time them stops with the error Use of uninitialized value in require...

peflanag

kraken

1

Hi, when I installed kraken database, I met some problems with kraken, so I decided to install this using kraken2 related command. But when I use roary with ‘-qc -k’...

zzzapperant

Hi @wwood I just want to know how can I change the lables of the x axis in the results of the roary plots? I want to label it according...

saras224

I have been using GFF3 files generated by Bakta and recently encountered a warning message when utilizing Roary. I would greatly appreciate it if you could kindly help me understand...

ryu1013

How can I know what subset a gene belongs to (core, softcore, shell, cloud), from the roary output? I expected to see this information in "gene_presence_absence.csv".

canarioviana

Hi, I have an issue understanding how Roary clusters the sequences after CDHIT step. The paper states : " Sequences are then clustered with MCL ([Enright et al., 2002]), and...

mweberr

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...

jhill4796

Roary needs Rscript 3 or higher Please upgrade and try again

1

Hi I'm getting the following error [rscript execution error: No such file or directory] using conda installation or aptitude this is what it shows when I run roary -a (roary)...

jhcuarta

hi i try to work with prokka to analize some genomes but i have this error : Error executing process > 'roary' Caused by: Missing output file(s) `roary/accessory_binary_genes.fa.newick` expected by...

Bjiornone

I would appreciate any suggestions to adapt the default parameters for ONT (Oxford Nanopore) long-read sequence data. Running prokka and roary with default parameters returns almost 3x the genes (pangenome)...

m-ocejo