Hi
I have high-quality draft genomes and I’m having issues running them on GrowthPred to calculate predicted ideal growth temperature. I’ve uploaded the following files (see below) and in all instances I’ve received the error “ERROR: sequence length not multiple of 3:” (see screenshot attached).
I’ve uploaded:
full genome fasta
feature only genome fasta (should only include the CDS regions)
GBK file obtained from ANTISMASH that should only include the CDS regions
Any advice?
Thank you!
I dont know this tool and could also not find it on galaxy (maybe I dont look good enough, your tag says you use local). But the error is clear, did you manually checked if the length of the CDS regions is indeed not a multiple of 3? If not, your input is not correct. So the advise would be to double check the lengths and maybe run the tool on a very small dataset where you are sure the CDS input is a multiple of 3.
Oh sorry I’m not too familiarized with the organization of galaxy. I find GrowthPred when I search for it in https://galaxy.pasteur.fr/.
I will check manually about the length… but is there a specific tool/software you recommend to extract CDS regions that are multiple of 3 in length?
Hi @Rosave
Since this tool is only deployed at this server, it is probably also part of a custom workflow or analysis path. Ask the authors via the email contact in their directory listing Galaxy@Pasteur - Galaxy Community Hub
Technically, yes. One is to get the sequences from a gene track in the UCSC table browser. Another is to use fasta manipulation tools (EMBOSS tool suite, etc). But you should confirm if those are appropriate or not for your use case/this tool and there might be a different recommended tool/method at that server.
