gapseq medium

[oohas2000]

Hi,
I am fairly new to Bioinformatics and I was trying to determine the suitable nutrient medium for my bacteria of interest. I was trying the "gapseq medium -m toy/ecoli-draft.RDS -p toy/ecoli-all-Pathways.tbl" command but I kept getting the following error:

"medium.sh: line 10: medium: command not found"

I am sure it's some silly mistake from my side but do you please mind suggesting the solution?

[Waschina]

Hi @Jagadrupa00

I am a little confused because gapseq does not have a file called medium.sh. Is this a script that you manually created?

Also, could you perhaps send the output of gapseq test ?

Best
Silvio

[oohas2000]

Yes, sorry, it was a personal file.

…

On Tue, Jul 25, 2023, 4:20 PM Silvio Waschina ***@***.***> wrote: Hi @Jagadrupa00 <https://github.com/Jagadrupa00> I am a little confused because gapseq does not have a file called medium.sh. Is this a script that you manually created? Also, could you perhaps send the output of gapseq test ? Best Silvio — Reply to this email directly, view it on GitHub <#187 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBG63OYVUDZUJ5WFGEVMG3TXR7I2NANCNFSM6AAAAAA2XCZ3UA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[oohas2000]

Another question I had regarding the medium it is generating: is the medium generated by gapseq minimal? And can it be used in wet-lab experiments?

[Waschina]

It is not necessarily a minimal media, but at least a chemically defined one. The medium prediction can provide some ideas about which nutrients might support growth. Still, we recommend checking available literature on experimental growth media for the strain or related microorganisms before running wet-lab experiments.