Silvio Waschina
Silvio Waschina
In the current development version, you can specify the number of cores using the "-K" option in the modules `gapseq find` and `gapseq find-transport`. Also, supplying a protein fasta instead...
There are different approached to this. However, the general goal is to have a gapfill-medium, that contains all essential nutrients to support the growth of the organism. The gapseq-predicted medium...
Hi! Unfortunately, this is not possible yet, but we are currently working on this option. This will be part of a major update to improve performance (i.e. reducing runtime). I'll...
Not yet. We have an experimental branch, where we are currently running tests with this options. We'll post updates here or in the duplicate issue #64 .
With the latest gapseq version, you can now use a multi-protein fasta file as genome input. Here's an example workflow: ```sh # Reaction+Pathway prediction gapseq find -p all -t Bacteria...
Hi! While the gapseq workflow itself is deterministic, the FBA solutions might be influenced by small differences in solver versions and the OS. Often there are several optimal solutions to...
Yes, I guess that can happen.
Hi! No, that is nothing to worry about. The warning occurs at the beginning of the draft network reconstruction, where gapseq tries to predict the biomass reactions (Archaea, Gram-pos. Bacteria,...
Feel free to re-open the issue if something remains unclear.
The option `-K` should work for `gapseq doall` since commit 74782d3 .