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Hi, I see; thanks for the clarification! The problem is some data loss from importing and exporting the model again. I just committed a quick fix for this, but we...

Reproducible example for the divergence in model attributes that could cause errors when a sbml is imported in R and used as input for gapfilling: ```R library(sybilSBML) library(sybil) mod.rds

I adapted the issue name to make it clearer

I completely agree with this and we will have some improvements in the future! The background for this is that gapseq was made not only for model generation but also...

hi @VadimDu, thanks for you kind feedback! You are right the tblastn step is time limiting at the moment. The reason for it is that we do not do a...

Hi @jdwinkler-lanzatech thanks for you suggestions! You are right and something like this (either blast everything at one and/or diamond) will be part of an upcoming release! A potential approach...

what about merging the media as proposed by Silvio?

I'm not sure if I get what you want to do. But if you want to use the predicted media but do not want to merge the media for the...

any updates on this? I checked the pull request locally and it seems to work with base branch!

thanks for your answer! The missing ``representative`` tag is really strange because it is actually there in the source assembly report: ``` curl -s ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/691/195/GCF_001691195.1_ASM169119v1/GCF_001691195.1_ASM169119v1_assembly_report.txt | grep "RefSeq category" #...