RagTag "patch" not outputting all the results

Hello, Thanks a lot for developing this tool. I am trying to use the RagTag patch to fill some gaps and improve a genome assembly. Basically, I have two genome assemblies of a wild tomato species, one is a Dovetail assembly and another is Pacbio Hifi assembly. The Dovetail assembly is scaffolded and has longer contiguity whereas the Pacbio is more fragmented. I am trying to use the Pacbio assembly as a query to fill the gaps and improve the scaffolds of the Dovetail target assembly. I am using the following command: ragtag.py patch Chile_Dovetail.fasta Chile_HiFi.fa -f 1000 --aligner nucmer --nucmer-params '-l 100 -c 500' -o patched

The program runs but I obtain only three output files named ragtag.patch.ctg.agp ragtag.patch.ctg.fasta ragtag.patch.err

The .err file is empty.

Can you please tell me how can I obtain all the necessary files and final patched.fasta file for downstream analyses?

I have installed the Ragtag on Ubuntu system.

Thanks. Anik

[DuttaAnik]

Hi there, The problem was solved. Everything ran perfectly. It was the external server that did not finish the job until the end. Many thanks for developing this tool.

Regards Anik

[malonge]

you can do something like this:

ragtag.py patch Chile_Dovetail.fasta Chile_HiFi.fa -f 1000 --aligner nucmer --nucmer-params '-l 100 -c 500' -o patched > ragtag.out 2> ragtag.err

And then share the contents of ragtag.err