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paulstothard / cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
https://paulstothard.github.io/cgview_comparison_tool/
GNU General Public License v3.0
30 stars 18 forks source link

gbff with multiple contigs a issue? #8

Closed dikshyantg closed 3 years ago

dikshyantg commented 3 years ago

I have this gbff file downloaded from NCBI and it has around 511 contigs , Is this the reason the CGC fails to give me a mapping against this gbff file? GCF_000238775.1_ASM23877v2_genomic.txt

paulstothard commented 3 years ago

The file will work but the program expects a .gbk file extension. The following commands worked for me:

mv GCF_000238775.1_ASM23877v2_genomic.txt test.gbk
docker pull pstothard/cgview_comparison_tool
docker run --rm -v "$(pwd)":/dir -w /dir pstothard/cgview_comparison_tool build_blast_atlas.sh -i test.gbk 
docker run --rm -v "$(pwd)":/dir -w /dir pstothard/cgview_comparison_tool build_blast_atlas.sh -p test