I sequenced some bacterial genomes and obtained consensus fasta from the original fastq after aligning against a reference genome. I now would like to create a comparative map (AKA, I reckon, Atlas map) of these consensuses to observe the differences between these isolates.
This map was generated using CGview (https://cgview.ca/), which is distributed as a server or docking Javascript application (https://js.cgview.ca/)\. The latter provides more computational power, so I used it. At least I tried.
Essentially, I ran docker, then made the links to my files (the consensus fasta, the reference file, and the annotation file) and re-ran docker:
```
~$ sudo docker pull pstothard/cgview_comparison_tool .$ sudo docker run --rm -v "$(pwd)":/dir -u "$(id -u)":"$(id -g)" -w /dir pstothard/cgview_comparison_tool build_blast_atlas.sh -p Eco ./Eco/reference_genome$ ln -s ~/AlnDir/Ref/K12_ref.fa ./K12_ref.fa ./Eco/comparison_genomes$ ln -s ~/AlnDir/Consensus/K12_Ho_Cns.fa ./K12_Ho.fa ./Eco/comparison_genomes$ ln -s ~/AlnDir/Consensus/HB101_Ho_Cns.fa ./HB101_Ho.fa ./Eco/features$ ln -s ~/Downloads/AlnDir/Ref/K12.gff3 ./K12_ref.gff .$ sudo docker run --rm -v "$(pwd)":/dir -u "$(id -u)":"$(id -g)" -w /dir pstothard/cgview_comparison_tool build_blast_atlas.sh -p Eco Creating maps for map type dna_vs_dna in Eco/maps_for_dna_vs_dna [Thursday March 07 11:03:25 2024] [Notice] Using the settings file Eco/project_settings_dna_vs_dna.conf. Maps drawn to Eco/maps_for_dna_vs_dna Creating maps for map type cds_vs_cds in Eco/maps_for_cds_vs_cds [Thursday March 07 11:03:25 2024] [Notice] Using the settings file Eco/project_settings_cds_vs_cds.conf. Maps drawn to Eco/maps_for_cds_vs_cds
```
Here, ~ is the Linux Home folder, . the top folder I have created for the project. CGView tells time that it has created the maps, but the folders marked as `map` are empty.
How do I run this app to create comparative maps?
Thank you
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