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 consesuses to observed differences between these isolates. Something like this:
This map was generated using CGview, which is distributed as a server or docking Javascript application. 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
