First of all, thank you for developing Pharokka. I have encountered two issues while using Pharokka v1.8.1.
Version
Pharokka: v1.8.1
Command
pharokka.py
-i ${genome_seq}
-o ./pharokka
-d /pharokka_db/pharokka_v1.8.0_databases
-p ${genome_name}
-g prodigal
-l ${genome_name}
--dnaapler
-t 8
issue 1: Genome is not always rotated to the actual beginning of the terL gene
After investigating the results, I think this issue may originate from dnaapler.
The rotated genome does not always start at the true beginning of the terL gene. It appears that dnaapler sometimes selects a Prodigal-predicted CDS whose start codon is not the actual ATG start codon. As a result, the rotation point is placed before the terL coding sequence rather than at its true start.
This can lead to the last gene in the rotated genome being truncated or completely missing from the final annotation.
issue 2: The last gene may lose its stop codon after genome rotation
Even when the rotation is correctly placed at the beginning of terL, another issue can occur.
If the last CDS overlaps with terL across the circular genome boundary, the final gene in the rotated sequence may no longer contain its stop codon. Consequently, the last CDS may be annotated as incomplete or may not be annotated correctly.
First of all, thank you for developing Pharokka. I have encountered two issues while using Pharokka v1.8.1.
Version
Pharokka: v1.8.1
Command
pharokka.py
-i ${genome_seq}
-o ./pharokka
-d /pharokka_db/pharokka_v1.8.0_databases
-p ${genome_name}
-g prodigal
-l ${genome_name}
--dnaapler
-t 8
issue 1: Genome is not always rotated to the actual beginning of the terL gene
After investigating the results, I think this issue may originate from dnaapler.
The rotated genome does not always start at the true beginning of the terL gene. It appears that dnaapler sometimes selects a Prodigal-predicted CDS whose start codon is not the actual ATG start codon. As a result, the rotation point is placed before the terL coding sequence rather than at its true start.
This can lead to the last gene in the rotated genome being truncated or completely missing from the final annotation.
issue 2: The last gene may lose its stop codon after genome rotation
Even when the rotation is correctly placed at the beginning of terL, another issue can occur.
If the last CDS overlaps with terL across the circular genome boundary, the final gene in the rotated sequence may no longer contain its stop codon. Consequently, the last CDS may be annotated as incomplete or may not be annotated correctly.