Trouble in assemble chloroplast by manual completion and get_organelle_from_assembly?

[curtainDian]

Mr. Kinggerm, I assembled some of my samples and got incomplete chloroplast. What I frequently meet is Multiple isolated embplant_pt components detected ! I loaded the fastg file of assembly in Bandage and removed the isolated short contigs in the down part of the picture, and used get_organelle_from_assembly.py . However, I still got incomplete chloroplast. According to these problem I wish I could get your advice:

1. Removing non-target contigs is quite difficult when meeting such complicated circos (many failed fastg loaded in bandage are like this). How to solve this situation?
2. Besides, I found that whem multiple components appeared in the get_org.log.txt, size my assembly.fastg was frequently smaller than that in complete chloroplast. So which parameter should be the better choice to adjust? (I set --max-reads inf --reduce-reads inf , and tried many word size values )?
3. After many rounds of adjustment in parameter , I still can't get complete result. Should I doubt the quality of my WGS data? Although I saw get_org.log and candidate reads I guess was sufficient. (usually the recruited ratio is more than 20%)
   I sincerely hope you could offer me some suggestions based on above. Thanks a lot !
   

get_org.log.txt