How to deal with incomplete chloroplast after adjusting many parameters ?

[curtainDian]

Mr. Kinggerm, I adjusted many parameters( decrease -w (from 60-95); max-reads inf; reduce-reads-for-coverage inf ; change reference chloroplast ), but there are still some samples which I can't get chloroplast from. From the log, "incomplete edge" and "mutiple isolated embplant_pt components detected ", both of them above appear frequently. How can I deal with the remaining incomplete results? Could you please offer more suggestions ? Thanks a lot ! one of the log files of failed assembly is below.
get_org.log.txt

[jjiami]

请问问题解决了吗？我用重测序数据组装叶绿体基因组，结果是成环的，但和参考比总是缺少1500bp左右，导致IRa区的最后一个基因rps19总是残缺的，但我用同样的方法组装另一个很近的物种就没有出现这种问题。您有什么想法吗？

[Kinggerm]

Please check the IR boundary movement (expansion/contraction) in the literature.

[Kinggerm]

Mr. Kinggerm, I adjusted many parameters( decrease -w (from 60-95); max-reads inf; reduce-reads-for-coverage inf ; change reference chloroplast ), but there are still some samples which I can't get chloroplast from. From the log, "incomplete edge" and "mutiple isolated embplant_pt components detected ", both of them above appear frequently. How can I deal with the remaining incomplete results? Could you please offer more suggestions ? Thanks a lot ! one of the log files of failed assembly is below. get_org.log.txt

For incomplete results, all guidelines we had were listed here. I don't think I have enough information to offer recommendations. However, you should always check the assembly graph before making any parameter adjustments.
There is no universal solution for all samples. A certain amount of samples could even contain gaps in the reads.