fail to circularize the cp genome assembly

[IntronQ]

I have tried the different augments to assemble the cp genome, but all the results are broken assembly graph .
I'm trying to assemble the raw reads directly using SPAdes, but I have no idea which SPAdes outputs are chosen for the next step and how to use getOrganelle (command line): use get_organelle_from_assembly.py to extract the target organelle genome sequence.
get_org.log.txt

[Kinggerm]

For the current GetOrganelle versions (<=1.7.7), you should use <spades_output_dir>/assembly_graph.fastg as the input of get_organelle_from_assembly.py.

Meanwhile, get_organelle_from_assembly.py can be able to utilize the scaffolding information only when the result is incomplete. This is disabled by default (see the option --spades-out-dir). To enable this, you have to input the spades output directory containing two files: scaffolds.fasta and scaffolds.paths using the flag --spades-out-dir, e.g. --spades-out-dir my_spades_dir. Please note that <spades_output_dir>/assembly_graph_with_scaffolds.gfa is currently not exploited by GetOrganelle.

[IntronQ]

Thanks for you replying! Here comes another problem. The command I used : <get_organelle_from_assembly.py -g dp_output/assembly_graph.fastg -F embplant_pt -o output --min-depth 10>, and the output information shows:

GetOrganelle v1.7.6.1

get_organelle_from_assembly.py isolates organelle genomes from assembly graph.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.8.13 (default, Mar 28 2022, 11:38:47) [GCC 7.5.0]
PLATFORM: Linux pbi 4.18.0-373.el8.x86_64 #1 SMP Tue Mar 22 15:11:47 UTC 2022 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.6.1; numpy 1.23.1; sympy 1.10.1; scipy 1.9.1
blastn not accessible!

I use conda to install the GetOrganelle. Can you help to fix this problem?

[Kinggerm]

Did you use a different GetOrganelle environment? According to the previous log, you should have blastn installed.

[IntronQ]

I use "conda activate “ to implement the script, and it works! But, there still comes the incomplete result. Do you have any suggestions for this situation？Many thanks!

Here is the command line I used:
<get_organelle_from_assembly.py -g dapiao_6_spades/dapiao_output/assembly_graph.fastg -F embplant_pt -o dapiao_9 --min-depth 10>
< join_spades_fastg_by_blast.py -g slimmed_assembly_graph.fastg -f ref.fasta >

The final output graph shows below.

slimmed_assembly_graph.slim.log.txt
get_org.log.txt

[Kinggerm]

The coverage seems high enough. I'm not sure of the reasons for the incomplete. Maybe you can try Velvet instead of SPAdes to get the assembly graph then use get_organelle_from_assembly.py to extract.

If it still fails,
You may follow the information in the log file

2022-12-30 09:04:57,920 - INFO: If the result is nearly complete, you can try join_spades_fastg_by_blast.py to fill N-gaps in-between contigs with a closely-related reference.
2022-12-30 09:04:57,920 - INFO: If you have questions for us, please provide us with the get_org.log.txt file and the post-slimming graph in the format you like!

It is also stated in the FAQ. You may check it out.