Comments (2)
Hi Ruben,
I guess your raw data contains two few mitogenome reads. So "--max-reads/--reduce-reads-for-coverage" won't help because GetOrganelle wasn't reducing the reads.
You could try to input a mitogenome sequence of a closely-related species as the seed (-s sequence.fasta). But I don't think that's the key issue here.
I think the most probable solution is increasing your genome skimming dataset, which is currently only 116M basepairs and likely insufficient for most animal mt assembly.
Best,
Jianjun
from getorganelle.
Hi Jianjun,
I will try with the -s parameter. I hope this could fix my problem.
Thanks a lot. I'll keep you updated!!!
Greetings,
Rubén.
from getorganelle.
Related Issues (20)
- Repeat of spades issues like #152 and #83 with update to getorganelle v1.7.7.0 HOT 3
- ERROR: Assembling failed due to SPAdes failure HOT 4
- More sequence.fasta?
- strand + or - ? HOT 1
- Issue : Invalid characters # Whitespace not allowed HOT 2
- Using embplant_mt and embplant_pt not possible HOT 2
- GetOrganelle aborts with error ("Killed") HOT 3
- Problems with canu-produced gfa processing HOT 1
- Program killed during early extension; RAM issue unlikely HOT 2
- ERROR: slimming the pre-assembled graph failed
- AssertionError: Invalid characters (e.g. space, non-ascii) for SPAdes in path: /home/ruizhang/zhaoliaocheng/Viburnum cpDNA/LYL47/plastome_output
- 2023-05-24 14:15:33,428 - INFO: Round 9: 10081574/10081574 AI 89119 AW 2714392 2023-05-24 14:15:33,428 - INFO: No more reads found and terminated ... 2023-05-24 14:16:02,153 - INFO: Extending finished. HOT 1
- incomplete assembly graph HOT 2
- Discrepancy between get_organelle_from_reads and summary_get_organelle_output logs HOT 1
- Set Startingpoint of Cicular Mitochondrial Genome HOT 2
- conda install error: conda version 23.5.0 too high HOT 2
- Please explain the output - multiple fasta HOT 1
- assembly_graph.fastg finished with no target organelle contigs found! HOT 7
- empty filtered paired HOT 2
- Problems with chloroplast genome assembly stagnation HOT 4
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