Comments (1)
Hi Charles,
Sorry for the delay (I just noticed that the stupid email system blocked github notifications). In short, If you assembled an animal mitogenome, you didn't need the "--genes" flag. You can just skip it.
The the "-s" is followed by the seed database, while "--genes" flag is followed by the label database. In fact, it's just the complete organelle genome used as seed, versus the genes used for labeling after assembly.
You won't find the "animal_mt.fasta" file in this repository, because, since 1.7.0, the default database has been isolated as another repo, GetOrganelleDB. But you can actually find them locally (GetOrganelle/GetOrganelleLib/LabelDatabase), after you install and initial GetOrganelle. If you don't assign a user one (no "--genes"), GetOrganelle will use the default one, which luckily works for your taxa.
However, while the fungus and animal mitogenomes are so divergent, our default database is currently limited for maybe 70% fungus and animal mitogenomes. Plant plastomes and mitogenomes won't have such a problem because of their slow rate. This is part of the reasons why we isolate the default database as an independent repo - we are going to update it and expand it in versions.
Thanks for the feedback. I'm going to update the recipe so that people could understand better. Please let me know if you have further questions.
Jianjun
from getorganelle.
Related Issues (20)
- 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
- Invalid information provided HOT 1
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