Comments (2)
Hi @quokkamole ,
Assembly of mitogenome usually really costs a lot of memory.
You can try to reduce the data usage by setting a smaller "--max-reads" value such as 40000000 or less. You can also try to increase the "-w" value, such as 103 or larger. However, both adjustments would risk incomplete result. But it's worth trying if you don't have enough physical memory.
Best,
Jianjun
from getorganelle.
Ok. Thank you. Nice pipeline BTW. I like it.
from getorganelle.
Related Issues (20)
- Errors in assembly effect evaluation HOT 3
- error using different seed HOT 1
- Plot assembly coverage? HOT 1
- Baiting for ITS1-5.8S-ITS2 ribosomal regions HOT 1
- Error with Mitochondrial Assembly
- Batch works HOT 2
- Error with OS return value: 22; Can anyone please help me with a solution ? HOT 5
- Using the GFA file (p_utg) exported by hifiasm for assembly with the error "Slimming failed." HOT 1
- Running getorganelle with raw target sequencing data error HOT 1
- [IRRELEVANT] Trying to install compas-wood with failed repodata HOT 1
- 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
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from getorganelle.