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ABORT: partitioning failed; increase redMemory. #2205
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This looks the same as #2035 or #2179 which unfortunately was fixed post the 2.2 release. You can either update the code to use the latest if you can compile canu locally from GitHub (or edit the code). On a related note, it seems you have extremely low coverage for your genome so there isn't really much here to assemble. Do you really only have 400k of data for a 12mb genome? You also would need to correct ONT data before assembling it but again, with this little coverage there isn't going to be anything to correct or assemble. |
Thank you! That worked for me. It's not actually 12mb - its a small region of a genome where a gene candidate is present so there is "low coverage" in that region but not actually. It's complicated is the short answer lol. Thank you for your help! |
System:
Linux AWS server (EC2 instance)
Version:
canu 2.2
Command:
./canu -p 011_full -d 01_canu genomeSize=12m -trimmed -stopOnLowCoverage=0.001 -nanopore /home/ec2-user/01_full.fastq
Error Message:
I have tried increasing the redMemory and the maxMemory and decreasing the stopOnLowCoverage but no matter what I do it gives me this error message. Can someone help me fix it?
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