Closed asylvz closed 3 months ago
Your assembly has only 5 input reads, and Shasta is definitely not designed for such a small assembly.
If you want to try anyway, to go past the MinHash phase I suggest adding --MinHash.allPairs
to your command line. This will cause all possible pairs of oriented reads to be used as alignment candidates. For a typical assembly this is prohibitively expensive, but if you only have a very small number of reads it will be fine.
As announced in the release notes for Shasta 0.12.0, the new assembly configuration Nanopore-ncm23-May2024
is only designed to be used with the new experimental high accuracy reads from the Oxford Nanopore 2023.12 data release. It will not work with reads of lower accuracy. In particular, it will not work with ONT R10 or R9 reads.
As a separate comment, the option --Assembly.mode2.suppressGfaOutput
you are using on your command line only applies to Mode 2 assembly and has no effect for Mode 3 assembly. Assembly configuration Nanopore-ncm23-May2024
uses Mode 3 assembly. There is currently no option to suppress GFA output in Mode 3 assembly.
I see, thank you so much.
Hello, I'm trying the newer version and getting the following error with a fasta of 5 ONT reads: