--restart-from last

[INFINITY1993]

Hi, there,

I have finished the metaspades assembly with default kmer set (21, 33 and 55), but now I also want to check the assembly results with kmer set (21,33,55 and 77). Could I use "--restart-from last" options ? will it start from kmer 77?

Best regards!

[asl]

Well, no, because "last" is k=55 in your case. You need to explicitly specify the k-mer set and the k-mer to restart from.

[INFINITY1993]

Thanks for your quick response.
spades.py
-o /data/home/soil_metagenome_anaysis/metaspades_assembly_out/s2
--meta
-1 /data/home/soil_metagenome_anaysis/cleandata/s2_1.fastq
-2 /data/home/soil_metagenome_anaysis/cleandata/s2_2.fastq
-t 60
-m 500
--restart-from k55
-k 21,33,55,77 \

metaspades_s2.log 2>&1

Is the settings right? Then it will run k55 again, or it will skip k55 and run k77?

[asl]

It will re-run k=55, as the last stage is always very special.

[INFINITY1993]

ok, I see. Thanks so much!