A question about SPAdes

Question

[Tong]

Hello everyone,

I have been using SPAdes using this command.

spades.py -k 111,113,127 --careful -o spades_output -1 s1-1.fastq -2 s1-2.fastq

If I do not misunderstand, SPAdes will choose the best k-mer based on the longest N50.

How can I know that which k-mer was chosen for the longest N50?

Thank you in advance.

[Istvan Albert]

don't the log state that? there are lots of files created there, just look into those

[Tong]

I already looked for it in the log file, but I could not find it.

By the way, thank you for your answer.

[samuel.a.odonnell]

I don't find this in the log file either. It says the kmers that were run but not which one was chosen. However is it always the last kmer tested?

A quick trick you can do to be sure, is just grab a part of the first header from the fastg file placed in the main output directory, e.g. "EDGE_20078450_length_31386" , and search for it within all the kmer fastg files. It is specific enough to find the original file.

[Istvan Albert]

I looked at a SPADES output we had. Another way that might work is that the scaffolds.fasta file is created only for the chosen kmer

find . -name 'scaff*' 

will tell you what directories contain this file.