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marbl / merqury

k-mer based assembly evaluation
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Quality value equal to Inf #48

Closed bistace closed 3 years ago

bistace commented 3 years ago

Hello and thank you for developing Merqury,

I have launched it on a plant genome and it finishes without crashing. However, the QVs I obtain are equal to inf, with k-mers specific to the assemblies equal to 0. The _only.bed and _only.wig files of the assembly are also empty. Here is the command I launched:

bash merqury/merqury.sh /env/cns/bigtmp2/reapr_pahang/reads/reads.meryl assembly_v2.fasta merqury_v2

Here is the content of the .qv file:

assembly_v2 0   405325924   inf 0

And finally, here is the spectra-cn log, could you please help me solve this issue? merqury_v2.spectra-cn.log

arangrhie commented 3 years ago

Hello, @bistace what is the genome size? Seems like you picked k=11, which seems too small. Of note, a 100 Mb genome requires k=18 ~ 19 under a tolerable collision rate of 0.001.

You could use $MERQURY/best_k.sh to estimate the recommended kmer size.

Best, Arang

bistace commented 3 years ago

You're right! I will launch everything again with k=21 as suggested by best_k.sh and report back to you if that solved my problem.

bistace commented 3 years ago

Hello,

changing the k-mer size to 21 corrected the errors and Merqury was able to finish successfully, as you predicted. Thanks a lot for your help!