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marbl / meryl

A genomic k-mer counter (and sequence utility) with nice features.
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ERROR: operation 'opNothing' cannot use sequence files as inputs. #23

Closed Gon1976 closed 3 years ago

Gon1976 commented 3 years ago

Hi, I am trying to estimate read accuracy for an assembly using this pipeline https://genome.cshlp.org/content/suppl/2020/09/02/gr.263566.120.DC1/Supplemental_Material_.pdf

I have the meryl database, and try to run the final step and I have this error: meryl -lookup -memory 40 -threads 16 -existence -sequence ../reads.fastq.gz -output k10.kmers -mers k10_filtered.meryl ERROR: operation 'opNothing' cannot use sequence files as inputs.

Any idea, what happen? thanks Gonzalo

brianwalenz commented 3 years ago

The command is meryl-lookup (one word), not meryl with option -lookup.

Gon1976 commented 3 years ago

I try it, but not founded the command? It is an installation problem maybe: meryl-lookup -memory 40 -threads 16 -existence -sequence reads.fastq.gz -output k10.kmers -mers k10_filtered.meryl -bash: meryl-lookup: no se encontró la orden (dont found the order)

arangrhie commented 3 years ago

add meryl/*/bin/ to your $PATH. https://github.com/marbl/meryl#installation

Gon1976 commented 3 years ago

I try it. Meryl was installed with canu, for some reason altough I add meryl to my path doesnt work. meryl command work, but not meryl-lookup I am doing something wrong?

meryl-lookup -memory 40 -threads 16 -existence -sequence reads.fastq.gz -output k10.kmers -mers k10_filtered.meryl -bash: meryl-lookup: no se encontró la orden [nanocruzi@hpc02 CanuAM64]$ echo $PATH /home//installs/canu-2.1.1/src/meryl/*/bin:

skoren commented 3 years ago

That path doesn't look right, you shouldn't rely on Canu to install meryl because it is not going to include/build everything and it would be under canu-2.1.1/build/bin. You should get meryl from it's own repo as either source or one of the releases.

Gon1976 commented 3 years ago

done, thanks