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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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parsnp: error: the following arguments are required: -d/--sequences #113

Closed Phylloxera closed 2 years ago

Phylloxera commented 2 years ago

parsnpv1.5.3 parsnp_linux/parsnp -r England1.fna -d genomes/*.fna -c -p 4 -o test3 runs fine parsnp_linux/parsnp –r CP030241.fasta –d fasta/*.fasta -x YES -o xyes_cno gives error in title. any ideas?

bkille commented 2 years ago

Hi @Phylloxera!

The -x argument is a "flag" that sets the xtrafast option to true, i.e. it takes no parameters. If that doesn't fix the problem, I'd recommend trying a more recent version of parsnp. Please let me know if neither of these options work!

-Bryce

Phylloxera commented 2 years ago

Thanks @bkille,

If -x is xtrafast, what is the flag for phipak? -x used to be the recombination detector: from: https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html Enable recombination detection/filter (-x) parsnp -r ./strep31/NC_011900.fna -d ./strep31 -p -c -x

It started working and I have no explanation why! First it gave a more reasonable error for -x YES as opposed to the one in the title and then started working swimmingly??? Probably not reproducible but I'm on a CENTOS server.

At present, version 1.5.3 is the most recent release on this repo with a precompiled binary.

Thanks again! Aaron

bkille commented 2 years ago

So the older version of parsnp actually had the xtrafast and phipack flags duplicated, i.e. -x would (and still does) activate the recombination detection. I'll update the --help documentation in the next release.

As far as getting a more updated binary goes, would you be interested in installing via conda? Its been our preferred route for some time, since it makes it easier to ensure that the dependencies are also installed and the correct versions.

Phylloxera commented 2 years ago

not a fan of conda... but if I containerize this (singularity), I'll be happy to do via conda within the container. right now I'm not getting any snps output with harvesttools, but that's an issue for a different repo :) in the past i've used the gui on a mac, but i'm wanting to run it all on linux so i can incorporate it into pipelines in the future.

thanks for the clarification.