parsnp: error: the following arguments are required: -d/--sequences
Phylloxera opened this issue · 4 comments
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?
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
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
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.
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.