cannot get ksnp3 to complete TOO FEW SPECIES
kSNP4 does SNP discovery and SNP annotation from whole genomes
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barryghall,
shea0
Hi,
I've tried lots of settings but this is the latest command:
kSNP3 -in ksnp.list -outdir ksnp-out -k 19 -vcf -NJ -core -ML
i have 15 genomes with several thousand SNPs. Parsnp runs fine and finds the expected number of SNPs but I cannot get kSNP3.0 to complete.. it always says no snps found. The .vcf output is empty.
It finishes with this message and hangs:
Number_SNPs: 1283
$count_snps: 0
Finished finding SNPs
Wed May 18 09:19:54 EST 2016
mv: No match.
Building parsimony tree
TOO FEW SPECIES
grep: RAxML_info.SNPs_all: No such file or directory
grep: RAxML_info.SNPs_all: No such file or directory
grep: RAxML_info.SNPs_all: No such file or directory
Number of most parsimonious trees from SNPs_all: 0
Score of those trees:
Running on Linux:
Linux version 3.10-3-amd64 (debian-kernel@lists.debian.org) (gcc version 4.7.2 (Debian 4.7.2-5) ) #1 SMP Debian 3.10.11-1 (2013-09-10)
Thanks for any help,
Theo
Hi ! I have the same problem here, although it works just fine with two other sets of data.
Maybe try doing what the previous post on "stuck at tree building step" suggests and check the input files ?
Sara
If your dataset is all of the same species, I'd recommend giving SPANDx a go (https://sourceforge.net/projects/spandx/). If your dataset is all sequence reads then you are good to go but if you want to include assemblies you'll need to convert these to sequence reads first using something like ART. Good Luck!
Derek
Hi
i have 85 genome, i want to compare the genotypes using kSNP, can someone send me the method and the protocol of comparison from A-Z with a little example please
thank you
should i concatenate all the genomes in an one fasta file?
thank you
Hi, I have the same problem and I can not find the solution. I will appreciate some help.
Arancha
kSNP3 has been replaced by kSNP4. Get kSNP4 from SourceForge and install it according to the kSNP4 User Guide.
Barry G. Hall
Director, Bellingham Research Institute
barryghall@gmail.com
http://www.bellinghamresearch.com http://www.bellinghamresearch.com/
Whenever you have a problem and ask for help be SURE to provide sufficient information for someone to actually help you. In this case you should have stated how many species you included in your input file. If it was fewer than 4 species it is impossible to make a phylogenetic tree.
kSNP3 has been replaced by kSNP4. Download kSNP4 from source forge and read the ENTIRE User Guide - including FAQ - before installing or trying to use kSNP4. If you still have problems follow all the instructions for asking for help and contact me directly if necessary.
Barry G. Hall
Director, Bellingham Research Institute
barryghall@gmail.com
http://www.bellinghamresearch.com http://www.bellinghamresearch.com/