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thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data
http://chibba.pgml.uga.edu/snphylo/
GNU General Public License v2.0
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Error in scan.vcf.marker(fn, method) #32

Open ketienne opened 5 years ago

ketienne commented 5 years ago

I am running snphylo as such:

$ ./snphylo.sh -v file.vcf -c 10 -P

Upon execution, these are my following messages:

Start to remove low quality data.

253268 low quality lines were removed.

Warning message: package ‘gdsfmt’ was built under R version 3.3.2 SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2) Start snpgdsVCF2GDS ... Extracting bi-allelic and polymorhpic SNPs. Scanning ... file: snphylo_asper.filtered.vcf Error in scan.vcf.marker(fn, method) : The file (file.filtered.vcf) has different numbers of columns. Calls: snpgdsVCF2GDS_R -> scan.vcf.marker Execution halted

Could you provide suggestions on how to fix his error? All decencies are installed.

Thanks for your attention to my question

jmf422 commented 3 years ago

I am having this same error too. @ketienne did you happen to figure out what the issue was?