An Error in PhylotaR

[ZQ1126]

Hi Dom,

I am now using phylotaR for processed the data in Blats+. During the processing of PhylotaR, it shows an error may need you help to solve. Below were the script I used and the Error it shows. The Script I Used:

library(phylotaR) wd<-'e:/Institute_Of_Bontany/WorldTree/TracheophytaTest' ncbi_dr<-'d:/blast/blast-2.7.1+/bin/' txid<-58023 setup(wd=wd,txid=txid,ncbi_dr=ncbi_dr,v=TRUE)

phylotaR: Implementation of PhyLoTa in R [v1.0.0]

Checking for valid NCBI BLAST+ Tools ... Found: [d:/blast/blast-2.7.1+/bin//makeblastdb] Found: [d:/blast/blast-2.7.1+/bin//blastn] Setting up pipeline with the following parameters: . blstn [d:/blast/blast-2.7.1+/bin//blastn] . btchsz [100] . date [2018-10-22] . mdlthrs [3000] . mkblstdb [d:/blast/blast-2.7.1+/bin//makeblastdb] . mncvrg [51] . mnsql [250] . mxevl [1e-10] . mxnds [1e+05] . mxrtry [100] . mxsql [2000] . mxsqs [50000] . ncps [1] . txid [58023] . v [TRUE] . wd [e:/Institute_Of_Bontany/WorldTree/TracheophytaTest]

run(wd=wd)

The Error it shows: Generating taxonomic dictionary ... Unexpected Error in FUN(X[[i]], ...) : Unable to get "PRNT" slot from object without slot basic category ("NULL")

Occurred [2018-10-23 09:06:12] Contact package maintainer for help. Error in stages_run(wd = wd, frm = 1, to = nstages, stgs_msg = stgs_msg) : Unexpected Error in FUN(X[[i]], ...) : Unable to get "PRNT" slot from object without slot basic category ("NULL")

Best Wishes, Qiang

[DomBennett]

Hi

This is likely due to an error in a taxonomic record downloaded from NCBI. It should be fixable by running the download step again. I've made some updates to phylotaR to better capture these kinds of errors.

Try:

# install newer version of phylotaR
devtools::install_github('ropensci/phylotaR')

# restart your pipeline
library(phylotaR)
wd <- 'e:/Institute_Of_Bontany/WorldTree/TracheophytaTest'
restart(wd = wd)

If you get a warning, try halting the pipeline (use Esc or ctrl+c) and restarting again.

If you get an error, ping me here again.

These issues are due to the occasional malformed record that is retrieved from NCBI. Re-downloading again often fixes the issue. I am working on a more elegant solution.

Thanks for using phylotaR!

Dom

P.S. @Cactusolo the above should work for you too.

[Cactusolo]

@DomBennett Thank you so much! It works now!

Miao

[ZQ1126]

Thanks for your kindly help, it works again. @DomBennett