Error: blastn failed to run. Check BLAST log files

[CesarDamian]

Hi. I'm trying to run the following commands

wd <- "C: / Project_Crass / 11_R / PhylotaR"
ncbi_dr <- "C: / Program Files / NCBI / blast-2.7.1 + / bin"
txid <- 3784
setUp (wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = T)
run (wd = "C: / Project_Crass / 11_R / PhylotaR")

but I get an error when the cluster stage starts

Error in runStgs (wd = wd, frm = 1, to = nstages, stgs_msg = stgs_msg): Unexpected Error in error (ps = ps, "blastn failed to run. Check BLAST log files."): Error: blastn failed to run. Check BLAST log files.

Could you guide me how I solve this error? I already performed the same procedure with different taxa and always stops at the CLUSTER stage. I attach the log file, thank you log.txt

[DomBennett]

Hi,

Sorry for the delay. This seems to be the same issue other people are having with windows. I've investigated and it appears to be due to differences in quotations in the arguments for blastn. I have updated the code to account for this OS difference.

I've run your same code on a windows machine and the pipeline completed without error.

Please try reinstalling phylotaR with the latest dev version and try again. You can reinstall phylotaR by running devtools::install_github('AntonelliLab/phylotaR') again.

If the error persists, please let me know.

Best, Dom

[DomBennett]

Closing due to inactivity.