Problem with makeblastdb

[jordandowell]

I keep getting errors when using makeblastdb. According to other reported issues, I was using Blast 2.14.0 and the current iteration of Blast, but neither had any impact.

Script used:

library(phylotaR)
wd <- 'phylotaOutput_9504'
ncbi_dr <- '/opt/homebrew/bin'

txid <- 9504
setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = TRUE)

PhylotaR output:

---

phylotaR: Implementation of PhyLoTa in R [v1.3.0]

Checking for valid NCBI BLAST+ Tools ...
Found: [/opt/homebrew/bin/makeblastdb]
Found: [/opt/homebrew/bin/blastn]
. . Running makeblastdb
Error: makeblastdb failed to run. Check BLAST log files.

Blast Log:

BLAST options error: Please provide a database name using -out

Session info:
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1

[jordandowell]

Adding more context, surprisingly, it works if I use a temporary directory.

example with temp folder

wd <- file.path(tempdir(), 'aotus')

setup for aotus, make sure aotus/ folder already exists

if (!dir.exists(wd)) {
dir.create(wd)
}

however replacing tempdir() with getwd() leads to the same errors above.