/path error when running ncbi-genome-download in a shell script

[KinSimon96]

Hello,

I need to download genome of multiple bacteria species, and to make it faster, I want to use a bash script:

`#!/bin/bash

species=(
"Bacillus anthracis"
"Bordetella bronchiseptica"
"Bordetella parapertussis"
"Bordetella pertussis"
"Candida albicans"
"Chlamydia pneumoniae"
"Chlamydia psittaci"
"Chlamydia trachomatis"
"Corynebacterium sp."
)

for s in "${species[@]}"; do
ncbi-genome-download --formats fasta,assembly-report bacteria --genera "$s"
done`

running ./dl_bacteria_genomes.sh, I have this following error:
File "/usr/lib/python3.8/os.py", line 213, in makedirs
makedirs(head, exist_ok=exist_ok)
[Previous line repeated 4 more times]
File "/usr/lib/python3.8/os.py", line 223, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/path'

If I download in the same linux pwd each species separately: ncbi-genome-download --formats fasta,assembly-report bacteria --genera "Bacillus anthracis", it's working correctly.

Any ideas of why this does not work using bash script ?

Thanks,
Simon

[kblin]

I can't reproduce this on my end copying your exact script. The downloads run as expected.