SyntaxError when running srst2

[cpavloud]

Hello!
I am trying to run srst2 in an HPC cluster to identify resistance genes and I get the error below:

Traceback (most recent call last):
File "/CCAS/home/cpavloudi/miniconda3/bin/srst2", line 5, in
from srst2.srst2 import main
File "/CCAS/home/cpavloudi/miniconda3/lib/python3.9/site-packages/srst2/srst2.py", line 308
print "Warning! MLST delimiter is " + delimiter + " but these genes may violate the pattern and cause problems:"
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Warning! MLST delimiter is " + delimiter + " but these genes may violate the pattern and cause problems:")?

Do you have any idea why this might be happening?

I checked if I have installed srst2 properly, but maybe something was wrong with my installation?

(base) srst2 --version
Traceback (most recent call last):
File "/CCAS/home/cpavloudi/miniconda3/bin/srst2", line 5, in
from srst2.srst2 import main
File "/CCAS/home/cpavloudi/miniconda3/lib/python3.9/site-packages/srst2/srst2.py", line 308
print "Warning! MLST delimiter is " + delimiter + " but these genes may violate the pattern and cause problems:"
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Warning! MLST delimiter is " + delimiter + " but these genes may violate the pattern and cause problems:")?

(base) getmlst.py -h
File "/CCAS/home/cpavloudi/miniconda3/bin/getmlst.py", line 128
print "No species matched your query."
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("No species matched your query.")?

(base) slurm_srst2.py -h
File "/CCAS/home/cpavloudi/miniconda3/bin/slurm_srst2.py", line 105
print "Could not determine forward/reverse read status for input file " + fastq
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Could not determine forward/reverse read status for input file " + fastq)?

[dannagifford]

I had this issue too. I solved it by running the scripts with python2, i.e. instead of
getmlst.py -h
run
python2.7 /usr/local/bin/getmlst.py -h
or wherever your scripts were actually installed to.