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.