Error when running goldrush_test_demo

[haraldgrove]

Hi

I've just started testing your program and ran into an issue when trying the demonstration.

I installed the software using conda as described and downloaded the github repository to find the demo-program.

When I ran the program (using slurm) I got the following error:

<...>
echo "Done GoldRush-Path! Golden path can be found in: goldrush_test_golden_path.fa"
Done GoldRush-Path! Golden path can be found in: goldrush_test_golden_path.fa
rm -f goldrush_test_silver_path_*.fq
Clean Done
goldrush-ulimit goldrush-edit --minimap2 -t4 -m/dev/shm goldrush_test_golden_path.fa test_reads.fq goldrush_test_golden_path.goldrush-edit-polished.fa
Running with 1030656 max processes: goldrush-edit --minimap2 -t4 -m/dev/shm goldrush_test_golden_path.fa test_reads.fq goldrush_test_golden_path.goldrush-edit-polished.fa
  File "/mnt/users/harag/.conda/envs/goldrush/bin/goldrush-edit", line 308
    while record := reader.read():
                  ^
SyntaxError: invalid syntax
make: *** [/mnt/users/harag/.conda/envs/goldrush/bin/goldrush.make:233: goldrush_test_golden_path.goldrush-edit-polished.fa] Error 1

The program had generated one file: goldrush_test_golden_path.fa. It's not quite the same name as in the README description, but is this the expected final output?

Can you tell what went wrong here?

-Harald

[lcoombe]

Hi @haraldgrove,

Did you install goldrush into a fresh conda environment, or into a pre-existing one? What version of python is installed? It looks like it's error-ing out at that walrus operator, which is only available in python 3.8+.

If your python version looks sufficient, it would help to see a conda list of the packages installed in your conda environment.

Due to the error, GoldRush did not generate the final expected output - the goldrush_test_golden_path.fa file is the output of the GoldPath stage, and is the 'golden path' - See our README, wiki or paper for more details about the steps of GoldRush.

Thank you for your interest in GoldRush! Lauren

[haraldgrove]

Sorry, I think the problem was on my end. I got a tip about checking which python3 file that was first in the path and it was not the one in the GoldRush environment (unlike python). After fixing that problem, the program ran to the end.

-Harald

[lcoombe]

Hi Harald - excellent, I'm glad to hear that you solved the issue!