Error running `phold run` in Colab Notebook
Closed this issue · 3 comments
Noonanav commented
Description
I was trying to run the Colab Notebook as published and encountered an error with limited explanation:
Running phold
Error occurred: Command 'phold run -i ./test_pharokka/test_pharokka.gbk -t 4 -o output_phold -p phold -f' returned non-zero exit status 1.
CPU times: user 22.1 ms, sys: 6.59 ms, total: 28.7 ms
Wall time: 4.87 s
Despite being connected to a T4 GPU, it appears phold is trying to run on a CPU (this could be the issue).
What I Did
Previous chunks ran as expected and generated output:
Database Downloads:
Downloading phynteny models. This will take a few minutes. Please be patient :)
Downloading pharokka database. This will take a few minutes. Please be patient :)
Downloading phold database. This will take a few minutes. Please be patient :)
CPU times: user 319 ms, sys: 46.1 ms, total: 365 ms
Wall time: 1min 36s
256
Run pharokka:
Input file ON602723.1.fna exists
Running pharokka
pharokka completed successfully.
Your output is in test_pharokka.
Zipping the output directory so you can download it all in one go.
Output directory has been zipped to test_pharokka.zip
CPU times: user 260 ms, sys: 22.1 ms, total: 282 ms
Wall time: 59.2 s
All expected output files were generated.
Run phold:
Running phold
Error occurred: Command 'phold run -i ./test_pharokka/test_pharokka.gbk -t 4 -o output_phold -p phold -f' returned non-zero exit status 1.
CPU times: user 22.1 ms, sys: 6.59 ms, total: 28.7 ms
Wall time: 4.87 s
gbouras13 commented
Hi @Noonanav ,
I reckon the issue isn't cpu - phold will run (just slower) if cpu only is available.
Would you mind downloading the .log file in the output_phold directory? If it exists?
George
gbouras13 commented
Hi @Noonanav ,
The issue was phynteny - it was breaking the notebook as it requires v1 of numpy (not 2).
I've changed the notebook - please try it again :)
George
Noonanav commented