Libgsl error from mash - cant run

[raw937]

• pharokka version: 1.7.1
• Python version: Python 3.10.8
• Operating System: Ubuntu 24.04

Description

Won't run. Had some errors.

Traceback (most recent call last): File "/home/docwhite/miniconda3/envs/pharokka/bin/pharokka.py", line 489, in main() File "/home/docwhite/miniconda3/envs/pharokka/bin/pharokka.py", line 128, in main ) = check_dependencies(args.skip_mash) File "/home/docwhite/miniconda3/envs/pharokka/bin/input_commands.py", line 540, in check_dependencies mash_major_version = int(mash_out.split(".")[0]) ValueError: invalid literal for int() with base 10: 'mash: error while loading shared libraries: libgsl'

What I Did

Command

pharokka.py -i phageX.fna -d ~/miniconda3/envs/pharokka/databases/ -t 8 -g prodigal-gv -o phageX_pharokka_gv

[raw937]

Same error when I tried to install base mash from conda. Traceback (most recent call last): File "/home/docwhite/miniconda3/envs/pharokka/bin/pharokka.py", line 489, in main() File "/home/docwhite/miniconda3/envs/pharokka/bin/pharokka.py", line 128, in main ) = check_dependencies(args.skip_mash) File "/home/docwhite/miniconda3/envs/pharokka/bin/input_commands.py", line 540, in check_dependencies mash_major_version = int(mash_out.split(".")[0]) ValueError: invalid literal for int() with base 10: 'mash: error while loading shared libraries: libgsl'

This fixed it: mamba install mash=2.2

All fixed and running again.

I would save this for others. Unsure it's a mash 2.3 or 2.1 issue. But, 2.2 works.