Inquiry on error for running protein annotation

[songmj86]

• pharokka version: 1.7.3
• Python version: 3.10.14
• Operating System: Ubuntu 22.04.4 LTS (GNU/Linux 5.15.0-101-generic x86_64)

Description

Hi. I am tyring to annotate the viral protein using following commands & the run was halted with the following error

Could you help me resolve this issue?

Thanks !

What I Did

Instllation command

conda create -y -c conda-forge -c bioconda -n Pharokka pharokka=1.7.3 ; conda activate Pharokka ;

Run command

conda activate Pharokka ; DB="/home/pharokka_v1.4.0_databases" ; In="/home/Protein.faa" ; Out="/home/Pharokka_Test" ; pharokka_proteins.py -d $DB -t 100 -i $In -o $Out ; conda deactivate ;

Output error

2024-07-15 22:16:39.315 | INFO | main:main:64 - Starting Pharokka v1.7.3 2024-07-15 22:16:39.317 | INFO | main:main:65 - Running pharokka_proteins.py to annotate proteins. 2024-07-15 22:16:39.317 | INFO | main:main:66 - Command executed: Namespace(infile='Protein.faa', outdir='/home/Pharokka_Test', database='/home/pharokka_v1.4.0_databases', threads='80', force=False, prefix='Default', evalue='1E-05', hmm_only=False, mmseqs2_only=False, citation=False) 2024-07-15 22:16:39.317 | INFO | main:main:67 - Repository homepage is https://github.com/gbouras13/pharokka 2024-07-15 22:16:39.317 | INFO | main:main:68 - Written by George Bouras: george.bouras@adelaide.edu.au 2024-07-15 22:16:39.317 | INFO | main:main:71 - Checking database installation. 2024-07-15 22:16:39.317 | INFO | main:main:75 - All databases have been successfully checked. 2024-07-15 22:16:39.317 | INFO | main:main:82 - Checking dependencies. 2024-07-15 22:16:39.462 | INFO | input_commands:check_dependencies:383 - Phanotate version found is v1.5.1 2024-07-15 22:16:39.462 | INFO | input_commands:check_dependencies:392 - Phanotate version is ok. 2024-07-15 22:16:39.465 | INFO | input_commands:check_dependencies:414 - MMseqs2 version found is v13.45111 2024-07-15 22:16:39.465 | INFO | input_commands:check_dependencies:423 - MMseqs2 version is ok. 2024-07-15 22:16:39.533 | INFO | input_commands:check_dependencies:447 - tRNAscan-SE version found is v2.0.12 2024-07-15 22:16:39.534 | INFO | input_commands:check_dependencies:458 - tRNAscan-SE version is ok. 2024-07-15 22:16:39.597 | INFO | input_commands:check_dependencies:482 - MinCED version found is v0.4.2 2024-07-15 22:16:39.598 | INFO | input_commands:check_dependencies:493 - MinCED version is ok. 2024-07-15 22:16:39.603 | INFO | input_commands:check_dependencies:519 - ARAGORN version found is v1.2.41 2024-07-15 22:16:39.604 | INFO | input_commands:check_dependencies:530 - ARAGORN version is ok. Traceback (most recent call last): File "/opt/anaconda3/envs/Pharokka/bin/pharokka_proteins.py", line 213, in main() File "/opt/anaconda3/envs/Pharokka/bin/pharokka_proteins.py", line 83, in main check_dependencies(False) # to check pharokka_proteins.py, don't need mash File "/opt/anaconda3/envs/Pharokka/bin/input_commands.py", line 544, 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'

[gbouras13]

Hi @songmj86

mash didnt install properly. Try mash v 2.2

try running

conda install mash==2.2

george

[songmj86]

Super fast response

Thanks!