fastANI error loading shared libraries libgsl.so.25

[CaitlinSelway]

Hi Laura,

I was installing this great tool this morning, but came across an error with libgsl.so.25.

$ btyper3 -i 2218710072.fna -o bytper3
Welcome to BTyper3!
You are initializing this run at 2022-07-19 08:56
You ran the following command:
/phe/tools/miniconda3/envs/btyper3/bin/btyper3 -i 2218710072.fna -o bytper3
Report bugs/concerns to Laura M. Carroll, laura.carroll@embl.de
Using FastANI to assign 2218710072 to a species at 2022-07-19 08:56
fastANI: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/phe/tools/miniconda3/envs/btyper3/bin/btyper3", line 10, in <module>
    sys.exit(main())
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/site-packages/btyper3/__init__.py", line 441, in main
    run_pipeline(args)
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/site-packages/btyper3/__init__.py", line 105, in run_pipeline
    final_species = get_species.run_fastani("species", fastani_path, infile, final_results_directory, prefix)
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/site-packages/btyper3/ani.py", line 60, in run_fastani
    proc.check_returncode()
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/subprocess.py", line 456, in check_returncode
    raise CalledProcessError(self.returncode, self.args, self.stdout,
subprocess.CalledProcessError: Command '['fastANI', '-q', '2218710072.fna', '--rl', '/tmp/tmp69n8g9vktxt', '-o', 'bytper3/btyper3_final_results/species/2218710072_species_fastani.txt']' returned non-zero exit status 127

After a quick google, the current gsl version 2.7.1 only provides libgsl.so.27. For anyone else that encounters this issue, I fixed it by downgrading the gsl version from 2.7.1 to 2.7. conda install gsl=2.7

Have a good day! Caitlin

[althonos]

Hi Caitlin, this looks more like a Bioconda issue, I'll be opening an issue there as well, this can likely be fixed by pinning an exact gsl version for the fastani package (at the moment it expects gsl>=2.7,<2.8).

[althonos]

Actually, this looks like it was fixed already in bioconda/bioconda-recipes#35517, have you updated your conda environment in the last month?