problem with fastANI in v.1.0.4 of pbptyper

[gaworj]

Hi,

First of all thank you for such amazing tool. I was trying to use other software for pbp typing and it was disaster.

I have installed pbptyper using mamba as suggested and encountered error with fastANI:

pbptyper --assembly ERR4991741_assembly.fna --prefix ERR4991741_pbp --outdir ERR4991741_pbptyper_out

Running TBLASTN for 1A...
TBLASTN results written to ERR4991741_pbptyper_out/ERR4991741_pbp-1A.tblastn.tsv

Running TBLASTN for 2B...
TBLASTN results written to ERR4991741_pbptyper_out/ERR4991741_pbp-2B.tblastn.tsv

Running TBLASTN for 2X...
TBLASTN results written to ERR4991741_pbptyper_out/ERR4991741_pbp-2X.tblastn.tsv

Running fastANI...
External command isn't available!

Command:
bash -c 'fastANI -q /mnt/SSD2/genome_analysis/Weronika/ERR4991741_230922/ERR4991741_assembly.fna -r /home/jang/anaconda3/envs/py3/envs/pbptyper/share/pbptyper-1.0.4/GCF_000006885.fna.gz -o
ERR4991741_pbptyper_out/ERR4991741_pbp.fastani.tsv'

Search path:
['/home/jang/anaconda3/envs/py3/envs/pbptyper/bin',
'/home/jang/biosoft/CRISPRCasFinder/bin',
'/home/jang/anaconda3/condabin',
'/home/jang/bin',
'/home/jang/.local/bin',
'/usr/local/sbin',
'/usr/local/bin',
'/usr/sbin',
'/usr/bin',
'/sbin',
'/bin',
'/usr/games',
'/usr/local/games',
'/snap/bin',
'/home/jang/biosoft/scripts',
'/home/jang/biosoft/KrakenTools-master',
'/home/jang/biosoft/pseudo-finder',
'/home/jang/biosoft',
'/home/jang/biosoft/sratoolkit.2.11.0-ubuntu64/bin',
'/home/jang/biosoft/seqstats',
'/home/jang/biosoft/fasta_tools/bin',
'/home/jang/biosoft/Polypolish/target/release',
'/home/jang/biosoft/seqtk',
'/home/jang/biosoft/assembly_accuracy',
'/home/jang/biosoft/bbmap',
'/home/jang/biosoft/extract_genes_ABRicate',
'/home/jang/biosoft/seqIO_extract',
'/home/jang/biosoft/blobtools',
'/home/jang/biosoft/dotPlotly']

Standard error:
fastANI: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

I have dig a little bit looking for fastANI issues and find your suggestion to downgrade gsl to v2.6 version.

Conda downgrading of gsl causes simultaneous downgrade of pbptyper so I run mamba reinstallation:

mamba create -n pbptyper -c conda-forge -c bioconda pbptyper gsl=2.6

Now it works like a charm!

Bests,
Jan