Drep error with fastANI

Hi Dr. Olm, I have installed fastANI but it is not working. Some error as below: (Compare) [youfen.qian@compute-0-4 Landfill_leachateGlobal]$ dRep check_dependencies mash.................................... all good (location = /share/data1/private/youfen.qian/software/miniconda3/envs/Compare/bin/mash) nucmer.................................. all good (location = /share/data1/private/youfen.qian/software/miniconda3/envs/Compare/bin/nucmer) checkm.................................. all good (location = /share/data1/private/youfen.qian/software/miniconda3/envs/Compare/bin/checkm) ANIcalculator........................... !!! ERROR !!! (location = None) prodigal................................ all good (location = /share/data1/private/youfen.qian/software/miniconda3/envs/Compare/bin/prodigal) centrifuge.............................. !!! ERROR !!! (location = None) nsimscan................................ !!! ERROR !!! (location = None) fastANI................................. !!! ERROR !!! (location = /share/data1/private/youfen.qian/software/miniconda3/envs/Compare/bin/fastANI)

File "/share/data1/private/youfen.qian/software/miniconda3/envs/Compare/lib/python3.7/site-packages/drep/d_cluster/compare_utils.py", line 298, in secondary_clustering ndb = compare_genomes(bdb, algorithm, data_folder, kwargs) File "/share/data1/private/youfen.qian/software/miniconda3/envs/Compare/lib/python3.7/site-packages/drep/d_cluster/compare_utils.py", line 368, in compare_genomes df = drep.d_cluster.external.run_pairwise_fastANI(genome_list, working_data_folder, kwargs) File "/share/data1/private/youfen.qian/software/miniconda3/envs/Compare/lib/python3.7/site-packages/drep/d_cluster/external.py", line 93, in run_pairwise_fastANI exe_loc = drep.get_exe('fastANI') File "/share/data1/private/youfen.qian/software/miniconda3/envs/Compare/lib/python3.7/site-packages/drep/init.py", line 100, in get_exe raise ValueError("{0} isn't working- make sure its installed".format(name)) ValueError: fastANI isn't working- make sure its installed

Thanks

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    Thanks for your help, it worked.
    Best regards.Pengfei.

                            Pengfei.hu

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On 2/21/2024 ***@***.***> wrote：

Hi all I was having the exact same issue and solved it with help from our server support team. They advised to install fastANI from source, and outside miniconda environment. I was folowing these commands: module purge module load pbs gsl/2.7.1 git clone -b v1.34 https://github.com/ParBLiSS/FastANI.git mkdir fastani cd FastANI ./bootstrap.sh ./configure --prefix=//fastani make make install Then export "/fastani/bin" under your $PATH using: export PATH=/fastani/bin:$PATH and then run dRep check_dependencies again, it should now recognize the fastANI and say all good! :) Hope it helps someone! Cheers, Tereza

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MrOlm / drep

Drep error with fastANI #218