Could not run Nucmer

[peflanag]

Hi,

I'm new to nucdiff. `I installed in a Conda environment on macOS and used the below code but Nucmer wouldn't run? Could anyone help me please?

/Users/peterflanagan/miniconda3/envs/nucdiff/bin/nucdiff /Volumes/IMRL/Peter_F/Recurrent_Isolates/All_Study_Analysis/SPAdes_Assembled/Fasta/01IE10.fasta /Volumes/IMRL/Peter_F/Recurrent_Isolates/All_Study_Analysis/SPAdes_Assembled/Fasta/16IE57.fasta /Volumes/IMRL/Peter_F/Recurrent_Isolates/All_Study_Analysis/Nucdiff Study12

Run NUCmer...

/bin/sh: /Users/peterflanagan/miniconda3/envs/nucdiff/bin/nucmer: /usr/local/bin/perl: bad interpreter: No such file or directory

Could not run nucmer. Please, check nucmer input parameters values.

[peflanag]

So just to update, it turns out I had to downgrade using

$ mamba install mummer=3.23=h6de7cb9_11

which allowed me to run nudiff. However, none of the output files int he results will open in Artemis. The purpose for me to use this program is that I have patients that have TB and I'm comparing two samples, one early with a later one over a year apart. I know that there is 1-3 SNPs between them but I wasn't to search where those SNPs are. So I assembled the early and late sample using SPAdes and used the early as the reference and the later sample as the query. Is there something I am doing wrong?

Cheers in advance!