nucmer won't run

[peflanag]

Hi,

Im not sure if I'm doing something stupid but installed mummer via mamba in its own env. I can run mummer -h and that's fine but if I try nucmer -h or ./nucmer -p [ref] [query] it fails with the following error:

zsh: /Users/peterflanagan/miniconda3/envs/mummer/bin/nucmer: bad interpreter: /usr/local/bin/perl: no such file or directory

Can someone tell me what I am doing wrong?

Cheers!

[peflanag]

To update, I updated perl and it ran for me but didn't output a .delta file. It only outputted a .error, .mgaps and .ntref file.

Basically I am trying to use some program that will compare an early isolate with a later one received from the same patient too see where the snp difference is after a number of years. I want to find the coordinate(s) so I can see what gene the SNP is in if there is a SNP difference. These samples should only have 1 to 2 SNP differences in them.

Cheers in advance!

[peflanag]

Hi again, I have tested this with other organisms that have a number of SNP differences between the reference and the query sample to make sure it wasn't my patent samples. Again nucmer failed with the error mummer and/or mgaps returned non-zero and the output folder only has an out.mgaps and out.ntref file as well as the .error file

Im just wondering am I doing something wrong to find the coordinates with differences between the reference and query sample?

Cheers,

P