Samtools missing binaries

[kaysahu]

Hello,

I have installed MIDAS using conda command in an empty virtual environment. I also installed samtools under the same conda environment. The installation is a success. But when I execute the run_midas.py command, I get the samtool error like the following. I double-check the $PATH and samtools is included in the $PATH. Samtools can be also run separately under the conda environment, but it looks like MIDAS couldn't find it.

run_midas.py --help comamnd works in the environment, however while processing fastq files, I run into this error. Kindly please advice regarding the same This is an example of my error:

[JuliaMcGonigle]

Hello,

I am having the same error. Please help, I would love to use your SNP calling program! Thanks.

[Eco-Luozhh]

Hello,

I am having the same error. Please help, I would love to use your SNP calling program! Thanks.

Hi, have u fix the error?

[qinghong2019]

I had the same problem before, I ended up install samtools v1.4 out of conda environment, and copy this binary and replace the samtools in bin in midas conda environment., and i module load Python/3.10.4-GCCcore-11.3.0 everytime I use it. and it worked!