hello, I am trying to run gatk cnv caller tutorial and I am facing an error with respect to reference fasta file. I have installed gatk using conda.
The code I am trying to run is:

    gatk PreprocessIntervals \
        -R ~/tutorial/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
        --padding 0 \
        -L ~/tutorial/tutorial_11684/gcnv-chr20XY-contig.list \
        -imr OVERLAPPING_ONLY \
        -O ~/output/chr20XY.interval_list

and the error i am getting is:

> A USER ERROR has occurred: The specified fasta file (file:///home/username/tutorial/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta) does not exist.

Please give some suggestions if there is any error in the code.
Have you checked to see if the file is readable?  You can use

    ls -lh
If it isn't readable, you can make it so using chmod.  For example, you could use

    chmod a+r <your_file>
