Can't find reference

[ktruve]

Hi,

I installed hap.py with apptainer. When trying to run with the following command: apptainer run hap.py_latest.sif /opt/hap.py/bin/hap.py truth.vcf comp.vcf -f HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed -o HG002_hg38_comp -r full_path_to.fasta

I get the following error: 2024-05-30 12:23:05,656 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. 2024-05-30 12:23:05,664 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. 2024-05-30 12:23:05,895 ERROR Please specify a valid reference path using -r. 2024-05-30 12:23:05,896 ERROR Traceback (most recent call last): 2024-05-30 12:23:05,896 ERROR File "/opt/hap.py/bin/hap.py", line 508, in 2024-05-30 12:23:05,896 ERROR main() 2024-05-30 12:23:05,896 ERROR File "/opt/hap.py/bin/hap.py", line 208, in main 2024-05-30 12:23:05,896 ERROR raise Exception("Please specify a valid reference path using -r.") 2024-05-30 12:23:05,896 ERROR Exception: Please specify a valid reference path using -r.

Please help me how to solve this problem. I have tried to write export HGREF=$ref_genome_path which doesn't help

Best, Katarina