Error when running with hg38/GRCh38 samples

[yaseminbridges]

Describe the bug FileNotFoundError when running with hg38 sample. The application attempts to access a file under a GRCh38 subdirectory in the data dependencies, however, this does not exist as they are named hg38.

Expected behavior The sample to run successfully without error of finding data dependency locations. Input data

Genome build hg38

Screenshots or pipeline output

Variable OMP_NUM_THREADS has been set to 1
INFO:    Using cached SIF image
VCF pre-processing
VCF quality filtering
Remove mitochondrial and unknown chromosome variants
Phrank scoring
join: /run/data_dependencies/phrank/hg19/gene_to_symbol_sorted.txt:16617: is not sorted: ENSG00000284015        MIR1281
Traceback (most recent call last):
  File "/run/phrank/src/run_phrank.py", line 33, in <module>
    if __name__ == "__main__": main(sys.argv[1], sys.argv[2])
  File "/run/phrank/src/run_phrank.py", line 27, in main
    p = Phrank(DAGFILE, DISEASEANNOTATIONS, DISEASEGENE, GENEANNOTATIONS)
  File "/usr/local/lib/python3.8/dist-packages/phrank/__init__.py", line 39, in __init__
    self._child_to_parent, self._parent_to_children = load_maps(dagfile)
  File "/usr/local/lib/python3.8/dist-packages/phrank/utils.py", line 3, in load_maps
    hpo_file = open(human_phenotype_map_file)
FileNotFoundError: [Errno 2] No such file or directory: '/run/data_dependencies/phrank/GRCh38/child_to_parent.txt'
Calculating phenotype similarities

[arine]

Hi @yaseminbridges ,

Thank you for providing the detailed information. It appears there is a mismatch in the genome build on the running command. When specifying the genome build, you should use hg38 instead of GRCh38. Please ensure that your configuration aligns with our instructions, which you can find here: Running with your sample.

If the issue persists after making this adjustment, please let us know, and we'll investigate further.

Best regards,

AIM Team