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immunogenomics / HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies
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Error running HLAassoc #13

Closed isabelleboothman closed 2 years ago

isabelleboothman commented 2 years ago

Hi, I ran the imputation using the Michigan server and am now trying to run HLAasssoc. I keep getting this error: Traceback (most recent call last): File "/home/iboothman/miniconda3/envs/myenv/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/home/iboothman/miniconda3/envs/myenv/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/iboothman/HLA-TAPAS/HLAassoc/HLAassoc.py", line 10, in from HLAassoc.src.reverse_map import reverse_map File "/home/iboothman/HLA-TAPAS/HLAassoc/HLAassoc.py", line 10, in from HLAassoc.src.reverse_map import reverse_map ModuleNotFoundError: No module named 'HLAassoc.src'; 'HLAassoc' is not a package

This is the code I ran:
python -m HLAassoc LINEAR \ --vcf /home/StorageArray02/Gianpiero/iboothman/HLA_imputation/Michigan/chr6.dose.vcf.gz \ --out /home/StorageArray02/Gianpiero/iboothman/HLA_imputation/Michigan/Random_Irish_samples_HLA. \ --pheno /home/StorageArray02/Gianpiero/iboothman/HLA_imputation/Random_Irish_samples_HATK.pheno \ --pheno-name Phenotype

Not sure why I am getting that error, thanks!

yluo86 commented 2 years ago

This might be a python error. Have you installed all the dependencies?

Are you able to run the toy example?

catheriz commented 2 years ago

Hi, Does the HLAssoc use dosage from the imputed file or GT for the analysis?

yluo86 commented 2 years ago

it uses GT. LINEAR and LOGISTIC use regression coded in PLINK, and OMNIBUS test uses haplotypes based on GT.