issue with plink and score function

[ishanparanjpe]

I am trying to generate scores (last step) for a plink formatted genotype file. I am not interested in prediction accuracy and only want to output scores.

nohup python $ldpred score --gf=$target_file --rf=$ldpred_output_file --out=$score_output_file --only-score > $nohup_log &

When I run this, I get the following error:

Calculating LDpred-inf risk scores Parsing PLINK bed file: /sc/private/regen/data/Regeneron/GSA/imputed_tgp_p3_plink/GSA_chr_all Traceback (most recent call last): File "/hpc/packages/minerva-centos7/ldpred/1.0.6/ldpred/LDpred.py", line 300, in main() File "/hpc/packages/minerva-centos7/ldpred/1.0.6/ldpred/LDpred.py", line 293, in main validate.main(p_dict) File "/hpc/packages/minerva-centos7/ldpred/1.0.6/ldpred/ldpred/validate.py", line 658, in main verbose=verbose, summary_dict=summary_dict) File "/hpc/packages/minerva-centos7/ldpred/1.0.6/ldpred/ldpred/validate.py", line 412, in calc_risk_scores prs_dict = get_prs(bed_file, rs_id_map, phen_map, only_score=only_score, verbose=verbose) File "/hpc/packages/minerva-centos7/ldpred/1.0.6/ldpred/ldpred/validate.py", line 12, in get_prs plinkf = plinkfiles.plinkfile.PlinkFile(genotype_file) File "/hpc/packages/minerva-centos7/py_packages/3.7/lib/python3.7/site-packages/plinkio/plinkfile.py", line 14, in init self.handle = cplinkio.open( path ) OSError: Error while trying to open the FAM plink file.

[bvilhjal]

Hi,

I apologize slow reply on this. You can use the --only-score

[May-Ibrahim]

Hi, I'm getting the same error although I'm using --only-score. I don't think the error is related to the use of only-score. It can't open the plink file although it is there.

Have you figured out how to fix it?

Thanks, May