search

bvilhjal / ldpred

MIT License
96 stars 57 forks source link

global name 'non_zero_chromosomes' is not defined #41

Closed gmgaous closed 5 years ago

gmgaous commented 5 years ago

Hi Bjarni, I downloaded the ldpred about one month ago (version 0.9.9). I am trying to run the validate script with

validate --vgf=./Olopade_chr1.imputed_common_SUMstat_newID --rf=./OUTPUT_pruning --out=./OUTPUT_validate_pruning --res_format=P+T

I get the an error similar to one posted before (see below).

Calculating P+T risk scores using p-value threshold of 1.000e+00 Traceback (most recent call last): File "/home/ggao5/.conda/envs/myPython2.7/bin/validate", line 11, in sys.exit(main()) File "/home/ggao5/.conda/envs/myPython2.7/lib/python2.7/site-packages/ldpred/validate.py", line 735, in main rs_id_map = parse_pt_res(weights_file) File "/home/ggao5/.conda/envs/myPython2.7/lib/python2.7/site-packages/ldpred/validate.py", line 400, in parse_pt_res non_zero_chromosomes.add(chrom) NameError: global name 'non_zero_chromosomes' is not defined

Guimin

bvilhjal commented 5 years ago

Hi, thanks for reporting this. I believe this has been fixed in the latest version.