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ghm17 / LOGODetect

LOGODetect is a powerful tool to identify small segments that harbor local genetic correlation between two traits/diseases.
GNU General Public License v3.0
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A bug! #13

Closed Rick-Chen-PKU closed 3 years ago

Rick-Chen-PKU commented 3 years ago

############### cd ./LOGODetect source ./Code/calculateLD.txt
for chr in $(seq 22) do Rscript ./Code/random_vector_generation.R ${chr} Rscript ./Code/aggregation.R ${chr} done ############### Hello! When I ran this code, it worked on the first and second chromosomes, but I ran on the third chromosome with a bug as shown in the figure below. And for the fourth and fifth chromosomes also appear the same problem, can you give me some advice?

微信图片_20210622172847
ghm17 commented 3 years ago

It seems that line 3 of calculateLD.txt (source Code/calculateLD/calculateLD_chr3.txt to calculate LD matrix in chr 3) did not function normally and was killed. Therefore when you ran random_vector_generation.R for chr 3, the required inputs of LD matrix were missing and the error message popped out. You may rerun line 3-22 of the script calculateLD.txt and see if the problem can be solved.

Rick-Chen-PKU commented 3 years ago

It seems that line 3 of calculateLD.txt (source Code/calculateLD/calculateLD_chr3.txt to calculate LD matrix in chr 3) did not function normally and was killed. Therefore when you ran random_vector_generation.R for chr 3, the required inputs of LD matrix were missing and the error message popped out. You may rerun line 3-22 of the script calculateLD.txt and see if the problem can be solved.

Thanked your reply！I will try again！