Query returning empty output

[kirk-broad]

There seems to a be a size limit to the query output. Using the same set of rsIDs, I will receive proper outputs (outputLD.txt, outputInfo.txt) when using an R2 threshold of 0.8, but as I lower the threshold, at a certain point (e.g. 0.3), I receive empty outputs.
This works:
topld_api -thres 0.8 -pop EUR -maf 0.01 -inFile my_rsIDs.txt -outputLD outputLD.txt -outputInfo outputInfo.txt
This does not work:
topld_api -thres 0.3 -pop EUR -maf 0.01 -inFile my_rsIDs.txt -outputLD outputLD.txt -outputInfo outputInfo.txt

If I then use a smaller subset of input SNPs, that same threshold of 0.3 will work correctly. I am using well below the input size limit of 500 SNPs that is noted in the AJHG 2022 paper.

For queries that we expect to return larger outputs (higher # of SNPs or lower R2 thresholds), is the best fix to just perform the queries in small batches?

Thank you for this great tool!

[linnabrown]

Hi Kirk, thank you for using our tool. I just tried -thres 0.3, and the program can give non-empty outputs for the example data. Could you share the input file with me and let me look deeper? Thank you.

[linnabrown]

I just update the web API code (remote code, no need git pull) and you can test it (still using topld_api -thres 0.3 -pop EUR -maf 0.01 -inFile my_rsIDs.txt -outputLD outputLD.txt -outputInfo outputInfo.txt)

[kirk-broad]

Thank you for the quick response, however I am still having the same issue after the update.

I've attached the input file that I am using. For this set of SNPs, it seems that any R2 threshold below 0.6 does not work. I am running the API on a remote cluster, so perhaps it's something on my end.

my_rsIDs.txt

[linnabrown]

I tried ./topld_api -thres 0.3 -pop AFR -maf 0.01 -inFile input2.txt -outputLD outputLD.txt -outputInfo outputInfo.txt and it works pretty well. Here are the result.
outputInfo.txt
outputLD.txt

[kirk-broad]

That works for me as well, but when I switch out "AFR" for "EUR", it does not work.

I'm guessing it has to do with the output size? For example, when run with -thres 0.6 -pop EUR, the resulting LD file has 17,741 rows, compared to just 7,814 rows when using -thres 0.6 -pop AFR.

[linnabrown]

I also got the empty file when using 0.3. Thank you for reporting this bug. I will take a deep look to revise the code.

[linnabrown]

I will maintain the website tonight and let you know when the website is ready.

[tsc22]

Hi. I am also having the same issue with empty output.

I am using ./topld_api -thres 0.9 -pop EUR -maf 0.01 -inFile input.txt -outputLD outputLD.txt -outputInfo outputInfo.txt. This worked for my file with 228 SNPs, but not 493SNPs, as attached.
228SNPs.txt
493SNPs.txt

[bioarpit1]

is there any update on this bug works with small test input but with larger input > 400 variant it gives empty output