In the MetaboAnalyst Causal Analysis workflow, on the SNP Filtering & Harmonization page, clicking Update and then Proceed results in no action, the workflow does not advance, and no error is shown. Persistent for the past few days.
Environment:– Windows 11, Google Chrome
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Hi @xia.lab team
Data used
On “SNP Filtering & Harmonization ”, selected the following options:
Use clumping to prune SNPs for LD Using proxy SNPs when a direct SNP query is absent Use steiger filtering- After Update (and/or Proceed), the workflow should run SNP filtering/harmonization and advance to the next step. But no loading/progress indicator or error message is shown.
The problem persists. Please take a look.
Data used
Exposure: L-Histidine (selected from the metabolite list)
Outcome: finn-b-F5_ADHD (selected from the public repository search)
On “SNP Filtering & Harmonization ”, selected the following options:
LD-based harmonization
Use clumping to prune SNPs for LD
Using proxy SNPs when a direct SNP query is absent
Allele Harmonization
⦿ Try to infer the forward strand alleles using allele frequency information
Remove Pleiotropic SNPs
⦿ Exclude SNPs associated with multiple metabolites
Steiger filtering
Use Steiger filtering
Click Update (button in the middle of the page).
Then click Proceed.
- After Update (and/or Proceed), the workflow should run SNP filtering/harmonization and advance to the next step. But no loading/progress indicator or error message is shown.
It processed, but I had to try multiple times. Now, it is stuck on the next pair. The process is random.
I took a look at this case, it is related to the study you selected: finn-b-F5_ADHD, which does not contain sample size information required for performing Steiger filtering. The server will be updated to provide better error message.
Possible solution:
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