# LD pruning not finishing running

**URL:** <https://discuss.hail.is/t/ld-pruning-not-finishing-running/2638>\
**Category:** Hail Query & hailctl\
**Created:** [April 27, 2022, 5:41pm UTC](https://discuss.hail.is/t/ld-pruning-not-finishing-running/2638 "2022-04-27T17:41:57Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![dlazarev](https://avatars.discourse-cdn.com/v4/letter/d/7c8e57/32.png) [@dlazarev](https://discuss.hail.is/u/dlazarev)\
**Post date:** [April 27, 2022, 5:41pm UTC](https://discuss.hail.is/t/ld-pruning-not-finishing-running/2638/1 "2022-04-27T17:41:57Z")

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Having some trouble running `ld_prune`. It doesn’t complete (seems to get stuck at some point).  
This is what I’m currently running:

```auto
pruned_variant_ht = hl.ld_prune(ukb_gt_filtered_mt.GT, r2=0.9, bp_window_size=1000000, block_size=2048)
ukb_gwas_filtered_mt = ukb_gwas_filtered_mt.semi_join_rows(pruned_variant_ht)

```

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<div class="post-metadata">

**Author:** ![dlazarev](https://avatars.discourse-cdn.com/v4/letter/d/7c8e57/32.png) [@dlazarev](https://discuss.hail.is/u/dlazarev)\
**Post date:** [April 28, 2022, 4:25pm UTC](https://discuss.hail.is/t/ld-pruning-not-finishing-running/2638/2 "2022-04-28T16:25:52Z")

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Resolved on Zulip.