# HailException: Cannot create BlockMatrix:

**URL:** <https://discuss.hail.is/t/hailexception-cannot-create-blockmatrix/1301>\
**Category:** Hail Query & hailctl\
**Created:** [February 19, 2020, 10:31am UTC](https://discuss.hail.is/t/hailexception-cannot-create-blockmatrix/1301 "2020-02-19T10:31:47Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![wonu](https://avatars.discourse-cdn.com/v4/letter/w/f17d59/32.png) [@wonu](https://discuss.hail.is/u/wonu)\
**Post date:** [February 19, 2020, 10:31am UTC](https://discuss.hail.is/t/hailexception-cannot-create-blockmatrix/1301/1 "2020-02-19T10:31:47Z")

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Hi,

I am using ld\_prune() after performing some variant filtering with the following command:

pruned\_variant\_table = hl.ld\_prune(scz\_varqc.GT, r2=0.2, bp\_window\_size=500000)  
scz\_varqc\_pruned = scz\_varqc.filter\_rows(hl.is\_defined(pruned\_variant\_table[scz\_varqc.row\_key]))

Response so far:  
[Stage 3:=====================================================\> (124 + 3) / 127]2020-02-17 13:56:23 Hail: INFO: ld\_prune: running local pruning stage with max queue size of 21572 variants  
[Stage 8:==================================================\>(16443 + 5) / 16448]2020-02-17 15:03:21 Hail: INFO: Coerced sorted dataset  
[Stage 23:=================================================\>(16446 + 2) / 16448]2020-02-18 08:43:32 Hail: INFO: wrote table with 1178530 rows in 16448 partitions to file:/tmp/hail.xvD6jqsyxN8t/vjAO0Iow8b  
[Stage 28:=================================================\>(16445 + 3) / 16448]2020-02-18 09:50:50 Hail: INFO: Coerced sorted dataset

I get the following error:  
FatalError: HailException: Cannot create BlockMatrix: filtered entry at row 0 and col 1

I am not sure why. I am running hail locally with version 0.2.24-9cd88d97bedd. Can you help please. Thank you!

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<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [February 19, 2020, 12:54pm UTC](https://discuss.hail.is/t/hailexception-cannot-create-blockmatrix/1301/2 "2020-02-19T12:54:21Z")

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This was a bug in ld\_prune that has since been fixed. Can you update to latest Hail? There are plenty of other bug fixes and performance improvements in the last 8 versions too!

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<div class="post-metadata">

**Author:** ![wonu](https://avatars.discourse-cdn.com/v4/letter/w/f17d59/32.png) [@wonu](https://discuss.hail.is/u/wonu)\
**Post date:** [February 19, 2020, 1:39pm UTC](https://discuss.hail.is/t/hailexception-cannot-create-blockmatrix/1301/3 "2020-02-19T13:39:22Z")

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Will do. Thanks!