Hi, I’m running the following: ht_0 = hl.read_table(test_ht_path) # Read in same ht for testing purposes ht_1 = hl.read_table(test_ht_path) # Join hts to get both MQRankSum annotations (created with lambda x: hl.agg.approx_cdf(x, k=10, _raw=True) ht = ht_0.annotate(first_MQRankSum=ht_0.info.MQRan…

Hi @klaricch , Do you have a full stacktrace from that error? That would help us pin down the cause.

Traceback (most recent call last): File "/tmp/715094ce17ce415c806d3cc28a2eaf4b/combine_cdfs.py", line 18, in <module> ht.raw_cdf_combined.show() File "<decorator-gen-540>", line 2, in show File "/opt/conda/default/lib/python3.10/site-packages/hail/typecheck/check.py", line 585, in wrapper …

Thanks! This is definitely a Hail bug. Is the table at test_ht_path something you could share with us, by any chance? That would be a huge help in fixing the bug. If so, you can email us at hail@broadinstitute.org to coordinate sharing the data. If not, I might ask you some more questions to figure …

Never mind, I’ve been able to reproduce the bug. I expect this to be fixed in our next release, but I’ll also try to find a workaround you can use in the meantime. I’ll keep you posted!

I think I have a working fix, but a workaround looks like it might be tricky. Are you able to wait for the next release (probably early January at the latest) for the fix? If not, I can build a custom wheel for you to install with the fix included.

Yeah waiting for the next release is fine

ArrayIndexOutOfBoundsException using _cdf_combine

Hail Query & hailctl

klaricch December 11, 2024, 7:55pm 6

OK, thank you!

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ArrayIndexOutOfBoundsException using _cdf_combine

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