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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Index out of bounds with the new tabix-based callableloci #328

Closed lbeltrame closed 10 years ago

lbeltrame commented 10 years ago

This occurs with a targeted sequencing dataset:

[0:apply]: IndexError: index -31 is out of bounds for axis 0 with size 17

This is repeated many times (with a slightly different output). I'm guessing there may be a race condition here.

chapmanb commented 10 years ago

Luca; Thanks for the heads up. I'm going to try and reproduce at scale here and see if I can isolate it. Apologies that development is a bit more unstable than normal. I'm trying to get in all of the major changes so we can test them early and often before the next release.

chapmanb commented 10 years ago

Luca; I could reproduce this error on systems with an older version of pysam. Could you ensure that you're upgraded to pysam 0.7.7 and see if that resolves the issue? If not, please feel let me know and we'll re-open and investigate further.

lbeltrame commented 10 years ago

I'm running an upgrade on the whole cluster as we speak. Once finished I'll rerun and test. As far as I could tell, the cluster ran 0.7.4.