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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
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Illegal instruction: 4 #125

Closed veronicatozzo closed 3 months ago

veronicatozzo commented 5 months ago

Hi there, I am following the Getting started tutorial and I am encountering an issue. Everything goes smoothly up to the test instruction 

dotnet bin/Release/net6.0/Nirvana.dll \
     -c Data/Cache/GRCh38 \
     --sd Data/SupplementaryAnnotation/GRCh38 \
     -r Data/References/Homo_sapiens.GRCh38.Nirvana.dat \
     -i HiSeq.10000.vcf.gz \
     -o HiSeq.10000

which output is

   ---------------------------------------------------------------------------
Nirvana                                             (c) 2022 Illumina, Inc.
Stromberg, Roy, Platzer, Siddiqui, Ouyang, et al                     3.18.1
---------------------------------------------------------------------------

Initialization                                         Time     Positions/s
---------------------------------------------------------------------------
Illegal instruction: 4

I've tried to start from the source code as well as from the binaries and I reach the same point with both. Following the installation via Docker is also a dead end, at the same point, it gets stuck for hours without producing any result or error code.

I am working with macOS 13.6 M2 Chip x86-x64, dotnet 6.0.26.

Any idea how to fix this? Thank you!

egidijusz commented 4 months ago

I have the same issue.

OS: Ubuntu 22.04 CPU: Intel Xeon X5650

.NET version 6.0.127

Update: after some research I think it's a hardware problem (in my case). Xeon X5650 does not support avx instructions, which are required for Nirvana (correct me if I'm wrong).

schreyers commented 3 months ago

If this helps, this can be added to bypass the AVX usage: https://github.com/Illumina/BlockCompression.

I had this fix and it got to the next step, but got a new / same error after. Issue raised is this: https://github.com/Illumina/Nirvana/issues/128

rajatshuvro commented 3 months ago

Please note that this tool is no longer being maintained. We have launched Illumina Connected Annotations built based on Nirvana. Please see: https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/ for details.