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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
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Illegal Instruction - Jasix.dll or netcoredeps issue #128

Closed schreyers closed 3 months ago

schreyers commented 3 months ago

Heya :) Not sure if its an issue or a setting missed, but:

After updating the BlockCompression to skip using AVX, the example test starts to run but then gives the Illegal Instruction error message. The stack trace points to the Jasix.dll (last thing called).

This line might mean that netcoredeps needs adding? I can't see netcoredeps anywhere though

openat(AT_FDCWD, "/opt/Nirvana/bin/Release/net6.0/netcoredeps/tls/x86_64/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)

CMD line is:

dotnet Nirvana.dll -c /opt/Nirvana/Data/Cache/GRCh37/Both --sd /opt/Nirvana/Data/SupplementaryAnnotation/GRCh37 -r /opt/Nirvana/Data/References/Homo_sapiens.GRCh37.Nirvana.dat -i /home/tmp_annotation/HiSeq.10000.vcf.gz -o /home/tmp_annotation/HiSeq_test

Is there a step missed in the setup maybe? thanks

Output from cmd is:

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

Initialization                                         Time     Positions/s
---------------------------------------------------------------------------
Cache                                               00:00:03.3
SA Position Scan                                    00:00:00.4       23,214

Reference                                Preload    Annotation   Variants/s
---------------------------------------------------------------------------
Illegal instruction
schreyers commented 3 months ago

Using VEP instead

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.