Error running DenoiseReadCounts on arm64 processor

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dbpiero

• June 01, 2021 10:22

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.2.0.0

b) Exact command used: gatk DenoiseReadCounts -I sample.counts.tsv --annotated-intervals annotated_intervals.tsv --standardized-copy-ratios sample.standardizedCR.tsv --denoised-copy-ratios sample.denoisedCR.tsv

c) Entire error log: A USER ERROR has occurred: Cannot load the required HDF5 library. HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.

Dear Administrators,

I try to run DenoiseReadCounts on new apple silicon chip (M1) with arm64 architecture, but I got this error: A USER ERROR has occurred: Cannot load the required HDF5 library. HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.

I created a docker with ubuntu 20.04 to launch gatk and I have already installed libhdf5-103:arm64 library and hdf5-tools inside but launching DenoiseReadCounts i get the same error. Is there a way to solve this issue?

Thanks

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  Genevieve Brandt (she/her)

  • June 01, 2021 18:15
  • Edited

  Hi dbpiero,

  It looks like a similar question was posted on our old forum, which has been archived here. Essentially, it looks like the issue is most likely coming from a file system permission issue. You can change the temporary directory with the java option `-Djava.io.tmpdir=tmp`. If that does not solve the issue, you could try using GATK from docker.

  Best,

  Genevieve

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  dbpiero

  • June 03, 2021 16:10

  Hi Genevieve,

  thank you for your answer. I've tried them but it still doesn't work. I add another warning, not seen before:

  16:00:21.248 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression980365261311152112.so
  : /tmp/libgkl_compression980365261311152112.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64-bit .so on a AAR
  CH64-bit platform))

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  Genevieve Brandt (she/her)

  • June 08, 2021 23:12

  Hi dbpiero,

  Unfortunately after looking into this further I found that currently the arm64 processor is not currently supported for running GATK. We do want you to be able to use the tools. In this case we may be able to patch the DenoiseReadCounts tool so that you can successfully run it without needing the HDF5 library. I created a ticket on our github for the team to look into this further. You can follow along at this link as it is being solved: https://github.com/broadinstitute/gatk/issues/7297

  I am sorry we do not have a better workaround at this point but you have come across an unsupported issue. Thank you for writing in so that we can find a solution as soon as possible.

  Best,

  Genevieve

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  dbpiero

  • June 09, 2021 13:04

  Hi Genevieve, thank you for your kind support.

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  Genevieve Brandt (she/her)

  • June 09, 2021 15:42

  You're welcome! :)

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