DeepTrio make_examples fails with 'Invalid interval' error at contig end (NT_113796.3)

[Pyramtee]

Hi,

I encountered an error while running the make_examples step in DeepTrio. The process terminates with an INVALID_ARGUMENT error related to an interval definition. I'm using Deeptrio v1.8.0 and GCF_000001405.40_GRCh38.p14_genomic.fna (downloaded from NCBI).

The error message from /logs/make_examples.log is as follows:

2025-04-21 03:39:31.680311: F ./third_party/nucleus/core/statusor.h:230] Non-OK-status: status_ status: INVALID_ARGUMENT: Invalid interval: reference_name: "NT_113796.3" start: 201709 end: 201709
Fatal Python error: Aborted

Current thread 0x00007f3b22dd2000 (most recent call first):
  File "/tmp/Bazel.runfiles_fte4asiy/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 1732 in writes_examples_in_region
  File "/tmp/Bazel.runfiles_fte4asiy/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 3064 in make_examples_runner
  File "/tmp/Bazel.runfiles_fte4asiy/runfiles/com_google_deepvariant/deeptrio/make_examples.py", line 424 in main
  File "/tmp/Bazel.runfiles_fte4asiy/runfiles/absl_py/absl/app.py", line 258 in _run_main
  File "/tmp/Bazel.runfiles_fte4asiy/runfiles/absl_py/absl/app.py", line 312 in run
  File "/tmp/Bazel.runfiles_fte4asiy/runfiles/com_google_deepvariant/deeptrio/make_examples.py", line 434 in <module>

I checked the reference genome's FASTA index (.fai file) and confirmed that the contig NT_113796.3 has a length of 201709 bp, maybe it's a off-by-one error?

Thank you for your time and help!

[danielecook]

@Pyramtee this is a bug that will be addressed in our next release.

In the meantime, you can see this past issue #912 (comment) which provides a workaround.

[Pyramtee]

Thanks!!