Error running conda build

[RuiLuo111]

I've been trying to run the conda build version 1.10.0 since I cannot use the Docker build. I tried to run make_examples.zip, but received error related to PythonNext TypeError. I have protobuf==3.20.3 installed, which should be the correct version.

Command:

python /.../DeepVariant/BINARYSUB/make_examples.zip
--mode calling
--ref /.../hg38.fa
--reads /.../possorted_genome_bam.bam
--sample_name HapMap
--examples /.../examples/HapMap.tfrecord.gz
--channel_list=read_base,base_quality,mapping_quality,strand,read_supports_variant,base_differs_from_ref

Error:

Traceback (most recent call last):
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 239, in
app.run(main)
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/absl_py/absl/app.py", line 312, in run
_run_main(main, args)
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/absl_py/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 229, in main
make_examples_core.make_examples_runner(options)
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 3613, in make_examples_runner
) = region_processor.process(region, n_stats, region_n)
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2264, in process
sample_reads = self.region_reads_norealign(
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2443, in region_reads_norealign
reads = reservoir_sample_reads(
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 1093, in reservoir_sample_reads
return utils.reservoir_sample(iterable_of_reads, k, random_generator)
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/third_party/nucleus/util/utils.py", line 117, in reservoir_sample
for i, item in enumerate(iterable):
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/third_party/nucleus/io/clif_postproc.py", line 95, in next
record, not_done = self._raw_next()
File "/tmp/rluo5/52141977/Bazel.runfiles_mln_u0qt/runfiles/com_google_deepvariant/third_party/nucleus/io/clif_postproc.py", line 154, in _raw_next
not_done = self._cc_iterable.PythonNext(record)
TypeError: PythonNext(): incompatible function arguments. The following argument types are supported:
1. (self: third_party.nucleus.io.python.sam_reader.SamIterable, read: EmptyProtoPtr) -> StatusOr

Invoked with: <third_party.nucleus.io.python.sam_reader.SamIterable object at 0x7ff03c76b530>,

I also tried other versions like 1.5.0 and 1.8.0, but they also could not work. I downloaded the zip files from: https://42basepairs.com/browse/gs/deepvariant/binaries/DeepVariant

Thanks!

[pichuan]

Hi @RuiLuo111 , our team doesn't officially maintain the conda version.
Last time I tried it was a year ago: #806 (comment)

At the end of that thread, the original poster shared a solution (Nov 2025). You can try that out too (I haven't tried it myself).

Let me know that worked for you.