Test+Docker profile fails: "ValueError: `call_variants_outputs` did not pass sanity check."

Description of the bug

Aug-12 14:30:26.359 [TaskFinalizer-10] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat)'

Caused by: Process NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) terminated with an error exit status (1)

Command executed:

/opt/deepvariant/bin/run_deepvariant \ --ref=reference.fasta \ --reads=hugelymodelbat_sorted_md.bam \ --output_vcf=hugelymodelbat_deepvar.vcf.gz \ --output_gvcf=hugelymodelbat_deepvar.g.vcf.gz \ --model_type=WGS \ \ --intermediate_results_dir=tmp \ --num_shards=2

cat <<-END_VERSIONS > versions.yml "NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT": deepvariant: 1.6.1 END_VERSIONS

Command exit status: 1

Command output: call_set_name: "hugelymodelbat" } end: 10821750 reference_name: "21" start: 10821734 is [[0], [1], [2]], which is invalid. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/usr/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1125, in _mappable_transform_call_variant_group_to_output_variant return _transform_call_variant_group_to_output_variant(**kwargs) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1030, in _transform_call_variant_group_to_output_variant canonical_variant, predictions = merge_predictions( File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 891, in merge_predictions raise ValueError('call_variants_outputs did not pass sanity check.') ValueError: call_variants_outputs did not pass sanity check. """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1419, in app.run(main) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/absl_py/absl/app.py", line 312, in run _run_main(main, args) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/absl_py/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1385, in main tmp_variant_file = dump_variants_to_temp_file(variant_generator) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1067, in dump_variants_to_temp_file tfrecord.write_tfrecords(variant_protos, temp.name) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/third_party/nucleus/io/tfrecord.py", line 190, in write_tfrecords for proto in protos: File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/haplotypes.py", line 91, in maybe_resolve_conflicting_variants for overlapping_candidates in _group_overlapping_variants(sorted_variants): File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/haplotypes.py", line 111, in _group_overlapping_variants for variant in sorted_variants: File "/usr/lib/python3.8/multiprocessing/pool.py", line 420, in return (item for chunk in result for item in chunk) File "/usr/lib/python3.8/multiprocessing/pool.py", line 868, in next raise value ValueError: call_variants_outputs did not pass sanity check.

real 0m5.169s user 0m2.696s sys 0m2.628s

Command error: call_set_name: "hugelymodelbat" } end: 10821750 reference_name: "21" start: 10821734 is [[0], [1], [2]], which is invalid. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/usr/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1125, in _mappable_transform_call_variant_group_to_output_variant return _transform_call_variant_group_to_output_variant(**kwargs) File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1030, in _transform_call_variant_group_to_output_variant canonical_variant, predictions = merge_predictions( File "/tmp/Bazel.runfiles_hekmsdb9/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 891, in merge_predictions raise ValueError('call_variants_outputs did not pass sanity check.') ValueError: call_variants_outputs did not pass sanity check. """

The above exception was the direct cause of the following exception:

real 0m5.169s user 0m2.696s sys 0m2.628s

Work dir: shortened/raredisease_test/work/b9/4ceb969843a4bba123687b3dfc7a11

Command used and terminal output

nextflow run nf-core/raredisease -resume -revision dev -profile test,docker -config test.config --outdir out

Relevant files

dag.overwrite = true

process { withName:"DEEPVARIANT" { //cpus = 20 //memory = 55.GB time = 2.d } withName:"GLNEXUS" { //cpus = 20 //memory = 55.GB time = 16.h }

}

System information

Nextflow version: 24.04.4.5917 Hardware: Desktop Executor: local Container engine: Docker OS: Ubuntu 22.04 Version of nf-core/raredisease: dev (2024-08-12)

nf-core / raredisease